squid/0000755000175000017520000000000010463223377012117 5ustar naolivbiolinuxsquid/00CHECKLIST0000640000175000017520000000214510463223377013511 0ustar naolivbiolinuxChecklist for a squid release. SRE, Wed Mar 6 08:52:52 2002 ------------------------------------- 1. Make sure is up to date w/ CVS. (Worry about commits here, and on HMMER and wren, if you have to.) % make distclean % cvs update Clean up any stray files. 2. Update the copyright, year stamps. - Makefile.in (release, relcode, date) - 00README (year only) - Licenses/COPYRIGHT.gnu (year only) - Licenses/gnu (year only) 3. Commit to CVS. % cvs commit 4. make a distribution package % autoconf <-- only wrasse. Must be autoconf >=2.52 % ./configure <-- makes a Makefile (needed for "make dist") % make dist 5. Build for our system (on whelk01 or some such) % cd squid-xxx % env CFLAGS="-O3" ./configure --enable-lfs prefix=/usr/seshare/ exec_prefix=/usr/seshare/`uname` % make % make check % make install <-- I don't need root to do this % ssh w001 % cd /nfs/wol2/people/eddy/src/squid/squid-xxx % ./configure <-- sets paths to /usr/local % sudo make install % logout % make distclean 6. Put on the FTP site. (on wrasse) % make ftpdist squid/00README0000640000175000017520000000265610463223377013144 0ustar naolivbiolinuxSQUID - library of functions for biological sequence analysis Copyright (C) 1992-2002 Washington University School of Medicine SQUID is a freely redistributable library of C code functions for sequence analysis. SQUID also includes a number of small utility programs. To install squid, see the file: INSTALL -- instructions for installing the programs If you have any questions about redistributing squid or using squid code in your own work, see the files: COPYRIGHT -- copyright notice, and information on my distribution policy LICENSE -- version 2 of the GNU Public License (see COPYRIGHT) For a web page with more information on squid, see: http://www.genetics.wustl.edu/eddy/software/#squid You can always download the latest stable release of squid from: ftp://ftp.genetics.wustl.edu/pub/eddy/software/squid.tar.gz The development codebase is available by anonymous CVS: cvs -d :pserver:anonymous@skynet.wustl.edu:/repository/sre login (password "anonymous") cvs -d :pserver:anonymous@skynet.wustl.edu:/repository/sre checkout squid If you encounter any bugs in this library, or you have any questions or comments, please e-mail me at the address below. Due to limited personal time, I may not respond, but I do read all my mail. Sean Eddy eddy@genetics.wustl.edu HHMI/Dept. of Genetics Washington University School of Medicine 660 South Euclid Box 8232 Saint Louis Missouri 63110 USA squid/Bugs/0000755000175000017520000000000010463223377013017 5ustar naolivbiolinuxsquid/Bugs/BUGTRAX0000644000175000017520000000643510463223377014066 0ustar naolivbiolinux# bug log started: SRE, Sun Apr 28 15:27:41 2002 # ID sq1 STATUS closed DESCRIPTION sfetch can't follow paths out of cwd if using SSI NOTED_DATE 6 Mar 02 NOTED_XREF - REPORTED_BY Zhirong Bao (bao@genetics) REPRODUCE_WITH Testsuite/bug-1-sfetch-paths REPRODUCE_ON any CLOSED_DATE 6 Mar 02 CLOSED_XREF - CLOSED_ACTION - // ID sq2 STATUS closed DESCRIPTION Fails to compile on Alpha. strtoull unresolved. NOTED_DATE SRE, Sun Apr 28 15:29:55 2002 NOTED_XREF STL6 p.41 REPORTED_BY Sam Griffiths-Jones (sgj@sanger.ac.uk) REPRODUCE_WITH ./configure; make REPRODUCE_ON waterbug (Alpha, Digital Unix) CLOSED_DATE 28 Apr 02 CLOSED_XREF STL6 p.41 CLOSED_ACTION - // ID sq3 TITLE weight segfaults, at end of alignment output STATUS CLOSED XREF - REPORTED_BY Robin Dowell CLOSED_DATE SRE, Fri Feb 20 08:36:09 2004 DESCRIPTION weight segfaulted on a_bacterial.stk: % valgrind weight -f .8 a_bacterial.stk shows a fault in MSAFree(). new->sqlen is being double free'd. fix: set to NULL after free'ing it in msa.c:MSASmallerAlignment(). // ID sq4 TITLE shuffle -0 and -1 have limited sequence length range STATUS CLOSED XREF - REPORTED_BY Mike Pheasant (m.pheasant@imb.uq.edu.au) OPENED_DATE SRE, Wed Jun 30 10:31:45 2004 CLOSED_DATE SRE, Wed Jun 30 10:31:46 2004 DESCRIPTION StrMarkov0() and StrMarkov1() were counting in floats. This limits length range to ~6 digits. Changes so it counts in integer, then normalizes to floating point probabilities; this gives a range of ~2GB sequence length (assuming 32-bit int). // ID sq5 TITLE FChoose(), DChoose() return impossible residues STATUS CLOSED XREF - REPORTED_BY Mike Pheasant (m.pheasant@imb.uq.edu.au) OPENED_DATE SRE, Thu Jul 1 11:40:10 2004 CLOSED_DATE SRE, Thu Jul 1 11:40:11 2004 DESCRIPTION Another problem w/ shuffle -0 and shuffle -1 was seen; they could generate residues that had never occurred in the original sequence. Problem is in FChoose(),DChoose(), where the "bulletproofing" against machine float representation was to choose 1 of N randomly, in the rare case that roll >= total_sum. To fix, force the bulletproofing to choose a nonzero p[i]. // ID sq6 TITLE Phylip output should only put - for gap chars. STATUS CLOSED XREF - REPORTED_BY Arno Meiler , Wed Jul 28 2004 OPENED_DATE SRE, Wed Jul 28 19:18:05 2004 CLOSED_DATE SRE, Wed Jul 28 19:18:06 2004 DESCRIPTION As of at least PHYLIP 3.6, . characters are not permitted as gaps, and Joe documents this. Rewrote the phylip parser, and changed the phylip example file in Formats. // ID sq7 TITLE seqsplit appends extra garbage characters STATUS CLOSED XREF - REPORTED_BY Tom Jones , Wed Aug 4 2004 OPENED_DATE SRE, Wed Aug 4 20:09:32 2004 CLOSED_DATE SRE, Wed Aug 4 20:09:33 2004 DESCRIPTION malloc of (length) instead of (length+1) for seqfrag. seqsplit may append garbage chars as a result, under many circumstances. // squid/Docs/0000755000175000017520000000000010463223377013007 5ustar naolivbiolinuxsquid/Docs/abstract.tex0000640000175000017520000000022610463223377015330 0ustar naolivbiolinux\begin{abstract} The {\tt squid} library is an evolving collection of C functions for nucleic acid and protein sequence analysis. \end {abstract} squid/Docs/formats.tex0000640000175000017520000005545710463223377015220 0ustar naolivbiolinux% -------------------------------------------------------------- % squid:formats.tex % SRE, Wed Jul 14 17:54:59 1999 % $CVS Id$ % -------------------------------------------------------------- \chapter {Sequence file formats} \section{Summary} The software can handle a number of different file formats. By default, it autodetects the file format, so you don't have to worry about converting formats. Most common file formats are recognized, including FASTA, Genbank, EMBL, Swissprot, PIR, and FASTA for unaligned sequences, and GCG MSF, Clustal, Phylip, and Stockholm format for multiple sequence alignments. Some parts of the source code call the autodetector the ``Babelfish''. The Babelfish has three drawbacks. First, it takes a small amount of time to do the autodetection. Second, the Babelfish is aggressive, and it makes mistakes when a file isn't one of the known formats -- in particular, it can recognize plain text files as SELEX alignments, because the SELEX format is so free-form. Third, because the Babelfish works by reading the first part of the file then rewinding it before starting to process it, you can't use the Babelfish on a nonrewindable stream: e.g. when you're taking sequence input from a UNIX pipe instead of a file, or when the file is gzipped and has to be decompressed before processing. In normal use, when you're using the software interactively from the command line on sequence files that you're familiar with, the Babelfish is very convenient and (relatively) safe. However, you'll find that there are times when you want to override the Babelfish -- particularly in high-throughput analysis, when you know the format your files are supposed to be in, and you'd rather increase robustness and sacrifice interactive flexibility. All the programs have an \verb+--informat + option that lets you specify the format and shut off the Babelfish. You \emph{must} use \verb+--informat+ to use compressed files, or to read sequence from a UNIX pipe... see below for more details on these tricks. \section{Formats recognized by the Babelfish} Recognized unaligned sequence file formats: \begin{tabular}{ll}\hline Format name & Note \\ \hline fasta & BLAST flatfile databases, etc.\\ genbank & NCBI Genbank flat file format.\\ embl & Includes both EMBL (DNA) and SWISSPROT (protein) databases.\\ pir & Protein Information Resource database (NBRF/Georgetown)\\ gcg & Wisconsin Genetics Computer Group; only allows one sequence per file.\\ gcgdata & I think this GCG database format is obsolete now.\\ \hline \end{tabular} Recognized multiple sequence alignment file formats: \begin{tabular}{ll}\hline Format name & Note \\ \hline stockholm & Pfam format. Allows databases of more than one alignment per file\\ selex & Old NeXagen RNA alignment format, adopted by early HMMER releases.\\ msf & GCG's alignment format.\\ clustal & ClustalV, ClustalW, and friends.\\ a2m & Aligned FASTA format; see comment below.\\ phylip & Format used by Felsenstein's PHYLIP phylogenetic inference software\\\hline \end{tabular} Aligned FASTA format (here called ``A2M'', though I believe that what Haussler's group at UCSC started calling A2M is yet another variant of aligned FASTA that's incompatible with this A2M) is only autodetected when an alignment file is expected. Otherwise an A2M file will be recognized as unaligned FASTA, and its gap characters (if any) will be parsed as sequence characters -- often not what you want. Alignment files may be used when unaligned files are expected -- the sequences will silently be de-aligned and read sequentially. The converse is not true; you can't give an unaligned sequence format when an alignment is expected (makes sense, right?). There is no provision for enforcing that single unaligned sequence formats really do contain just a single sequence. An attempt to convert a multisequence file to GCG format will silently ``succeed'', and the file may look ok to your eye, but that multisequence ``GCG'' file is illegal. The data will be corrupted if you try to read that file back in, possibly without generating any error messages. It turns out that other formats work too, but they're undocumented, not subjected to any quality control testing at software release time, and prone to change without notice at my slightest whim. (In other words, even less supported than the software already is.) The brave, curious, or desperate are invited to peruse \prog{seqio.c} and \prog{squid.h}. \section{Special tricks} \subsection{Reading from standard input (probably UNIX-only)} If you give ``-'' as a sequence filename, the software will read the sequences from standard input rather than from a file. You will need to specify the format of the incoming data using the \verb+--informat+ option. Any format except SELEX can be read from standard input. This lets you use any program downstream in a standard UNIX pipe. There is one limitation: you can't use ``-'' more than once on a command line, for obvious reasons. (How is it supposed to read more than one file from one standard input stream?) If you do, behavior of the software is undefined -- in other words, the software don't check for whether you're making this mistake, so God help you if you do. \subsection{Reading from gzip'ed files (probably UNIX-only)} A sequence file in any format except SELEX can be compressed by gzip, and read in its compressed form. The software looks for the suffix \prog{.gz} to detect gzip'ed files. This allows you to save disk space by keeping sequence files gzip'ed, if you like. gzip is not built in; the software needs to find a gzip executable in your current PATH. If for some reason you name a file with a \prog{.gz} suffix and it's \emph{not} a gzip-compressed file, the software will still try to decompress it, and peculiar things may happen. \section{FASTA format, the recommended unaligned format} FASTA is probably the simplest of formats for unaligned sequences. FASTA files are easily created in a text editor. Each sequence is preceded by a line starting with \verb+>+. The first word on this line is the name of the sequence. The rest of the line is a description of the sequence (free format). The remaining lines contain the sequence itself. You can put as many letters on a sequence line as you want. \textbf{Example of a simple FASTA file:} \begin{verbatim} >seq1 This is the description of my first sequence. AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCA CGACGTAGATGCTAGCTGACTCGATGC >seq2 This is a description of my second sequence. CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG CATCGTCAGTTACTGCATGCTCG \end{verbatim} For better or worse, FASTA is not a documented standard. Minor (and major) variants are in widespread use in the bioinformatics community, all of which are called ``FASTA format''. My software attempts to cater to all of them, and is tolerant of common deviations in FASTA format. Certainly anything that is accepted by the database formatting programs in NCBI BLAST or WU-BLAST (e.g. setdb, pressdb, xdformat) will also be accepted by my software. Blank lines in a FASTA file are ignored, and so are spaces or other gap symbols (dashes, underscores, periods) in a sequence. Other non-amino or non-nucleic acid symbols in the sequence are also silently ignored, mostly because some people seem to think that ``*'' or ``.'' should be added to protein sequences to (redundantly) indicate the end of the sequence. The parser will also accept unlimited line lengths, which allows it to accomodate the enormous description lines in the NCBI NR databases. On the other hand, any FASTA files \emph{generated} by my software adhere closely to community standards, and should be usable by other software packages (BLAST, FASTA, etc.) that are more picky about parsing their input files. That means you can run a sloppy FASTA file thru \prog{sreformat} to clean it up. Partly because of this tolerance, the software may have a difficult time dealing with files that are \textit{not} in FASTA format, especially if you're relying on the Babelfish to do format autodetection. Some (now mercifully uncommon) file formats are so similar to FASTA format that they be erroneously called FASTA by the Babelfish and then quietly but lethally misparsed. An example is the old NBRF file format. If you're using \verb+--informat+, things will be more robust, and the software should simply refuse to accept a non-FASTA file -- but you shouldn't count on this, because files perversely similar to FASTA will still confuse the parser. (The gist of these caveats applies to all formats, not just FASTA.) \section{SELEX, the quick and dirty alignment format} An example of a simple SELEX alignment file: \begin{verbatim} # Example selex file seq1 ACGACGACGACG. seq2 ..GGGAAAGG.GA seq3 UUU..AAAUUU.A seq1 ..ACG seq2 AAGGG seq3 AA...UUU \end{verbatim} SELEX is an interleaved multiple alignment format that arose as a simple, intuitive format that was easy to write and manipulate manually in a text editor. It is usually easy to convert other alignment formats into SELEX format, even with a couple of lines of Perl, but it can be harder to go the other way, since SELEX is more free-format than other alignment formats. For instance, GCG's MSF format and the output of the CLUSTALV multiple alignment program are similar interleaved formats that can be converted to SELEX just by stripping a small number of non-sequence lines out. Because SELEX evolved to accomodate different user input styles, it is very tolerant of various inconsistencies such as different gap symbols, varying line lengths, etc. Each line contains a name, followed by the aligned sequence. A space, dash, underscore, or period denotes a gap. If the alignment is too long to fit on one line, the alignment is split into multiple blocks, separated by blank lines. The number of sequences, their order, and their names must be the same in every block (even if a sequence has no residues in a given block!) Other blank lines are ignored. You can add comments to the file on lines starting with a \verb+#+. SELEX stands for ``Systematic Evolution of Ligands by Exponential Enrichment'' -- it refers to the Tuerk and Gold technology for evolving families of small RNAs for particular functions \cite{Tuerk90b}. SELEX files were what we used to keep track of alignments of these small RNA families, at a company then called NeXagen, in Boulder. It's an interesting piece of historical baggage. With the development of HMMER and more need for annotated alignments in Pfam, SELEX format later evolved into ``extended SELEX'', with a reserved comment style that allowed structural markup and other annotations, but that became unwieldy. We now use Stockholm format (see below) for highly annotated alignments. (Extended SELEX is deprecated and undocumented.) Still, the basic SELEX format remains a useful ``lowest common denominator'' alignment format, and has been retained. \subsubsection {Detailed specification of a SELEX file} \begin{enumerate} \item Any line beginning with a \verb+#=+ as the first two characters is a parsed machine comment in extended SELEX, and is now deprecated. \item All other lines beginning with a \verb+%+ or \verb+#+ as the first character are user comments. User comments are ignored by all software. Anything may appear on these lines. Any number of comments may be included in a SELEX file, and at any point. \item Lines of data consist of a name followed by a sequence. The total length of the line must be smaller than 4096 characters. \item Names must be a single word. Any non-whitespace characters are accepted. No spaces are tolerated in names: names MUST be a single word. Names must be less than 32 characters long. \item In the sequence, any of the characters \verb+-_.+ or a space are recognized as gaps. Any other characters are interpreted as sequence. Sequence is case-sensitive. There is a common assumption by my software that upper-case symbols are used for consensus (match) positions and lower-case symbols are used for inserts. This language of ``match'' versus ``insert'' comes from the hidden Markov model formalism \cite{Krogh94}. To almost all of my software, this isn't important, and it immediately converts the sequence to all upper-case after it's read. \item Multiple different sequences are grouped in a block of data lines. Blocks are separated by blank lines. No blank lines are tolerated between the sequence lines in a block. Each block in a multi-block file of a long alignment must have its sequences in the same order in each block. The names are checked to verify that this is the case; if not, only a warning is generated. (In manually constructed files, some users may wish to use shorthand names in subsequent blocks after an initial block with full names -- but this isn't recommended.) \end{enumerate} \section{Stockholm, the recommended multiple sequence alignment format} While we recommend a community standard format (FASTA) for unaligned sequence files, the recommended multiple alignment file format is not a community standard. The Pfam Consortium developed a format (based on extended SELEX) called ``Stockholm format''. The reasons for this are two-fold. First, there really is no standard accepted format for multiple sequence alignment files, so we don't feel guilty about inventing a new one. Second, the formats of popular multiple alignment software (e.g. CLUSTAL, GCG MSF, PHYLIP) do not support rich documentation and markup of the alignment. Stockholm format was developed to support extensible markup of multiple sequence alignments, and we use this capability extensively in both RNA work (with structural markup) and the Pfam database (with extensive use of both annotation and markup). \subsection{A minimal Stockholm file} \begin{verbatim} # STOCKHOLM 1.0 seq1 ACDEF...GHIKL seq2 ACDEF...GHIKL seq3 ...EFMNRGHIKL seq1 MNPQTVWY seq2 MNPQTVWY seq3 MNPQT... \end{verbatim} The simplest Stockholm file is pretty intuitive, easily generated in a text editor. It is usually easy to convert alignment formats into a ``least common denominator'' Stockholm format. For instance, SELEX, GCG's MSF format, and the output of the CLUSTALV multiple alignment program are all similar interleaved formats. The first line in the file must be \verb+# STOCKHOLM 1.x+, where \verb+x+ is a minor version number for the format specification (and which currently has no effect on my parsers). This line allows a parser to instantly identify the file format. In the alignment, each line contains a name, followed by the aligned sequence. A dash or period denotes a gap. If the alignment is too long to fit on one line, the alignment may be split into multiple blocks, with blocks separated by blank lines. The number of sequences, their order, and their names must be the same in every block. Within a given block, each (sub)sequence (and any associated \verb+#=GR+ and \verb+#=GC+ markup, see below) is of equal length, called the \textit{block length}. Block lengths may differ from block to block; the block length must be at least one residue, and there is no maximum. Other blank lines are ignored. You can add comments to the file on lines starting with a \verb+#+. All other annotation is added using a tag/value comment style. The tag/value format is inherently extensible, and readily made backwards-compatible; unrecognized tags will simply be ignored. Extra annotation includes consensus and individual RNA or protein secondary structure, sequence weights, a reference coordinate system for the columns, and database source information including name, accession number, and coordinates (for subsequences extracted from a longer source sequence) See below for details. \subsection{Syntax of Stockholm markup} There are four types of Stockholm markup annotation, for per-file, per-sequence, per-column, and per-residue annotation: \begin{wideitem} \item {\emprog{#=GF }} Per-file annotation. \prog{} is a free format text line of annotation type \prog{}. For example, \prog{#=GF DATE April 1, 2000}. Can occur anywhere in the file, but usually all the \prog{#=GF} markups occur in a header. \item {\emprog{#=GS }} Per-sequence annotation. \prog{} is a free format text line of annotation type \prog{tag} associated with the sequence named \prog{}. For example, \prog{#=GS seq1 SPECIES_SOURCE Caenorhabditis elegans}. Can occur anywhere in the file, but in single-block formats (e.g. the Pfam distribution) will typically follow on the line after the sequence itself, and in multi-block formats (e.g. HMMER output), will typically occur in the header preceding the alignment but following the \prog{#=GF} annotation. \item {\emprog{#=GC <...s...>} Per-column annotation. \prog{<...s...>} is an aligned text line of annotation type \prog{}. \verb+#=GC+ lines are associated with a sequence alignment block; \prog{<...s...>} is aligned to the residues in the alignment block, and has the same length as the rest of the block. Typically \verb+#=GC+ lines are placed at the end of each block. \item {\emprog{#=GR <.....s.....>} Per-residue annotation. \prog{<...s...>} is an aligned text line of annotation type \prog{}, associated with the sequence named \prog{}. \verb+#=GR+ lines are associated with one sequence in a sequence alignment block; \prog{<...s...>} is aligned to the residues in that sequence, and has the same length as the rest of the block. Typically \verb+#=GR+ lines are placed immediately following the aligned sequence they annotate. \end{wideitem} \subsection{Semantics of Stockholm markup} Any Stockholm parser will accept syntactically correct files, but is not obligated to do anything with the markup lines. It is up to the application whether it will attempt to interpret the meaning (the semantics) of the markup in a useful way. At the two extremes are the Belvu alignment viewer and the HMMER profile hidden Markov model software package. Belvu simply reads Stockholm markup and displays it, without trying to interpret it at all. The tag types (\prog{#=GF}, etc.) are sufficient to tell Belvu how to display the markup: whether it is attached to the whole file, sequences, columns, or residues. HMMER uses Stockholm markup to pick up a variety of information from the Pfam multiple alignment database. The Pfam consortium therefore agrees on additional syntax for certain tag types, so HMMER can parse some markups for useful information. This additional syntax is imposed by Pfam, HMMER, and other software of mine, not by Stockholm format per se. You can think of Stockholm as akin to XML, and what my software reads as akin to an XML DTD, if you're into that sort of structured data format lingo. The Stockholm markup tags that are parsed semantically by my software are as follows: \subsubsection{Recognized #=GF annotations} \begin{wideitem} \item [\emprog{ID }] Identifier. \emprog{} is a name for the alignment; e.g. ``rrm''. One word. Unique in file. \item [\emprog{AC }] Accession. \emprog{} is a unique accession number for the alignment; e.g. ``PF00001''. Used by the Pfam database, for instance. Often a alphabetical prefix indicating the database (e.g. ``PF'') followed by a unique numerical accession. One word. Unique in file. \item [\emprog{DE }] Description. \emprog{} is a free format line giving a description of the alignment; e.g. ``RNA recognition motif proteins''. One line. Unique in file. \item [\emprog{AU }] Author. \emprog{} is a free format line listing the authors responsible for an alignment; e.g. ``Bateman A''. One line. Unique in file. \item [\emprog{GA }] Gathering thresholds. Two real numbers giving HMMER bit score per-sequence and per-domain cutoffs used in gathering the members of Pfam full alignments. See Pfam and HMMER documentation for more detail. \item [\emprog{NC }] Noise cutoffs. Two real numbers giving HMMER bit score per-sequence and per-domain cutoffs, set according to the highest scores seen for unrelated sequences when gathering members of Pfam full alignments. See Pfam and HMMER documentation for more detail. \item [\emprog{TC }] Trusted cutoffs. Two real numbers giving HMMER bit score per-sequence and per-domain cutoffs, set according to the lowest scores seen for true homologous sequences that were above the GA gathering thresholds, when gathering members of Pfam full alignments. See Pfam and HMMER documentation for more detail. \end{wideitem} \subsection{Recognized #=GS annotations} \begin{wideitem} \item [\emprog{WT }] Weight. \emprog{} is a positive real number giving the relative weight for a sequence, usually used to compensate for biased representation by downweighting similar sequences. Usually the weights average 1.0 (e.g. the weights sum to the number of sequences in the alignment) but this is not required. Either every sequence must have a weight annotated, or none of them can. \item [\emprog{AC }] Accession. \emprog{} is a database accession number for this sequence. (Compare the \prog{#=GF AC} markup, which gives an accession for the whole alignment.) One word. \item [\emprog{DE }] Description. \emprog{} is one line giving a description for this sequence. (Compare the \prog{#=GF DE} markup, which gives a description for the whole alignment.) \end{wideitem} \subsection{Recognized #=GC annotations} \begin{wideitem} \item [\emprog{RF}] Reference line. Any character is accepted as a markup for a column. The intent is to allow labeling the columns with some sort of mark. \item [\emprog{SS_cons}] Secondary structure consensus. For protein alignments, DSSP codes or gaps are accepted as markup: [HGIEBTSCX.-_], where H is alpha helix, G is 3/10-helix, I is p-helix, E is extended strand, B is a residue in an isolated b-bridge, T is a turn, S is a bend, C is a random coil or loop, and X is unknown (for instance, a residue that was not resolved in a crystal structure). For RNA alignments the symbols \verb+>+ and \verb+<+ are used for base pairs (pairs point at each other). \verb-+- indicate definitely single-stranded positions, and any gap symbol indicates unassigned bases or single-stranded positions. This description roughly follows \cite{Konings89}. RNA pseudoknots are represented by alphabetic characters, with upper case letters representing the 5' side of the helix and lower case letters representing the 3' side. Note that this limits the annotation to a maximum of 26 pseudoknots per sequence. \item [\emprog{SA_cons}] Surface accessibility consensus. 0-9, gap symbols, or X are accepted as markup. 0 means <10\% accessible residue surface area, 1 means <20\%, 9 means <100\%, etc. X means unknown structure. \end{wideitem} \subsection{Recognized #=GR annotations} \begin{wideitem} \item [\emprog{SS}] Secondary structure consensus. See \prog{#=GC SS_cons} above. \item [\emprog{SA}] Surface accessibility consensus. See \prog{#=GC SA_cons} above. \end{wideitem} squid/Docs/gsi-format.tex0000640000175000017520000000576210463223377015607 0ustar naolivbiolinux% Mon Dec 5 15:23:18 1994 \section{GSI format} {\tt GSI} (``generic sequence index'') is a format for indexing sequence databases. Database retrieval programs such as {\tt sfetch} can read GSI files when they are available to enable fast retrieval of a sequence from large databases. GSI files are created from sequence databases by Perl scripts. Scripts are currently provided for indexing GenBank, SwissProt, GenPept, FASTA, and PIR formatted databases. \subsection {GSI programmatic details} A single GSI file indexes one or more files in a sequence database. It is a binary file consisting of a number of fixed-length records. There are three types of records: one header record, one file record for every file in the database, and one keyword record for every sequence retrieval key. (The retrieval key is usually the sequence name, but may also be a database accession number.) Every GSI record is 38 bytes long and contains three fields: 32 bytes of text (31 bytes plus a trailing NUL byte), a 2 byte network short, and a 4 byte network long. (``Network short'' and ``network long'' refer to portable integer variables of fixed size and byte order. See Perl manuals for a few more details.) The first record is a header. It contains a short identifying text string (``GSI''), then the number of files indexed ({\tt nfiles}), and the number of keywords indexed ({\tt nkeys}). The next {\tt nfiles} records (records 1..{\tt nfiles}) map file numbers onto file names. The three fields are \verb+ +. These records must be in numerical order according to their file numbers. Because of the 31-character restriction on filename lengths, the sequence files will generally have to be in the same directory as the GSI index file. The file format number is defined in {\tt squid.h}: \begin{tabular}{rl} 0 & Unknown \\ 1 & Intelligenetics\\ 2 & Genbank\\ 4 & EMBL\\ 5 & GCG single sequence\\ 6 & Strider \\ 7 & FASTA\\ 8 & Zuker\\ 9 & Idraw\\ 12 & PIR\\ 13 & Raw\\ 14 & SQUID\\ 16 & GCG data library \\ 101& Stockholm alignment\\ 102& SELEX alignment\\ 103& GCG MSF alignment\\ 104& Clustal alignment\\ 105& A2M (aligned FASTA) alignment\\ 106& Phylip\\ \end{tabular} The remaining records ({\tt nfiles}+1..{\tt nfiles+nkeys}) are for mapping keys onto files and disk offsets. The three fields are \verb+ +. These records must be sorted in alphabetic order by their retrieval keys, because the function GSIGetOffset() locates a keyword in the index file by a binary search. \subsection{Relevant functions} \begin{description} \item[GSIOpen()] Opens a GSI index file. \item[GSIGetRecord()] Gets three fields from the current record. \item[GSIGetOffset()] Looks up a keyword in a GSI index and returns a filename, file format, and disk offset in the file. \item[SeqfilePosition()] Repositions an open sequence file to a given disk offset. \item[GSIClose()] Closes an open GSI index file. \end{description} squid/Docs/intro.tex0000640000175000017520000000003110463223377014652 0ustar naolivbiolinux\section {Introduction} squid/Docs/macros.tex0000644000175000017520000000514610463223377015023 0ustar naolivbiolinux% customizations used in the User's Guide % Description-like environment for documenting functions/APIs. % puts the description label in a minipage with a large hanging % indent. % Good christ this took a long time to develop. % hanging indent trick stolen from Peter Wilson's hanging.sty @CTAN % minipage allows multi-line label, and puts item on next line. % customized list inspired by Kopka/Daly _Guide to LaTeX_ p.213 % SRE, Wed Dec 27 11:37:18 2000 % \newenvironment{sreapi}{% \begin{list}{}{% \renewcommand{\makelabel}[1]{% \begin{minipage}{\textwidth}% \hangindent10em\hangafter1\noindent% {\bfseries\texttt{##1}\vspace{0.8em}}% \end{minipage}% }}}% {\end{list}} % Description-like environment for producing lists like: % % label stuff, stuff, stuff % % label2 more stuff, more stuff, % more stuff. % \begin{sreitems}{Longest label} \item[label] stuff, ... \end{sreitems} % SRE, Wed Dec 27 11:59:43 2000 % \newenvironment{sreitems}[1]{% \begin{list}{}{% \settowidth{\labelwidth}{#1}% \setlength{\leftmargin}{\labelwidth}% \addtolength{\leftmargin}{\labelsep}% }} {\end{list}} \DefineVerbatimEnvironment{sreoutput}{Verbatim}{fontsize=\scriptsize,xleftmargin=2.0\parindent}% \makeatletter \newcommand{\listoffaqs}{\@starttoc{faq}} \newenvironment{srefaq}[1] {\addcontentsline{faq}{faq}{#1}\begin{sloppypar}\noindent\slshape\small\begin{quote}\textbf{$\triangleright$ #1}} {\end{quote}\end{sloppypar}} \newcommand{\l@faq}[2]{\@dottedtocline{0}{0pt}{0pt}{#1}{#2}} \makeatother % Consistent font styles % \software{} for the name of a software package % \database{} for the name of a database % \prog{} for a program or file name % \emprog{} for an emphasized program or file name % \user{} for a typed user command % \response{} for an output line following a \user command % \newcommand{\software}[1]{\textsc{#1}} \newcommand{\database}[1]{\textsc{#1}} \newcommand{\prog}[1]{{\small\bfseries\texttt{#1}}} \newcommand{\emprog}[1]{{\small\bfseries\texttt{#1}}} \newcommand{\user}[1]{\indent\indent{\small\bfseries\texttt{> #1}}} \newcommand{\response}[1]{\indent\indent{\small\bfseries\texttt{#1}}} % The ``wideitem'' environment is mostly obsolete, but % it gets used in converted manpages. % \newenvironment{wideitem}{\begin{list} {} { \setlength{\labelwidth}{2in}\setlength{\leftmargin}{1.5in}}} {\end{list}} % The following are used as temp vars in how man pages are % converted into LaTeX w/ rman; see ``make manpages'' in Makefile. % \newlength{\sresavei} \newlength{\sresaves}squid/Docs/main.tex0000640000175000017520000000114410463223377014451 0ustar naolivbiolinux \documentstyle[jmb]{article} \setcounter{secnumdepth}{0} \input{psfig} \addtolength{\oddsidemargin}{-.5in} \addtolength{\textwidth}{1in} \addtolength{\topmargin}{-.5in} \addtolength{\textheight}{1in} \renewcommand{\baselinestretch}{1.2} \title{The SQUID sequence function library} \author{Sean R. Eddy \\ MRC Laboratory of Molecular Biology\\ Hills Road\\ Cambridge CB2 2QH\\ England\\ sre@mrc-lmb.cam.ac.uk} \begin{document} \bibliographystyle{jmb} \nocite{TitlesOn} \maketitle \input{abstract} \input{formats} \input{selex} \input{squid-format} \input{gsi-format} \bibliography{master} \end{document} squid/Docs/selex.tex0000640000175000017520000001464410463223377014656 0ustar naolivbiolinux\section{ SELEX alignment file format } \subsection{ Example of a simple SELEX format file} \begin{verbatim} # Example selex file seq1 ACGACGACGACG. seq2 ..GGGAAAGG.GA seq3 UUU..AAAUUU.A seq1 ..ACG seq2 AAGGG seq3 AA...UUU \end{verbatim} SELEX is an interleaved multiple alignment format that evolved as an intuitive format. SELEX files are easy to write and manipulate manually with a text editor. It is usually easy to convert other alignment formats into SELEX format; the output of the CLUSTALV multiple alignment program and GCG's MSF format are similar interleaved formats. Because it evolved to accomodate different user input styles, it is very tolerant of various inconsistencies such as different gap symbols, varying line lengths, etc. As the format evolved, more features have been added. To maintain compatibility with past alignment files, the new features are added using a reserved comment style. These extra features are usually maintained by automated SELEX-generating software, such as the {\tt koala} sequence alignment editor or my {\tt cove} and {\tt hmm} sequence analysis packages. This extra information includes consensus and individual RNA or protein secondary structure, per-sequence weights, a reference coordinate system for the columns, and database source information including name, accession number, and coordinates (for subsequences extracted from a longer source sequence). \subsection {Specification of a SELEX file} \begin{enumerate} \item Any line beginning with a \verb+#=+ as the first two characters is a machine ``comment''. \verb+#=+ comments are reserved for additional data about the alignment. Usually these features are maintained by software such as the {\tt koala} editor, not by hand. \item All other lines beginning with a \verb+%+ or \verb+#+ as the first character is a user comment. User comments are ignored by all software. Any number of comments may be included. \item Lines of data consist of a name followed by a sequence. The total length of the line must be smaller than 1024 characters. \item Names must be a single word. Any non-whitespace characters are accepted. No spaces are tolerated in names: names MUST be a single word. \item In the sequence, any of the characters \verb+-_.+ or a space are recognized as gaps. Gaps are converted to a '.'. Any other characters are interpreted as sequence. Sequence is case-sensitive. There is a common assumption by my software that upper-case symbols are used for consensus (match) positions and lower-case symbols are used for inserts. This language of ``match'' versus ``insert'' comes from the hidden Markov model formalism \cite{Krogh94}. To almost all of my software, this isn't important, and it immediately converts the sequence to all upper-case after it's read. \item Multiple different sequences are grouped in a block of data lines. Blocks are separated by blank lines. No blank lines are tolerated between the sequence lines in a block. Each block in a multi-block file of a long alignment must have its sequences in the same order in each block. The names are checked to verify that this is the case; if not, only a warning is generated. (In manually constructed files, some users may wish to use shorthand names after the first block with full names, but this isn't recommended.) \end{enumerate} \subsection {Special comments} \subsubsection {Secondary structure} I use one-letter codes to indicate secondary structures. Secondary structure strings are aligned to sequence blocks just like additional sequences. For RNA secondary structure, the symbols \verb+>+ and \verb+<+ are used for base pairs (pairs point at each other). \verb-+- indicate other single-stranded positions, {\tt .} indicates unassigned bases. This description follows \cite{Konings89}. For protein secondary structure, I use {\tt E} to indicate residues in $\beta$-sheet, {\tt H} for those in $\alpha$-helix, {\tt L} for those in loops, and {\tt .} for unassigned residues. RNA pseudoknots are represented by alphabetic characters, with upper case letters representing the 5' side of the helix and lower case letters representing the 3' side. Note that this restricts the annotation to a maximum of 26 pseudoknots per sequence. Lines beginning with \verb+#=SS+ or \verb+#=CS+ are individual or consensus secondary structure data, respectively. \verb+#=SS+ individual secondary structure lines must immediately follow the sequence they are associated with. There can only be one \verb+#=SS+ per sequence. \verb+#=CS+ consensus secondary structure predictions precede all the sequences in each block. There can only be one \verb+#=CS+ per file. \subsubsection {Reference coordinate system} Alignments are usually numbered by some reference coordinate system, often a canonical molecule. For instance, tRNA positions are numbered by reference to the positions of yeast tRNA-Phe. A line beginning with \verb+#=RF+ preceding the sequences in a block gives a reference coordinate system. Any non-gap symbol in the \verb+#=RF+ line indicates that sequence positions in its columns are numbered. For instance, the \verb+#=RF+ lines for a tRNA alignment would have 76 non-gap symbols for the canonical numbered columns; they might be the aligned tRNA-Phe sequence itself, or they might be just X's. \subsubsection {Sequence header} Additional per-sequence information can be placed in a header before any blocks appear. These lines, one per sequence and in exactly the same order as the sequences appear in the alignment, are formatted like \verb+#=SQ +. This information includes a sequence weight (for compensating for biased representation of subfamilies of sequences in the alignment); source information, if the sequence came from a database, consisting of identifier, accession number, and source coordinates; and a description of the sequence. If a \verb+#=SQ+ line is present, all the fields must be present. If no information is available for a field, use '-' for all the fields except the source coordinates, which would be given as '0'. \subsubsection {Author} The first non-comment, non-blank line of the file may be a \verb+#=AU+ ``author'' line. There is a programmatic interface for alignment-generating programs to record a short comment like \verb+11 November 1993, by Feng-Doolittle v. 2.1.1+, and this comment will be recorded on the \verb+#=AU+ line by \verb+WriteSELEX()+. squid/Docs/squid-format.tex0000640000175000017520000000575110463223377016150 0ustar naolivbiolinux\newpage \section {SQUID format} SQUID format is a sequence database format similar to the PIR, GenBank, and EMBL formats. The primary difference is that SQUID format may optionally contain secondary structure annotation information for the sequence. No other sequence format allows secondary structure annotation, which is why SQUID format became necessary. An example SQUID format file: \begin{verbatim} NAM DY9990 SRC HSTGYA M27547 76..169::196 DES Human Tyr-tRNA gene, clone pM6. SEQ +SS 1 ccttcgatagctcagctggtagagcggaggactgtagactgcggaaacgt >>>>>>>..>>>>........<<<<.>>>>>................... 51 ttgtggacatccttaggtcgctggttcaattccggctcgaagga .........<<<<<.....>>>>>.......<<<<<<<<<<<<. ++ NAM DY9991 SRC HSTRNAYE M55611 1..93::93 DES Human Tyr-tRNA precursor. SEQ +SS 1 ccttcgatagctcagctggtagagcggaggactgtagcctgtagaaacat >>>>>>>..>>>>........<<<<.>>>>>................... 51 ttgtggacatccttaggtcgctggttcgattccggctcgaagg .........<<<<<.....>>>>>.......<<<<<<<<<<<< ++ NAM DA0260 SEQ 1 GGGCGAAUAGUGUCAGCGGGAGCACACCAGACUUGCAAUCUGGUAGGGAG 51 GGUUCGAGUCCCUCUUUGUCCACCA ++ \end{verbatim} \subsection {Specification of a SQUID file} \begin{enumerate} \item There must be a line of the form \verb+NAM +. \item There may be an optional line \verb+SRC ..::+, which specified a database source for this sequence, giving the database identifier (name), accession number, start and end position in the database sequence, and the original length of the database sequence, respectively. If a \verb+SRC+ line is present, all of these values must be specified. If any values are unknown, they may be set to \verb+-+ in the case of \verb++ and \verb++ and \verb+0+ in the case of \verb++, \verb+, and \verb++, and in these cases the values will be ignored. \item There may be an optional line \verb+DES + giving a one-line description of the sequence. \item There must be a line of the form \verb-SEQ +SS- or \verb-SEQ-. If the line contains \verb-+SS-, it means that the record contains secondary structure annotation interleaved with the sequence. \item The sequence (and optional structure) immediately follow. There may be optional numbering either before or after the sequence. The number of characters per line is unimportant. Spaces and tabs are ignored. There must be no non-numeric non-space characters on any lines except sequence or structure annotation characters. Structure annotation is fairly free-form; any alphabetic character or character in the set \verb/_.-*?<>{}[]()!@#$%^&=+;:'|`~"\/ is accepted. There must be one such character for every sequence character (preferably aligned to the sequence, but in fact this is not checked for). Note that spaces in the secondary structure annotation are not permitted, except where they are aligned to gaps in the sequence. \item Sequence records are separated by a line of the form \verb-++-. \end{enumerate} squid/Docs/ssi-format.tex0000640000175000017520000006671710463223377015632 0ustar naolivbiolinux% SRE, Mon Dec 25 13:00:46 2000 \documentclass[12pt]{report} \usepackage{fancyvrb} \usepackage{fullpage} \usepackage{times} \usepackage{epsfig} %\usepackage{html} % From the LaTeX2html translator \usepackage{apalike} \setcounter{secnumdepth}{2} \input{macros} \begin{document} \bibliographystyle{apalike} \section{SSI format} SSI format (Sequence/Subsequence Index format) indexes flatfile databases by names and/or accessions, enabling fast retrieval. An SSI index is a binary file that stores sequence names or accessions as \emph{keys} that it can look up rapidly. It differentiates between \emph{primary keys} and \emph{secondary keys}. There is one and only one primary key per sequence. There can be more than one secondary key per sequence. Both primary and secondary keys must be unique identifiers (no two records have the same key). A program (like HMMER's distributed PVM implementation) that needs to step through each sequence one at a time can refer to the list of primary keys. A program solely concerned with flexible sequence retrieval (such as SQUID's \prog{sfetch}) might consult an SSI index with accessions as primary keys, and names as secondary keys. A single SSI file can index multiple sequence data files. This allows indexing multifile databases (e.g. Genbank flatfile distributions). The SSI format is relatively simple and may prove useful for other indexing tasks besides sequence names. HMMER uses SSI format to index HMM files. \subsection{Special features of SSI} SSI superceded 1994's GSI format after human genome sequence files started exceeding 2 GB filesystem limitations, and after problems in the HMMER PVM implementation had to be hacked around. SSI has the following additional features compared to GSI. \begin{description} \item[Separate primary key section] Primary keys are set apart in a separate section, enabling programs to step through a guaranteed one-to-one mapping of keys to sequences. A secondary key section adds many-to-one mapping of keys to sequences. \item[Arbitrary filename and key lengths] File name lengths and key name lengths are effectively unlimited. \item[64-bit indexing] For sequence files exceeding 2GB, on architectures that support 64-bit filesystems (such as IRIX, Solaris, Tru64 UNIX, FreeBSD...), SSI supports 64-bit indexing; depending on the system, file sizes may theoretically be allowed to range up to millions of terabytes. \item[Fast subsequence extraction] SSI can be used to greatly accelerate \emph{subsequence} extraction from very long sequences (example: human chromosome contigs). The sequence file must meet certain formatting conditions for this to work; see below for details. \end{description} \subsection{SSI API in SQUID} \subsubsection{Functions for using a SSI index file:} \begin{sreapi} \item[int SSIOpen(char *filename, SSIFILE **ret\_sfp)] Opens the SSI index file \prog{filename} and returns a \prog{SSIFILE *} stream through \prog{ret\_sfp}. Returns 0 on success, nonzero on failure. The caller must eventually close this stream using \prog{SSIClose()}. More than one index can be open at once. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_NOFILE} & failed to open file; doesn't exist or not readable\\ \prog{SSI\_ERR\_BADMAGIC} & not a SSI file \\ \prog{SSI\_ERR\_NO64BIT} & it has 64-bit offsets, and we can't support that\\ \prog{SSI\_ERR\_FORMAT} & file appears to be corrupted\\ \prog{SSI\_ERR\_MALLOC} & malloc failed \\ \end{tabular} \item[int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret\_fh, SSIOFFSET *ret\_offset)] Looks up the string \prog{key} in the open index \prog{sfp}. \prog{key} can be either a primary or secondary key. If \prog{key} is found, \prog{*ret\_fh} contains a unique handle on the file that contains {key} (suitable for an \prog{SSIFileInfo()} call, or for comparison to the handle of the last file that was opened for retrieval), and \prog{offset} is filled in with the offset in that file. Returns 0 on success, non-zero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_NO\_SUCH\_KEY} & key not found \\ \prog{SSI\_ERR\_NODATA} & fread() failed, file appears to be corrupted\\ \end{tabular} \item[int SSIGetOffsetByNumber(SSIFILE *sfp, int nkey, int *ret\_fh, SSIOFFSET *offset)] Retrieves information for primary key number \prog{nkey}. \prog{nkey} ranges from 0..\prog{nprimary-1}. When the key is found, \prog{*ret\_fh} contains a unique handle on the file that contains {key} (suitable for an SSIFileInfo() call, or for comparison to the handle of the last file that was opened for retrieval), and \prog{offset} is filled in with the offset in that file. Returns 0 on success, non-zero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_SEEK\_FAILED} & failed to reposition in index file\\ \prog{SSI\_ERR\_NO\_SUCH\_KEY} & key not found \\ \prog{SSI\_ERR\_NODATA} & fread() failed, file appears to be corrupted\\ \end{tabular} \item[int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested\_start, int *ret\_fh, SSIOFFSET *record\_offset, SSIOFFSET *data\_offset, int *ret\_actual\_start)] Implements \prog{SSI\_FAST\_SUBSEQ}. Looks up the string \prog{key} in the open index \prog{sfp}, and asks for the nearest offset to a subsequence starting at position \prog{requested\_start} in the sequence (numbering the sequence 1..L). \prog{key} can be either a primary or secondary key. If \prog{key} is found, \prog{*ret\_fh} contains a unique handle on the file that contains {key} (suitable for an SSIFileInfo() call, or for comparison to the handle of the last file that was opened for retrieval); \prog{record\_offset} contains the disk offset to the start of the record; \prog{data\_offset} contains the disk offset either exactly at the requested residue, or at the start of the line containing the requested residue; \prog{ret\_actual\_start} contains the coordinate (1..L) of the first valid residue at or after \prog{data\_offset}. \prog{ret\_actual\_start} is $\leq$ \prog{requested\_start}. Returns 0 on success, non-zero on failure. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_NO\_SUBSEQS} & this file or key doesn't allow subseq lookup\\ \prog{SSI\_ERR\_NO\_SUCH\_KEY} & key not found \\ \prog{SSI\_ERR\_RANGE} & the requested\_start is out of bounds\\ \prog{SSI\_ERR\_NODATA} & fread() failed, file appears to be corrupted\\ \end{tabular} \item[int SSISetFilePosition(FILE *fp, SSIOFFSET *offset] Uses \prog{offset} to sets the file position for \prog{fp} (usually an open sequence file) relative to the start of the file. Hides the details of system-dependent shenanigans necessary for file positioning in large ($>2$ GB) files. Behaves just like \prog{fseek(fp, offset, SEEK\_SET)} for 32 bit offsets and $<2$ GB files. Returns 0 on success, nonzero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_SEEK\_FAILED} & failed to reposition the file\\ \end{tabular} \item[int SSIFileInfo(SSIFILE *sfp, int fh, char **ret\_filename, int *ret\_format)] Given a file handle \prog{fh} in an open index file \prog{sfp}, retrieve file name \prog{ret\_filename} and the file format \prog{ret\_format}. \prog{ret\_filename} is a pointer to a string maintained internally by \prog{sfp}. It should not be free'd; \prog{SSIClose(sfp)} will take care of it. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_BADARG} & no such file n\\ \end{tabular} \item[void SSIClose(SSIFILE *sfp)] Close an open \prog{SSIFILE *}. \end{sreapi} \subsubsection{Skeleton example code for using a SSI index file:} \small\begin{verbatim} SSIFILE *sfp; FILE *fp; int fh; char *seqfile; int fmt; SSIOFFSET offset; SSIOpen(``foo.gsi'', &sfp); /* Finding an entry by name * (by number, with SSIGetOffsetByNumber(), is analogous) */ SSIGetOffsetByName(sfp, ``important_key'', &fh, &offset); SSIGetFileInfo(sfp, fh, &seqfile, &fmt); fp = fopen(seqfile, ``r''); /* more usually SeqfileOpen(), using fmt */ SSIFilePosition(fp, &offset); /* read the entry from there, do whatever... */ free(seqfile); fclose(fp); SSIClose(sfp); \end{verbatim}\normalsize \subsubsection{Functions for creating a SSI index file:} \begin{sreapi} \item[int SSIRecommendMode(char *file)] Examines the file and determines whether it should be indexed with large file support or not; returns \prog{SSI\_OFFSET\_I32} for most files, \prog{SSI\_OFFSET\_I64} for large files, or -1 on failure. \item[SSIINDEX *SSICreateIndex(int mode)] Creates and initializes a SSI index structure. Sequence file offset type to be used is specified by \prog{mode}, which may be either \prog{SSI\_OFFSET\_I32} or \prog{SSI\_OFFSET\_I64}. Returns a pointer to the new structure, or NULL on failure. The caller must free this structure with \prog{SSIFreeIndex()} when done. \item[int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret\_offset)] Fills \prog{ret\_offset} with the current disk offset of \prog{fp}, relative to the start of the file. {mode} is the type of offset to use; it must be either \prog{SSI\_OFFSET\_I32} or \prog{SSI\_OFFSET\_I64}. Returns 0 on success, non-zero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_NO64BIT} & 64-bit mode unsupported on this system\\ \prog{SSI\_ERR\_TELL\_FAILED} & failed to determine position in file\\ \end{tabular} \item[int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret\_fh)] Adds the sequence file \prog{filename}, which is known to be in format \prog{fmt}, to the index \prog{g}. Creates and returns a unique filehandle \prog{ret\_fh} for associating primary keys with this file using \prog{SSIAddPrimaryKeyToIndex()}. Returns 0 on success, non-zero on failure. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_TOOMANY\_FILES} & exceeded file number limit\\ \prog{SSI\_ERR\_MALLOC} & a malloc() failed\\ \end{tabular} \item[int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl)] Set \prog{SSI\_FAST\_SUBSEQ} for the file indicated by filehandle \prog{fh} in the index \prog{g}, setting parameters \prog{bpl} and \prog{rpl} to the values given. \prog{bpl} is the number of bytes per sequence data line. \prog{rpl} is the number of residues per sequence data line. Caller must be sure that \prog{bpl} and \prog{rpl} do not change on any line of any sequence record in the file (except for the last data line of each record). If this is not the case in this file, \prog{SSI\_FAST\_SUBSEQ} will not work, and this routine should not be called. Returns 0 on success, non-zero on failure. \item[int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh, SSIOFFSET *r\_off, SSIOFFSET *d\_off, int L)] Puts a primary key \prog{key} in the index \prog{g}, while telling the index that this primary key is in the file associated with filehandle \prog{fh} and its record starts at position \prog{r\_off} in that file. \prog{d\_off} and \prog{L} are optional; they may be left unset by passing NULL and 0, respectively. (If one is provided, both must be provided.) If they are provided, \prog{d\_off} gives the position of the first line of sequence data in the record, and \prog{L} gives the length of the sequence in residues. They are used when \prog{SSI\_FAST\_SUBSEQ} is set for the sequence file. If \prog{SSI\_FAST\_SUBSEQ} is not set for the file, \prog{d\_off} and \prog{L} will be ignored even if they are available, so it doesn't hurt for the indexing program to provide them; typically it won't know whether it's safe to set \prog{SSI\_FAST\_SUBSEQ} for the whole file until the whole file has been read and every key has already been added to the index. Through \prog{ret\_kh} it provides a ``handle'' - a unique identifier for the primary key - that any subsequent calls to \prog{SSIAddSecondaryKeyToIndex()} will use to associate one or more secondary keys with this primary key. Returns 0 on success, non-zero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_TOOMANY\_KEYS} & exceeded primary key limit\\ \prog{SSI\_ERR\_TOOMANY\_FILES} & filenum exceeds file limit\\ \prog{SSI\_ERR\_MALLOC} & a malloc() failed\\ \end{tabular} \item[int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey)] Puts a secondary key \prog{key} in the index \prog{g}, associating it with a primary key \prog{pkey} that has already been added to the index by \prog{SSIAddPrimaryKeyToIndex()}. Returns 0 on success, non-zero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_TOOMANY\_KEYS} & exceeded secondary key limit\\ \prog{SSI\_ERR\_MALLOC} & a malloc() failed\\ \end{tabular} \item[int SSIWriteIndex(char *file, SSIINDEX *g)] Writes complete index \prog{g} in SSI format to a binary file \prog{file}. Does all overhead of sorting the primary and secondary keys, and maintaining the association of secondary keys with primary keys during and after the sort. Returns 0 on success, non-zero on error. Error codes:\\ \begin{tabular}{ll} \prog{SSI\_ERR\_NOFILE} & an fopen() failed\\ \prog{SSI\_ERR\_FWRITE} & an fwrite() failed\\ \prog{SSI\_ERR\_MALLOC} & a malloc() failed\\ \end{tabular} \item[void SSIFreeIndex(SSIINDEX *g)] Free an index structure. \end{sreapi} \subsubsection{Other SSI functions:} \begin{sreapi} \item[char *SSIErrorString(int n)] Returns a pointer to an internal string corresponding to error \prog{n}, a return code from any of the functions in the API that return non-zero on error. \end{sreapi} \subsection{Detailed specification of SSI binary format} There are four sections to the SSI file: \begin{sreitems}{\textbf{Secondary keys}} \item[\textbf{Header}] Contains a magic number indicating GSI version number, and various information about the number and sizes of things in the index. \item[\textbf{Files}] Contains one or more \emph{file records}, one per sequence file that's indexed. These contain information about the individual files. \item[\textbf{Primary keys}] Contains one or more \emph{primary key records}, one per primary key. \item[\textbf{Secondary keys}] Contains one or more \emph{secondary key records}, one per secondary key. \end{sreitems} All numeric quantities are stored as unsigned integers of known size in network (bigendian) order, for maximum crossplatform portability of the index files. \prog{sqd\_uint16}, \prog{sqd\_uint32}, and \prog{sqd\_uint64} are typically typedef'd as \prog{unsigned short}, \prog{unsigned int}, and \prog{unsigned long long} or \prog{unsigned long} at SQUID compile-time. Values may need to be cast to signed quantities, so only half of their dynamic range is valid (e.g. 0..32,767 for values of type \prog{sqd\_uint16}; 0..2,146,483,647 (2 billion) for \prog{sqd\_uint32}; and 0..9.22e18 (9 million trillion) for \prog{sqd\_uint64}). These typedef's are handled automatically by the \prog{./configure} script (see \prog{squidconf.h.in} before configuration, \prog{squidconf.h} after configuration). If necessary, \prog{./configure}'s guess can be overridden in \prog{squidconf.h} after configuration. \subsubsection{Header section} The header section contains: \vspace{1em} \begin{tabular}{llrr} Variable & Description & Bytes & Type \\\hline \prog{magic} & SSI version magic number. & 4 & \prog{sqd\_uint32}\\ \prog{flags} & Optional behavior flags (see below) & 4 & \prog{sqd\_uint32}\\ \prog{nfiles} & Number of files in file section. & 2 & \prog{sqd\_uint16}\\ \prog{nprimary} & Number of primary keys. & 4 & \prog{sqd\_uint32}\\ \prog{nsecondary} & Number of secondary keys. & 4 & \prog{sqd\_uint32}\\ \prog{flen} & Length of filenames (incl. '\verb+\0+') & 4 & \prog{sqd\_uint32}\\ \prog{plen} & Length of primary key names (incl. '\verb+\0+') & 4 & \prog{sqd\_uint32}\\ \prog{slen} & Length of sec. key names (incl. '\verb+\0+') & 4 & \prog{sqd\_uint32}\\ \prog{frecsize} & \# of bytes in a file record & 4 & \prog{sqd\_uint32}\\ \prog{precsize} & \# of bytes in a primary key record & 4 & \prog{sqd\_uint32}\\ \prog{srecsize} & \# of bytes in a sec. key record & 4 & \prog{sqd\_uint32}\\ \prog{foffset} & disk offset, start of file records & \dag & \dag\\ \prog{poffset} & disk offset, start of primary key recs & \dag & \dag\\ \prog{soffset} & disk offset, start of sec. key records & \dag & \dag\\ \end{tabular} \vspace{1em} The optional behavior flags are: \vspace{1em} \begin{tabular}{lll} Flag & Value& Note\\ \hline \prog{SSI\_USE64} & $1 \ll 0$ & Large sequence files; all key offsets 64 bit.\\ \prog{SSI\_USE64\_INDEX} & $1 \ll 1$ & Large index; GSI file itself uses 64-bit offsets.\\\hline \end{tabular} \vspace{1em} The optional behavior flags define whether the SSI file uses large file (64-bit) offsets. This issue is discussed in greater detail below (see ``Large sequence files and large indices''). Briefly: if \prog{SSI\_USE64} is set, the sequence file is large, and all sequence file offsets are 64-bit integers. If \prog{SSI\_USE64\_INDEX} is set, the index file itself is large, and \prog{foffset}, \prog{poffset}, and \prog{soffset} (that is, all offsets within the index file itself, indicated as \dag\ in the above table) are 64-bit integers. \footnote{In the current API it is not expected that \prog{SSI\_USE64\_INDEX} would ever be set. The current index-writing API keeps the entire index in RAM (it has to sort the keys), and would presumably have to be modified or replaced to be able to generate very large indices.} The reason to explicitly record various record sizes (\prog{frecsize}, \prog{precsize}, \prog{srecsize}) and index file positions (\prog{foffset}, \prog{poffset}, \prog{soffset}) is to allow future extendibility. More fields might be added without breaking older SSI parsers. The format is meant to be both forwards- and backwards-compatible. \subsubsection{File section} The file section consists of \prog{nfiles} file records. Each record is \prog{frecsize} bytes long, and contains: \vspace{1em} \begin{tabular}{llrr} Variable & Description & Bytes & Type \\\hline \prog{filename} & Name of file (possibly including full path) & \prog{flen} & char *\\ \prog{format} & Format code for file; see squid.h for definitions & 4 & \prog{sqd\_uint32} \\ \prog{flags} & Optional behavior flags & 4 & \prog{sqd\_uint32} \\ \prog{bpl} & Bytes per sequence data line & 4 & \prog{sqd\_uint32} \\ \prog{rpl} & Residues per sequence data line & 4 & \prog{sqd\_uint32} \\\hline \end{tabular} \vspace{1em} When a SSI file is written, \prog{frecsize} is equal to the sum of the sizes above. When a SSI file is read by a parser, it is possible that \prog{frecsize} is larger than the parser expects, if the parser is expecting an older version of the SSI format: additional fields may be present, which increases \prog{frecsize}. The parser will only try to understand the data up to the \prog{frecsize} it expected to see, but still knows the absolutely correct \prog{frecsize} for purposes of skipping around in the index file. Normally the SSI index resides in the same directory as the sequence data file(s), so \prog{filename} is relative to the location of the SSI index. In the event this is not true, \prog{filename} can contain a full path. \prog{format} is a SQUID sequence file format code; e.g. something like \prog{SQFILE\_FASTA} or \prog{MSAFILE\_STOCKHOLM}. These constants are defined in \prog{squid.h}. Only one possible optional behavior flag is defined: \vspace{1em} \begin{tabular}{lll} Flag & Value& Note\\ \hline \prog{SSI\_FAST\_SUBSEQ} & $1 \ll 0$ & Fast subseq retrieval is possible for this file.\\\hline \end{tabular} \vspace{1em} When \prog{SSI\_FAST\_SUBSEQ} is set, \prog{bpl} and \prog{rpl} are nonzero. They can be used to calculate the offset of subsequence positions in the data file. This is described in the optional behavior section below. \subsubsection{Primary key section} The primary key section consists of \prog{nprimary} records. Each record is \prog{precsize} bytes long, and contains: \vspace{1em} \begin{tabular}{llrr} Variable & Description & Bytes & Type \\\hline \prog{key} & Key name (seq name, identifier, accession) & \prog{plen}& char *\\ \prog{fnum} & File number (0..nfiles-1) & 2 & \prog{sqd\_uint16}\\ \prog{offset1} & Offset to start of record & \ddag & \ddag \\ \prog{offset2} & Offset to start of sequence data & \ddag & \ddag \\ \prog{len} & Length of data (e.g. seq length, residues) & 4 & \prog{sqd\_uint32} \\\hline \end{tabular} \vspace{1em} The offsets are sequence file offsets (indicated by \ddag). They are 4 bytes of type \prog{sqd\_uint32} normally, 8 bytes of type \prog{sqd\_uint32} if \prog{SSI\_USE64} is set, and \prog{sizeof(fpos\_t)} bytes of type \prog{fpos\_t} if \prog{SSI\_FPOS\_T} is set. \prog{offset2} and \prog{len} are only meaningful if \prog{SSI\_FAST\_SUBSEQ} is set on this key's file. \prog{offset2} gives the absolute disk position of line 0 in the sequence data. \prog{len} is necessary for bounds checking in a subsequence retrieval, to be sure we don't try to reposition the disk outside the valid data. \subsubsection{Secondary key section} The secondary key section consists of \prog{nsecondary} records. Each record is \prog{srecsize} bytes long, and contains: \vspace{1em} \begin{tabular}{llrr} Variable & Description & Bytes & Type \\\hline \prog{key} & Key name (seq name, identifier, accession) & \prog{slen}& char *\\ \prog{pkey} & Primary key & \prog{plen}& char *\\\hline \end{tabular} \vspace{1em} All data are kept with the primary key records. Secondary keys are simply translated to primary keys, then the primary key has to be looked up. \subsection{Optional behaviors} \subsubsection{Large sequence files and large indices: 64-bit operation} Normally a SSI index file can be no larger than 2 GB, and can index sequence files that are no larger than 2 GB each. This is due to limitations in the ANSI C/POSIX standards, which were developed for 32-bit operating systems and filesystems. Most modern operating systems allow larger 64-bit file sizes, but as far as I'm aware (Dec 2000), there are no standard interfaces yet for working with positions (offsets) in large files. On many platforms, SSI can extend to full 64-bit capabilities, but on some platforms, it cannot. To understand the limitations (of SSI, and possibly of my understanding) you need to understand some details about what's happening behind the SSI API and how I understand C API's to modern 64-bit OS's and hardware. First, some information on ANSI C APIs for file positioning. ANSI C provides the portable functions \prog{fseek()} and \prog{ftell()} for manipulating simple offsets in a file. They store the offset in a \prog{long} (which ranges up to 2 GB). The Standard says we're allowed to do arithmetic on this value if the file is binary. ANSI C also provides \prog{fgetpos()} and \prog{fsetpos()} which store file positions in an opaque data type called \prog{fpos\_t}. Modern operating systems with large file support define \prog{fpos\_t} in a way that permits files $>$2 GB. However, \prog{fpos\_t} is an opaque type. It has two disadvantages compared to a simple arithmetic type like \prog{long}: first, we're not allowed to do arithmetic on it, and second, we can't store it in a binary file in an architecture-independent manner. We need both features for SSI, unfortunately. \footnote{Surely the professional C community has the same problem; does \emph{everyone} hack around \prog{fpos\_t}?} Therefore we have to rely on system dependent features. Most operating systems provide a non-compliant library call that returns an arithmetic offset. Fully 64-bit systems typically give us a 64-bit \prog{off\_t} and functions \prog{ftello()}/\prog{fseeko()} that work with that offset. Many systems provide a ``transitional interface'' where all normally named functions are 32-bits, but specially named 64-bit varieties are available: e.g. \prog{off\_t} is 32 bits, but \prog{off64\_t} is 64 bits and we have functions \prog{ftello64()} and \prog{fseeko64()}. Some systems provide a \prog{ftell64()} and \prog{fseek64()} that work on offsets of type \prog{long long}. Many popular systems may even provide more than one of these models, depending on compiler flags. And, unfortunately, some systems provide none of these models (FreeBSD for example). There, we will exploit the fact that most systems (including FreeBSD) do in fact implement \prog{fpos\_t} as a simple arithmetic type, such as an \prog{off\_t}, so we can misuse it. At compile time, SQUID's \prog{./configure} script tests for the system's capabilities for 64-bit file offsets, and configures a section in the \prog{squidconf.h} file. (The configuration includes a custom autoconf macro, \prog{SQ\_ARITHMETIC\_FPOS\_T()}, to test \prog{fpos\_t} and define \prog{ARITHMETIC\_FPOS\_T} if it is.) Four possible 64-bit models are tested in the following order; if one of them is possible, it will be used, and the constant \prog{HAS\_64BIT\_FILE\_OFFSETS} is set. \begin{enumerate} \item has \prog{ftello()}, \prog{fseeko()}; sizeof(\prog{off\_t}) $= 8$. \item has \prog{ftello64()}, \prog{fseeko64()}; sizeof(\prog{off64\_t}) $= 8$. \item has \prog{ftell64()}, \prog{fseek64()} \item \prog{fpos\_t} is an arithmetic 64-bit type; (mis)use \prog{fgetpos()}, \prog{fsetpos()}. \end{enumerate} \subsubsection{Fast subsequence retrieval} In some files (notably vertebrate chromosome contigs) the size of each sequence is large. It may be slow to extract a subsequence by first reading the whole sequence into memory -- or even prohibitive, if the sequence is so large that it can't be stored in memory. If the sequence data file is very consistently formatted so that each line in each record (except the last one) is of the same length, in both bytes and residues, we can determine a disk offset of the start of any subsequence by direct calculation. For example, a simple well-formatted FASTA file with 50 residues per line would have 51 bytes per sequence line (counting the '\verb+\0+') (\prog{bpl}=51, \prog{rpl}=50). Position $i$ in a sequence $1..L$ will be on line $l = (i-1)/\mbox{\prog{rpl}}$, and line $l$ starts at disk offset $l * \mbox{\prog{bpl}}$ relative to the start of the sequence data. If there are no nonsequence characters in the data line except the terminal '\verb+\0+' (which is true iff \prog{bpl} = \prog{rpl}+1 and 1 residue = 1 byte), position $i$ can be precisely found: \[ \mbox{relative offset of residue $i$} = \left((i-1)/\mbox{\prog{rpl}}\right)*\mbox{\prog{bpl}} + (i-1) \% \mbox{ \prog{rpl}} \] Even for sequence data lines with extra characters (e.g. spaces, coordinates, whatever), fast subsequence retrieval is possible; a parser can be positioned at the beginning of the appropriate line $l$, which starts at residue $(l*\mbox{\prog{rpl}}) + 1$, and it can start reading from there (e.g. the line that $i$ is on) rather than the beginning of the whole sequence record. The program that creates the index is responsible for determining if \prog{bpl} and \prog{rpl} are consistent throughout a file; if so, it may set the \prog{SSI\_FAST\_SUBSEQ} flag for the file. Then any record whose primary key carries the optional data offset (\prog(offset2)) and sequence length data is available for subsequence position calculations by \prog{SSIGetSubseqOffset()}. \end{document}squid/Formats/0000755000175000017520000000000010463223377013532 5ustar naolivbiolinuxsquid/Formats/a2m0000640000175000017520000002214110463223377014130 0ustar naolivbiolinux>GLB2_MORMR ...PIVD..SGSVSPLSDAEKNKIRAAW.DIVYKNYEKNGVDILVKFFTGTPAAQAFFPK FKGLTTADALKKSSDVRWHAERIINAVNDAVKSMDDTEKMSMKLQELSVKHAQSFYVDRQ YFKVLAGII.........ADTTAPGDAGFEKLMSMICILLSSAY....... >GLBZ_CHITH MKFIILALCVAAASALSGDQIGLVQST.YGKVKG....DSVGILYAVFKADPTIQAAFPQ FVGK.DLDAIKGGAEFSTHAGRIVGFLGGVIDDLP...NIGKHVDALVATH.KPRGVTHA QFNNFRAAFIAYLKGHV..DYTAAVEAAWGATFDAFFGAVFAK.......M >HBA2_BOSMU ...V...........LSAADKGNVKAAW.GKVGGHAAEYGAEALERMFLSFPTTKTYFPH FD.LSH.....GSAQVKGHGAKVAAALTKAVGHLDD...LPGALSELSDLHAHKLRVDPV NFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR...... >HBA2_GALCR ...V...........LSPTDKSNVKAAW.EKVGAHAGDYGAEALERMFLSFPTTKTYFPH FD.LSH.....GSTQVKGHGKKVADALTNAVLHVDD...MPSALSALSDLHAHKLRVDPV NFKLLRHCLLVTLACHHPAEFTPAVHASLDKFMASVSTVLTSKYR...... >HBA4_SALIR ...S...........LSAKDKANVKAIW.GKILPKSDEIGEQALSRMLVVYPQTKAYFSH WASVAP.....GSAPVKKHGITIMNQIDDCVGHMDD...LFGFLTKLSELHATKLRVDPT NFKILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKYR...... >HBAD_CHLME ...M...........LTADDKKLLTQLW.EKVAGHQEEFGSEALQRMFLTYPQTKTYFPH FD.LHP.....GSEQVRGHGKKVAAALGNAVKSLDN...LSQALSELSNLHAYNLRVDPA NFKLLAQCFQVVLATHLGKDYSPEMHAAFDKFLSAVAAVLAEKYR...... >HBAD_PASMO ...M...........LTAEDKKLIQQIW.GKLGGAEEEIGADALWRMFHSYPSTKTYFPH FD.LSQ.....GSDQIRGHGKKVVAALSNAIKNLDN...LSQALSELSNLHAYNLRVDPV NFKFLSQCLQVSLATRLGKEYSPEVHSAVDKFMSAVASVLAEKYR...... >HBAZ_HORSE ...S...........LTKAERTMVVSIW.GKISMQADAVGTEALQRLFSSYPQTKTYFPH FD.LHE.....GSPQLRAHGSKVAAAVGDAVKSIDN...VAGALAKLSELHAYILRVDPV NFKFLSHCLLVTLASRLPADFTADAHAAWDKFLSIVSSVLTEKYR...... >HBA_AILME ...V...........LSPADKTNVKATW.DKIGGHAGEYGGEALERTFASFPTTKTYFPH FD.LSP.....GSAQVKAHGKKVADALTTAVGHLDD...LPGALSALSDLHAHKLRVDPV NFKLLSHCLLVTLASHHPAEFTPAVHASLDKFFSAVSTVLTSKYR...... >HBA_ANSSE ...V...........LSAADKGNVKTVF.GKIGGHAEEYGAETLQRMFQTFPQTKTYFPH FD.LQP.....GSAQIKAHGKKVAAALVEAANHIDD...IAGALSKLSDLHAQKLRVDPV NFKFLGHCFLVVLAIHHPSLLTPEVHASMDKFLCAVATVLTAKYR...... >HBA_COLLI ...V...........LSANDKSNVKAVF.AKIGGQAGDLGGEALERLFITYPQTKTYFPH FD.LSH.....GSAQIKGHGKKVAEALVEAANHIDD...IAGALSKLSDLHAQKLRVDPV NFKLLGHCFLVVVAVHFPSLLTPEVHASLDKFVLAVGTVLTAKYR...... >HBA_ERIEU ...V...........LSATDKANVKTFW.GKLGGHGGEYGGEALDRMFQAHPTTKTYFPH FD.LNP.....GSAQVKGHGKKVADALTTAVNNLDD...VPGALSALSDLHAHKLRVDPV NFKLLSHCLLVTLALHHPADFTPAVHASLDKFLATVATVLTSKYR...... >HBA_FRAPO ...V...........LSAADKNNVKGIF.GKISSHAEDYGAEALERMFITYPSTKTYFPH FD.LSH.....GSAQVKGHGKKVVAALIEAANHIDD...IAGTLSKLSDLHAHKLRVDPV NFKLLGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGNVLTAKYR...... >HBA_MACFA ...V...........LSPADKTNVKAAW.GKVGGHAGEYGAEALERMFLSFPTTKTYFPH FD.LSH.....GSAQVKGHGKKVADALTLAVGHVDD...MPQALSALSDLHAHKLRVDPV NFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR...... >HBA_MACSI ...V...........LSPADKTNVKDAW.GKVGGHAGEYGAEALERMFLSFPTTKTYFPH FD.LSH.....GSAQVKGHGKKVADALTLAVGHVDD...MPQALSALSDLHAHKLRVDPV NFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR...... >HBA_MESAU ...V...........LSAKDKTNISEAW.GKIGGHAGEYGAEALERMFFVYPTTKTYFPH FD.VSH.....GSAQVKGHGKKVADALTNAVGHLDD...LPGALSALSDLHAHKLRVDPV NFKLLSHCLLVTLANHHPADFTPAVHASLDKFFASVSTVLTSKYR...... >HBA_PAGLA ...V...........LSSADKNNIKATW.DKIGSHAGEYGAEALERTFISFPTTKTYFPH FD.LSH.....GSAQVKAHGKKVADALTLAVGHLED...LPNALSALSDLHAYKLRVDPV NFKLLSHCLLVTLACHHPAEFTPAVHSALDKFFSAVSTVLTSKYR...... >HBA_PHACO ...V...........LSAADKNNVKGIF.TKIAGHAEEYGAEALERMFITYPSTKTYFPH FD.LSH.....GSAQIKGHGKKVVAALIEAVNHIDD...ITGTLSKLSDLHAHKLRVDPV NFKLLGQCFLVVVAIHHPSALTPEVHASLDKFLCAVGTVLTAKYR...... >HBA_PONPY ...V...........LSPADKTNVKTAW.GKVGAHAGDYGAEALERMFLSFPTTKTYFPH FD.LSH.....GSAQVKDHGKKVADALTNAVAHVDD...MPNALSALSDLHAHKLRVDPV NFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR...... >HBA_PROLO ...V...........LSPADKANIKATW.DKIGGHAGEYGGEALERTFASFPTTKTYFPH FD.LSP.....GSAQVKAHGKKVADALTLAVGHLDD...LPGALSALSDLHAYKLRVDPV NFKLLSHCLLVTLACHHPAEFTPAVHASLDKFFTSVSTVLTSKYR...... >HBA_TRIOC ...V...........LSANDKTNVKTVF.TKITGHAEDYGAETLERMFITYPPTKTYFPH FD.LHH.....GSAQIKAHGKKVVGALIEAVNHIDD...IAGALSKLSDLHAQKLRVDPV NFKLLGQCFLVVVAIHHPSVLTPEVHASLDKFLCAVGNVLSAKYR...... >HBB1_VAREX ...V..........HWTAEEKQLICSLW.GKI..DVGLIGGETLAGLLVIYPWTQRQFSH FGNLSSPTAIAGNPRVKAHGKKVLTSFGDAIKNLDN...IKDTFAKLSELHCDKLHVDPT NFKLLGNVLVIVLADHHGKEFTPAHHAAYQKLVNVVSHSLARRYH...... >HBB2_TRICR ...V..........HLTAEDRKEIAAIL.GKV..NVDSLGGQCLARLIVVNPWSRRYFHD FGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLDN...LREYYADLSVTHSLKFYVDPE NFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY....... >HBB2_XENTR ...V..........HWTAEEKATIASVW.GKV..DIEQDGHDALSRLLVVYPWTQRYFSS FGNLSNVSAVSGNVKVKAHGNKVLSAVGSAIQHLDD...VKSHLKGLSKSHAEDLHVDPE NFKRLADVLVIVLAAKLGSAFTPQVQAVWEKLNATLVAALSHGYF...... >HBBL_RANCA ...V..........HWTAEEKAVINSVW.QKV..DVEQDGHEALTRLFIVYPWTQRYFST FGDLSSPAAIAGNPKVHAHGKKILGAIDNAIHNLDD...VKGTLHDLSEEHANELHVDPE NFRRLGEVLIVVLGAKLGKAFSPQVQHVWEKFIAVLVDALSHSYH...... >HBB_CALAR ...V..........HLTGEEKSAVTALW.GKV..NVDEVGGEALGRLLVVYPWTQRFFES FGDLSTPDAVMNNPKVKAHGKKVLGAFSDGLTHLDN...LKGTFAHLSELHCDKLHVDPE NFRLLGNVLVCVLAHHFGKEFTPVVQAAYQKVVAGVANALAHKYH...... >HBB_COLLI ...V..........HWSAEEKQLITSIW.GKV..NVADCGAEALARLLIVYPWTQRFFSS FGNLSSATAISGNPNVKAHGKKVLTSFGDAVKNLDN...IKGTFAQLSELHCDKLHVDPE NFRLLGDILVIILAAHFGKDFTPECQAAWQKLVRVVAHALARKYH...... >HBB_EQUHE ...V..........QLSGEEKAAVLALW.DKV..NEEEVGGEALGRLLVVYPWTQRFFDS FGDLSNPAAVMGNPKVKAHGKKVLHSFGEGVHHLDN...LKGTFAQLSELHCDKLHVDPE NFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH...... >HBB_LARRI ...V..........HWSAEEKQLITGLW.GKV..NVADCGAEALARLLIVYPWTQRFFAS FGNLSSPTAINGNPMVRAHGKKVLTSFGEAVKNLDN...IKNTFAQLSELHCDKLHVDPE NFRLLGDILIIVLAAHFAKDFTPDSQAAWQKLVRVVAHALARKYH...... >HBB_MANSP ...V..........HLTPEEKTAVTTLW.GKV..NVDEVGGEALGRLLVVYPWTQRFFDS FGDLSSPDAVMGNPKVKAHGKKVLGAFSDGLNHLDN...LKGTFAQLSELHCDKLHVDPE NFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH...... >HBB_ORNAN ...V..........HLSGGEKSAVTNLW.GKV..NINELGGEALGRLLVVYPWTQRFFEA FGDLSSAGAVMGNPKVKAHGAKVLTSFGDALKNLDD...LKGTFAKLSELHCDKLHVDPE NFNRLGNVLIVVLARHFSKDFSPEVQAAWQKLVSGVAHALGHKYH...... >HBB_RABIT ...V..........HLSSEEKSAVTALW.GKV..NVEEVGGEALGRLLVVYPWTQRFFES FGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDN...LKGTFAKLSELHCDKLHVDPE NFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH...... >HBB_SPECI ...V..........HLSDGEKNAISTAW.GKV..HAAEVGAEALGRLLVVYPWTQRFFDS FGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLDN...LKGTFASLSELHCDKLHVDPE NFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALAHKYH...... >HBB_SPETO ...V..........HLTDGEKNAISTAW.GKV..NAAEIGAEALGRLLVVYPWTQRFFDS FGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLDN...LKGTFASLSELHCDKLHVDPE NFKLLGNMIVIVMAHHLGKDFTPEAQAAFQKVVAGVANALSHKYH...... >HBB_SUNMU ...V..........HLSGEEKACVTGLW.GKV..NEDEVGAEALGRLLVVYPWTQRFFDS FGDLSSASAVMGNPKVKAHGKKVLHSLGEGVANLDN...LKGTFAKLSELHCDKLHVDPE NFRLLGNVLVVVLASKFGKEFTPPVQAAFQKVVAGVANALAHKYH...... >HBB_TACAC ...V..........HLSGSEKTAVTNLW.GHV..NVNELGGEALGRLLVVYPWTQRFFES FGDLSSADAVMGNAKVKAHGAKVLTSFGDALKNLDN...LKGTFAKLSELHCDKLHVDPE NFNRLGNVLVVVLARHFSKEFTPEAQAAWQKLVSGVSHALAHKYH...... >HBB_TRIIN ...V..........HLTPEEKALVIGLW.AKV..NVKEYGGEALGRLLVVYPWTQRFFEH FGDLSSASAIMNNPKVKAHGEKVFTSFGDGLKHLED...LKGAFAELSELHCDKLHVDPE NFRLLGNVLVCVLARHFGKEFSPEAQAAYQKVVAGVANALAHKYH...... >HBB_TUPGL ...V..........HLSGEEKAAVTGLW.GKV..DLEKVGGQSLGSLLIVYPWTQRFFDS FGDLSSPSAVMSNPKVKAHGKKVLTSFSDGLNHLDN...LKGTFAKLSELHCDKLHVDPE NFRLLGNVLVRVLACNFGPEFTPQVQAAFQKVVAGVANALAHKYH...... >HBB_URSMA ...V..........HLTGEEKSLVTGLW.GKV..NVDEVGGEALGRLLVVYPWTQRFFDS FGDLSSADAIMNNPKVKAHGKKVLNSFSDGLKNLDN...LKGTFAKLSELHCDKLHVDPE NFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH...... >HBE_PONPY ...V..........HFTAEEKAAVTSLW.SKM..NVEEAGGEALGRLLVVYPWTQRFFDS FGNLSSPSAILGNPKVKAHGKKVLTSFGDAIKNMDN...LKTTFAKLSELHCDKLHVDPE NFKLLGNVMVIILATHFGKEFTPEVQAAWQKLVSAVAIALAHKYH...... >HBF1_URECA ..............GLTTAQIKAIQDHWFLNIKGCLQAAADSIFFKYLTAYPGDLAFFHK FSSV.PLYGLRSNPAYKAQTLTVINYLDKVVDALGG..NAGALMKAKVPSH.DAMGITPK HFGQLLKLVGGVFQEEF..SADPTTVAAWGDAAGVLVAAM..........K >LGB1_PEA GFTDKQEALVNSSSE.FKQNLPGYSILFYTIVLEKAP..AAKGL................ FSFLKDTAGVEDSPKLQAHAEQVFGLVRDSAAQLRTKGEVVLGNATLGAIHVQKGVTNP. HFVVVKEALLQTIKKASGNNWSEELNTAWEVAYDGLATAIKKAMKT....A >LGB1_VICFA GFTEKQEALVNSSSQLFKQNPSNYSVLFYTIILQKAP..TAKAM................ FSFLKDSAGVVDSPKLGAHAEKVFGMVRDSAVQLRATGEVVLDGKD.GSIHIQKGVLDP. HFVVVKEALLKTIKEASGDKWSEELSAAWEVAYDGLATAIK....A....A >MYG_ESCGI ...V...........LSDAEWQLVLNIW.AKVEADVAGHGQDILIRLFKGHPETLEKFDK FKHLKTEAEMKASEDLKKHGNTVLTALGGILKKKGH...HEAELKPLAQSHATKHKIPIK YLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKELGFQG >MYG_HORSE ...G...........LSDGEWQQVLNVW.GKVEADIAGHGQEVLIRLFTGHPETLEKFDK FKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGH...HEAELKPLAQSHATKHKIPIK YLEFISDAIIHVLHSKHPGNFGADAQGAMTKALELFRNDIAAKYKELGFQG >MYG_LYCPI ...G...........LSDGEWQIVLNIW.GKVETDLAGHGQEVLIRLFKNHPETLDKFDK FKHLKTEDEMKGSEDLKKHGNTVLTALGGILKKKGH...HEAELKPLAQSHATKHKIPVK YLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKELGFQG >MYG_MOUSE ...G...........LSDGEWQLVLNVW.GKVEADLAGHGQEVLIGLFKTHPETLDKFDK FKNLKSEEDMKGSEDLKKHGCTVLTALGTILKKKGQ...HAAEIQPLAQSHATKHKIPVK YLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKELGFQG >MYG_MUSAN ..................VDWEKVNSVW.SAVESDLTAIGQNILLRLFEQYPESQNHFPK FKN.KSLGELKDTADIKAQADTVLSALGNIVKKKGS...HSQPVKALAATHITTHKIPPH YFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKAANFQG >MYG_PROGU ...G...........LSDGEWQLVLNVW.GKVEGDLSGHGQEVLIRLFKGHPETLEKFDK FKHLKAEDEMRASEELKKHGTTVLTALGGILKKKGQ...HAAELAPLAQSHATKHKIPVK YLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKELGFQG >MYG_SAISC ...G...........LSDGEWQLVLNIW.GKVEADIPSHGQEVLISLFKGHPETLEKFDK FKHLKSEDEMKASEELKKHGTTVLTALGGILKKKGQ...HEAELKPLAQSHATKHKIPVK YLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELGFQG squid/Formats/clustal0000640000175000017520000000466310463223377015131 0ustar naolivbiolinuxCLUSTAL W(1.5) multiple sequence alignment REF -----GCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAAATCTGGAGGTC-CTGTGT A0380 -----GGGCTCGTAGATCAG-CGGTAGATCGCTTCCTTCGCAAGGAAGAGGCC-CTGGGT A0500 -----GGGCTCGTAGATCAG-TGGCAGATCGCTTCCTTCGCAAGGAAGAGGCC-CGGGGT A0501 -----GGGCTCGTAGATCAG-GGGTAGATCACTCCCTTGGCATGGGAGAGGCC-CCGGGT A0502 -----GGGCCCATAGCTCAG-TGGTAGAGTGCCTCCTTTGCAAGGAGGATGCC-CAGGGT A1140 -----GGGCCCTAAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGGGTC-GACGGT A1180 -----GGGCCCTTAGCTCAGCTGGGAGAGCACCTGCCTTGCACGCAGGGGGTC-GACGGT A1540 -----GGAGCCTTAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTC-AGCGGT A1660 -----GGGGCTATAGCTCAGCTGGGAGAGCGCTTGCATGGCATGCAAGAGGTC-AGCGGT A1661 -----GGGGGCATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTC-TGCGGT A1662 -----GGGGCTATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTC-TGCGGT A3920 -----GGGGGTATAGTATAATTGGTAGTACAGCAATCTTGCTCAATGCTTGTC--AAGGT A6360 -----GGGCGTGTGGCGTAGTTGGTAGCGCGTTCGCTTAGCATGCGAAAGGTC-TCCGGT A6400 -----GGGCGTGTGGCGTAGTCGGTAGCGCGCTCCCTTAGCATGGGAGAGGTC-TCCGGT A7680 -----GGGGGCGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTA-CCGGGA A7681 -----GGGGGCGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTA-CCGGGA A9990 -----GGGGGATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTA-GCGGGA A9991 -----GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTA-GCGGGA C0500 GCCAAGGTGGCAGAATTCGGC--CCAACGCATCCGCCTGCAGAGCGGAACCCCCGCCGGT C1140 -----GGCAACAAGGCCAAGCGGCTAAGGCATGGGTCTGCAACACCCTGATC--ATCGGT * * * * REF TCGATCCACAGAATTCGCACCA A0380 TCAAATCCCAGCGAGTCCACCA A0500 TCAAATCCCCGCGAGTCCACCA A0501 TCAAATCCCGGCGAGTCCACCA A0502 TCGAATCCCTGTGGGTCCACCA A1140 TCGATCCCGTTAGGGTCCACCA A1180 TCGATCCCGTTAGGGTCCACCA A1540 TCGATCCCGCTAGGCTCCACCA A1660 TCGATCCCGCTTAGCTCCACCA A1661 TCGATCCCGCGCGCTCCCACCA A1662 TCGATCCCGCATAGCTCCACCA A3920 TCAAATCCTTGTATCTCCACCA A6360 TCGACTCCGGACTCGTCCACCA A6400 TCGATTCCGGACTCGTCCACCA A7680 TCGATACCCGGCGCCTCCACCA A7681 TCGATACCCGGCGCCTCCACCA A9990 TCGATGCCCGCATCCTCCACCA A9991 TCGATGCCCGCATTCTCCACCA C0500 TCAAATCCGGCCCTTGGCTCCA C1140 TCGAATCCGATTGTTGCCTCCA ** * * * *** squid/Formats/embl0000640000175000017520000001552110463223377014374 0ustar naolivbiolinuxID XXPHA21 standard; DNA; PHG; 1635 BP. XX AC X02501; M23775; XX SV X02501.1 XX DT 28-JAN-1986 (Rel. 08, Created) DT 12-SEP-1993 (Rel. 36, Last updated, Version 3) XX DE Bacteriophage 21 DNA for left end sequence with genes 1 and 2 XX KW overlapping genes. XX OS Bacteriophage 21 OC Viruses; dsDNA viruses, no RNA stage; Tailed phages; Siphoviridae. XX RN [1] RP 1-1635 RX MEDLINE; 85237525. RA Miller G., Feiss M.; RT "Sequence of the left end of phage 21 DNA"; RL J. Mol. Biol. 183:246-249(1985). XX DR SWISS-PROT; P36693; TERL_BPP21. DR SWISS-PROT; P36694; TERS_BPP21. XX CC Data kindly reviewed (06-MAR-1986) by M. Feiss XX FH Key Location/Qualifiers FH FT source 1..1635 FT /db_xref="taxon:10743" FT /organism="Bacteriophage 21" FT misc_feature 1..177 FT /note="bacteriophage 21 cos segment" FT misc_feature complement(31..41) FT /note="integrative host factor (IHF) binding sequence 1" FT misc_feature 75..85 FT /note="IHF binding sequence 2" FT misc_feature 175..185 FT /note="IHF binding sequence 3" FT RBS 178..181 FT /note="pot. SD-sequence" FT CDS 189..737 FT /db_xref="SWISS-PROT:P36694" FT /note="gp 1 (aa 1-182)" FT /transl_table=11 FT /protein_id="CAA26342.1" FT /translation="MKVNKKRLAEIFNVDPRTIERWQSQGLPCASKGSKGIESVFDTAM FT AIQWYAQRETDIENEKLRKELDDLRAAAESDLQPGTIDYERYRLTKAQADAQELKNARE FT DGVVLETELFTFILQRVAQEISGILVRVPLTLQRKYPDISPSHLDVVKTEIAKASNVAA FT KAGENVGGWIDDFRRAEGS" FT RBS 699..702 FT /note="pot. SD-sequence" FT CDS 709..>1635 FT /db_xref="SWISS-PROT:P36693" FT /note="gp 2 (aa 1-309)" FT /transl_table=11 FT /protein_id="CAA26343.1" FT /translation="MISDAQKAANAAGAIATGLLSLIIPVPLTTVQWANKHYYLPKESS FT YTPGRWETLPFQVGIMNCMGNDLIRTVNLIKSARVGYTKMLLGVEAYFIEHKSRNSLLF FT QPTDSAAEDFMKSHVEPTIRDVPALLELAPWFGRKHRDNTLTLKRFSSGVGFWCLGGAA FT AKNYREKSVDVVCYDELSSFEPDVEKEGSPTLLGDKRIEGSVWPKSIRGSTPKIKGSCQ FT IEKAANESAHFMRFYVPCPHCGEEQYLKFGDDASPFGLKWEKNKPESVFYLCEHHGCVI FT HQSELDQSNGRWICENTGMWTRDGLMFF" XX SQ Sequence 1635 BP; 411 A; 356 C; 436 G; 432 T; 0 other; gggcggcgac ctcgcggttt ttcactattt atgaaaattt ttcagggaaa atcgtgtcgg 60 tacttctcga atataacttt ttgttttttt taatattgca tccgtaaagg tccgacatga 120 aagtgtccga aaatgccttt ttctggcgtt ttcatgtcgg gccttgtatt tgataatggg 180 ttgttttcat gaaggttaat aaaaagaggc ttgccgaaat tttcaacgtg gacccgcgga 240 cgattgaacg ctggcagtct cagggactcc cttgcgcctc caaaggtagt aagggcattg 300 aatctgtatt tgatactgcc atggcaattc agtggtatgc gcagagggaa actgatatcg 360 aaaacgaaaa gctccgcaaa gaactggacg atttgcgtgc ggcagcggag tcagatttac 420 aacccggcac cattgactat gaacgctacc ggctcacaaa agcgcaggca gatgcgcagg 480 aactgaaaaa tgcccgtgaa gacggagtag tgctggaaac tgaactgttt accttcattc 540 tgcaacgtgt ggcacaggag atttcgggga tacttgtgcg tgtgccgttg acattacagc 600 gtaaatatcc ggacatttca ccatcacacc ttgatgtggt gaaaactgaa atcgcgaaag 660 cctccaatgt tgcagctaag gccggtgaaa acgtgggcgg gtggatcgat gatttcagac 720 gcgcagaagg cagctaatgc agccggtgcg atagctacag ggcttttatc tctcattatt 780 cctgttccac tgacgacagt tcagtgggcc aataaacatt attaccttcc taaagagtcg 840 tcttataccc cggggcgatg ggaaacactg ccgtttcagg ttggcatcat gaactgtatg 900 ggcaacgatc tgattcgcac ggttaacctg attaaatctg cccgtgttgg ttatacaaag 960 atgttgctgg gagtggaggc ttattttatt gagcataaat cacgcaacag ccttcttttt 1020 cagcccacgg actcagctgc tgaagatttt atgaaatctc atgttgagcc aacgataagg 1080 gatgttcctg cattgctgga gctggctcca tggttcggaa gaaaacaccg cgataatacg 1140 ctcaccctga agcgtttttc ctccggtgtg gggttctggt gtctgggtgg tgcggcagca 1200 aaaaactacc gtgaaaaatc cgtggatgtg gtctgttatg acgagctttc ctcgttcgaa 1260 ccggatgttg aaaaagaggg ttcgccaacc ctgctggggg ataaacgtat tgagggctct 1320 gtatggccaa aatccattcg cggctcgacg ccaaaaatca aaggctcctg tcagatcgaa 1380 aaagccgcta acgagtcggc acacttcatg cgtttttatg tgccctgtcc gcactgtggg 1440 gaggagcagt atctgaaatt tggcgatgat gcctcgcctt tcggtcttaa gtgggagaag 1500 aataagccag aaagtgtttt ctacctttgc gagcatcatg gctgtgtgat ccatcagtct 1560 gagcttgacc agagtaacgg gcggtggatc tgtgaaaaca cgggcatgtg gacccgtgac 1620 ggcctgatgt ttttc 1635 // ID XXPHI80 standard; DNA; PHG; 233 BP. XX AC X01639; XX SV X01639.1 XX DT 02-JUL-1986 (Rel. 09, Created) DT 02-JUL-1986 (Rel. 09, Last updated, Version 1) XX DE Bacteriophage phi 80 DNA-fragment with replication origin XX KW origin of replication. XX OS Bacteriophage phi-80 OC Viruses; dsDNA viruses, no RNA stage; Tailed phages; Siphoviridae; OC Lambda phage group; bacteriophage lambda. XX RN [1] RP 1-233 RX MEDLINE; 79135017. RA Grosschedl R., Hobom G.; RT "DNA sequences and structural homologies of the replication origins of RT lambdoid bacteriophages"; RL Nature 277:621-627(1979). XX FH Key Location/Qualifiers FH FT source 1..233 FT /db_xref="taxon:10713" FT /organism="Bacteriophage phi-80" FT rep_origin 40..187 FT /note="origin of replication of phi 21" FT misc_feature 40..128 FT /note="pot. binding site for initiator protein" FT repeat_region 50..55 FT /note="multiple repeated sequence I" FT misc_feature 61..66 FT /note="inverted repeat of sequence I" FT repeat_region 71..76 FT /note="direct repeat of I" FT misc_feature 82..87 FT /note="inverted repeat of I" FT repeat_region 92..97 FT /note="direct repeat of I" FT misc_feature 103..108 FT /note="inverted repeat of I" FT repeat_region 113..117 FT /note="imp. direct repeat of I" FT misc_feature 129..155 FT /note="pot. region of replicational primer start site" FT misc_feature 156..187 FT /note="pot. binding site for initiator protein" XX SQ Sequence 233 BP; 91 A; 51 C; 48 G; 43 T; 0 other; ggaccaaata aaaacatctc agaatggtgc atcctcaaaa cgagggaaaa tcccctaaaa 60 cgagggataa aacatccctc aaattggggg attgctatcc ctcaaaacag ggggacacaa 120 aagacactat tacaaaagaa aaaagaaaag attattcgtc agagaattct ggcgaatcct 180 ctgaccagcc agaaaacgac ctttctgtgg tgaaaccgga tgctgcaatt cag 233 // squid/Formats/fasta0000640000175000017520000000350610463223377014553 0ustar naolivbiolinux>AC3.1 CE05131 (CAMBRIDGE) MAQTLLSRHFRGVNCYFIFLNFAGWLMDLHLSTFMQFIPLFPVFGGYCTGLLTQIFRIDDSFQTTYTAFTICLVASALNS CFVRKHQAISKISSKYLLDNVTYCIVIFLLNIYPVIAASLLYLSMLNKSEQVELVKSVYPNLVDKFASLPNYVVFDSNIW AIVFFAFIFFGCTYTLVLIVTTTYQMFKILDDNRKHISASNYAKHRATLRSLLAQFTTCFLIVGPASLFSLLVVIRYEHS QVATHWTIVALTLHSSANAIIIPLRIISISTVYSPEYKNSNGAKYCSNNNNPLTSNFPSFKLVNKLFRLLMILFYYFKLK VPDLLSFCDFTHFDNPESKFYKIHIAKIRLNCSLIF >AC3.2 CE05132 UDP-GLUCURONOSYLTRANSFERASE (CAMBRIDGE) MLHFLSVLRSEETNFLKISKLKKLKTCILNFSIKYGLFEFVKVNHQISILGMYTFLFLLLSLLAVDAGKILVYSPSISRS HLISNGRIADALVDAGHDVVMFITEYEPLTEFTGTKKAKVITMKGFSTKFAEDMDGIGEYLLSSSRLSFLERLMFEKTCT GACDDLMTRREELEQLRAYNFDVAFSEQIDLCGVGIVRYLGIKNHLWISTTPIMDAVSYNLGIPAPSSYVPTIEENDNGD KMDFWQRTFNLYMKIGSILIHRYGTDGTTEVFRKYIPDFPNVREIAANSSLCFVNSDEVLDLPRPTITKAIYVGGLGIPK VSKPLDKKFTNIMSKGKEGVVIISLGSIIPFGDLPAAAKEGVLRAIQEISDYHFLIKIAKGDNNTKKLVEGIKNVDVAEW LPQVDILSHPRLKLFVMHGGINGLVETAIQAVPTVIVPVFADQFRNGRMVEKRGIGKVLLKLDIGYESFKNTVLTVLNTP SYKKNAIRIGKMMRDKPFSPEERLTKWTQFAIDHGVLEELHVEGSRLNTIIYYNLDVIAFVLFVFVAVLHVFIYAFKFLC CDCYDLISYSSPSSCSFSSILVYSPSISRSHLISNGRIADALVDAGHDVVMFITEYEPLTEFTGTKKAKVRSTMIIQWTI LGSTLLLIQEQIFWKGLCTKNGSLIFVMVICFKILNTKSNILNLDLMARREELEQLRAYNFDVAFSEQIDLCGVRIVRYL GIKNHLWISTTPIMDAVSYNLGIPAPSSYVPTIEENDNGDKMDFWQRTFSLYMKIGAILIHRYATDSTTEVFRKYIPDFP NVREIAANSSLCFVNSDEVLDLPRLTITKTIYVGGLGTPNISQHLDNVFAKIMSKGKRGVIIISLGSFVQFGDFPVNIKK EVFRAISELSEYHFLIKISKDDTNTKTLTKEISNVDLVHWFPQVDLLSNPRLKLFIMHGGINGLVEKFF >AC3.3 CE05133 (CAMBRIDGE) MRFIAIAALIASSVLLAEATTIRDKRQSCGCAPRVQPSCSCQRTTYTQPQQYSCSCQNTAPVQKSCSCAQPVQQQTYQIQ ASQCAPACQQSCQNQCQSAPSVSQCQSTCQQSCQTSSCYTPTTPAPVQCQPSCMPACEQSCVVQTPAPVQCVPQCQQQCQ QQCVQTQPIQQCQPQCQQQCVQQCAPTTTAAPQIIKINMEISAQCVPQCQQSCQQQCVQQQVPAQQCNQQCTQQCQTTCQ QAVPQCQQQCAPQCQQPSAPQCQQCQNTCQQAAPVCQQQCAPQCQQQSAPACQQCQTSCQQTQQCQQQCTPQCQQPSAPQ CQQCQSACQAPVATTAAPQVVTIILEASVSQSAQCEPQCQQSCQQQCVQQQQPMQQCAPACTQSCSQSCSAAQPAQMPCQ TQSVNSCSCQQNYSPCGNGQCCKRK squid/Formats/formattest.pl0000640000175000017520000000637210463223377016263 0ustar naolivbiolinux#! /usr/local/bin/perl $binpath = shift; # Suck in the regression data on our file format test suite. # print "Format test suite...\t"; open(DAT,"regression.dat") || die "failed to open regression.dat"; $nfiles = 0; while () { if (/^\#/) { next; } if (/^(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)/) { $filename[$nfiles] = $1; $format[$nfiles] = $2; $seqtype[$nfiles] = $3; $nseq[$nfiles] = $4; $nres[$nfiles] = $5; $shortest[$nfiles] = $6; $longest[$nfiles] = $7; if ($8 eq "yes") { $autodetect[$nfiles] = 1; } else { $autodetect[$nfiles] = 0; } if ($9 eq "yes") { $is_alignment[$nfiles] = 1; } else { $is_alignment[$nfiles] = 0; } if ($10 eq "yes") { $is_singleseq[$nfiles] = 1; } else { $is_singleseq[$nfiles] = 0; } $nfiles++; } } close(DAT); # Test 1. # Run seqstat on every file in two modes; # autodetecting (if format allows it), then forcing a format with --informat. # for ($i = 0; $i < $nfiles; $i++) { if ($autodetect[$i]) { $output = `$binpath/seqstat $filename[$i]`; if ($? != 0) { die "seqstat failed, autodetecting, on $filename[$i]"; } ($ns, $nr, $fr, $to) = &parse_seqstat($output); if ($ns != $nseq[$i] || $nr != $nres[$i] || $fr != $shortest[$i] || $to != $longest[$i]) { die "seqstat regression failed, autodetecting, on $filename[$i]"; } } $output = `$binpath/seqstat --informat $format[$i] $filename[$i]`; if ($? != 0) { die "seqstat failed, using --informat, on $filename[$i]"; } ($ns, $nr, $fr, $to) = &parse_seqstat($output); if ($ns != $nseq[$i] || $nr != $nres[$i] || $fr != $shortest[$i] || $to != $longest[$i]) { die "seqstat regression failed, using --informat, on $filename[$i]"; } } # Test 2. # Reformatting tests. # for ($i = 0; $i < $nfiles; $i++) { for ($j = 0; $j < $nfiles; $j++) { if (! $is_alignment[$i] && $is_alignment[$j]) { next; } # can't convert unaligned to aligned if (! $is_singleseq[$i] && $is_singleseq[$j]) { next; } # can't convert multiple seqs to single seq format `$binpath/sreformat --informat $format[$i] $format[$j] $filename[$i] > formattest.tmp`; if ($? != 0) { die "sreformat failed ($format[$i] to $format[$j]) on $filename[$i]"; } $output = `$binpath/seqstat --informat $format[$j] formattest.tmp`; if ($? != 0) { die "seqstat failed after sreformat ($format[$i] to $format[$j]) on $filename[$i]"; } ($ns, $nr, $fr, $to) = &parse_seqstat($output); if ($ns != $nseq[$i] || $nr != $nres[$i] || $fr != $shortest[$i] || $to != $longest[$i]) { die "seqstat regression failed after sreformat ($format[$i] to $format[$j]) on $filename[$i]"; } } } print "passed.\n"; unlink "formattest.tmp"; # Function: parse_seqstat(file) # # Returns the number of sequences in the file, # and their maximum and minimum length, and their avg. len. # Dies if 'seqstat' fails. # sub parse_seqstat { local($output) = shift; my ($nseq, $nres, $fromlen, $tolen); if ($output =~ /Number of sequences:\s+(\d+)/) {$nseq = $1; } if ($output =~ /Total # residues:\s+(\d+)/) {$nres = $1; } if ($output =~ /Smallest:\s+(\d+)/) {$fromlen = $1; } if ($output =~ /Largest:\s+(\d+)/) {$tolen = $1; } ($nseq, $nres, $fromlen, $tolen); } squid/Formats/gcg0000640000175000017520000003200510463223377014211 0ustar naolivbiolinux Free format documentation can precede a GCG file. In principle it's possible for this documentation to confuse Babelfish autodetection, if it looks like the header of a different sequence file format. HIVHXB2CG Length: 9718 March 10, 1993 14:11 Type: N Check: 1730 .. 1 TGGAAGGGCT AATTCACTCC CAACGAAGAC AAGATATCCT TGATCTGTGG 51 ATCTACCACA CACAAGGCTA CTTCCCTGAT TAGCAGAACT ACACACCAGG 101 GCCAGGGATC AGATATCCAC TGACCTTTGG ATGGTGCTAC AAGCTAGTAC 151 CAGTTGAGCC AGAGAAGTTA GAAGAAGCCA ACAAAGGAGA GAACACCAGC 201 TTGTTACACC CTGTGAGCCT GCATGGAATG GATGACCCGG AGAGAGAAGT 251 GTTAGAGTGG AGGTTTGACA GCCGCCTAGC ATTTCATCAC ATGGCCCGAG 301 AGCTGCATCC GGAGTACTTC AAGAACTGCT GACATCGAGC TTGCTACAAG 351 GGACTTTCCG CTGGGGACTT TCCAGGGAGG CGTGGCCTGG GCGGGACTGG 401 GGAGTGGCGA GCCCTCAGAT CCTGCATATA AGCAGCTGCT TTTTGCCTGT 451 ACTGGGTCTC TCTGGTTAGA CCAGATCTGA GCCTGGGAGC TCTCTGGCTA 501 ACTAGGGAAC CCACTGCTTA AGCCTCAATA AAGCTTGCCT TGAGTGCTTC 551 AAGTAGTGTG TGCCCGTCTG TTGTGTGACT CTGGTAACTA GAGATCCCTC 601 AGACCCTTTT AGTCAGTGTG GAAAATCTCT AGCAGTGGCG CCCGAACAGG 651 GACCTGAAAG CGAAAGGGAA ACCAGAGCTC TCTCGACGCA GGACTCGGCT 701 TGCTGAAGCG CCCGCACGGC AAGAGGCGAG GGGCGGCGAC TGGTGAGTAC 751 GCCAAAAATT TTGACTAGCG GAGGCTAGAA GGAGAGAGAT GGGTGCGAGA 801 GCGTCAGTAT TAAGCGGGGG AGAATTAGAT CGATGGGAAA AAATTCGGTT 851 AAGGCCAGGG GGAAAGAAAA AATATAAATT AAAACATATA GTATGGGCAA 901 GCAGGGAGCT AGAACGATTC GCAGTTAATC CTGGCCTGTT AGAAACATCA 951 GAAGGCTGTA GACAAATACT GGGACAGCTA CAACCATCCC TTCAGACAGG 1001 ATCAGAAGAA CTTAGATCAT TATATAATAC AGTAGCAACC CTCTATTGTG 1051 TGCATCAAAG GATAGAGATA AAAGACACCA AGGAAGCTTT AGACAAGATA 1101 GAGGAAGAGC AAAACAAAAG TAAGAAAAAA GCACAGCAAG CAGCAGCTGA 1151 CACAGGACAC AGCAATCAGG TCAGCCAAAA TTACCCTATA GTGCAGAACA 1201 TCCAGGGGCA AATGGTACAT CAGGCCATAT CACCTAGAAC TTTAAATGCA 1251 TGGGTAAAAG TAGTAGAAGA GAAGGCTTTC AGCCCAGAAG TGATACCCAT 1301 GTTTTCAGCA TTATCAGAAG GAGCCACCCC ACAAGATTTA AACACCATGC 1351 TAAACACAGT GGGGGGACAT CAAGCAGCCA TGCAAATGTT AAAAGAGACC 1401 ATCAATGAGG AAGCTGCAGA ATGGGATAGA GTGCATCCAG TGCATGCAGG 1451 GCCTATTGCA CCAGGCCAGA TGAGAGAACC AAGGGGAAGT GACATAGCAG 1501 GAACTACTAG TACCCTTCAG GAACAAATAG GATGGATGAC AAATAATCCA 1551 CCTATCCCAG TAGGAGAAAT TTATAAAAGA TGGATAATCC TGGGATTAAA 1601 TAAAATAGTA AGAATGTATA GCCCTACCAG CATTCTGGAC ATAAGACAAG 1651 GACCAAAGGA ACCCTTTAGA GACTATGTAG ACCGGTTCTA TAAAACTCTA 1701 AGAGCCGAGC AAGCTTCACA GGAGGTAAAA AATTGGATGA CAGAAACCTT 1751 GTTGGTCCAA AATGCGAACC CAGATTGTAA GACTATTTTA AAAGCATTGG 1801 GACCAGCGGC TACACTAGAA GAAATGATGA CAGCATGTCA GGGAGTAGGA 1851 GGACCCGGCC ATAAGGCAAG AGTTTTGGCT GAAGCAATGA GCCAAGTAAC 1901 AAATTCAGCT ACCATAATGA TGCAGAGAGG CAATTTTAGG AACCAAAGAA 1951 AGATTGTTAA GTGTTTCAAT TGTGGCAAAG AAGGGCACAC AGCCAGAAAT 2001 TGCAGGGCCC CTAGGAAAAA GGGCTGTTGG AAATGTGGAA AGGAAGGACA 2051 CCAAATGAAA GATTGTACTG AGAGACAGGC TAATTTTTTA GGGAAGATCT 2101 GGCCTTCCTA CAAGGGAAGG CCAGGGAATT TTCTTCAGAG CAGACCAGAG 2151 CCAACAGCCC CACCAGAAGA GAGCTTCAGG TCTGGGGTAG AGACAACAAC 2201 TCCCCCTCAG AAGCAGGAGC CGATAGACAA GGAACTGTAT CCTTTAACTT 2251 CCCTCAGGTC ACTCTTTGGC AACGACCCCT CGTCACAATA AAGATAGGGG 2301 GGCAACTAAA GGAAGCTCTA TTAGATACAG GAGCAGATGA TACAGTATTA 2351 GAAGAAATGA GTTTGCCAGG AAGATGGAAA CCAAAAATGA TAGGGGGAAT 2401 TGGAGGTTTT ATCAAAGTAA GACAGTATGA TCAGATACTC ATAGAAATCT 2451 GTGGACATAA AGCTATAGGT ACAGTATTAG TAGGACCTAC ACCTGTCAAC 2501 ATAATTGGAA GAAATCTGTT GACTCAGATT GGTTGCACTT TAAATTTTCC 2551 CATTAGCCCT ATTGAGACTG TACCAGTAAA ATTAAAGCCA GGAATGGATG 2601 GCCCAAAAGT TAAACAATGG CCATTGACAG AAGAAAAAAT AAAAGCATTA 2651 GTAGAAATTT GTACAGAGAT GGAAAAGGAA GGGAAAATTT CAAAAATTGG 2701 GCCTGAAAAT CCATACAATA CTCCAGTATT TGCCATAAAG AAAAAAGACA 2751 GTACTAAATG GAGAAAATTA GTAGATTTCA GAGAACTTAA TAAGAGAACT 2801 CAAGACTTCT GGGAAGTTCA ATTAGGAATA CCACATCCCG CAGGGTTAAA 2851 AAAGAAAAAA TCAGTAACAG TACTGGATGT GGGTGATGCA TATTTTTCAG 2901 TTCCCTTAGA TGAAGACTTC AGGAAGTATA CTGCATTTAC CATACCTAGT 2951 ATAAACAATG AGACACCAGG GATTAGATAT CAGTACAATG TGCTTCCACA 3001 GGGATGGAAA GGATCACCAG CAATATTCCA AAGTAGCATG ACAAAAATCT 3051 TAGAGCCTTT TAGAAAACAA AATCCAGACA TAGTTATCTA TCAATACATG 3101 GATGATTTGT ATGTAGGATC TGACTTAGAA ATAGGGCAGC ATAGAACAAA 3151 AATAGAGGAG CTGAGACAAC ATCTGTTGAG GTGGGGACTT ACCACACCAG 3201 ACAAAAAACA TCAGAAAGAA CCTCCATTCC TTTGGATGGG TTATGAACTC 3251 CATCCTGATA AATGGACAGT ACAGCCTATA GTGCTGCCAG AAAAAGACAG 3301 CTGGACTGTC AATGACATAC AGAAGTTAGT GGGGAAATTG AATTGGGCAA 3351 GTCAGATTTA CCCAGGGATT AAAGTAAGGC AATTATGTAA ACTCCTTAGA 3401 GGAACCAAAG CACTAACAGA AGTAATACCA CTAACAGAAG AAGCAGAGCT 3451 AGAACTGGCA GAAAACAGAG AGATTCTAAA AGAACCAGTA CATGGAGTGT 3501 ATTATGACCC ATCAAAAGAC TTAATAGCAG AAATACAGAA GCAGGGGCAA 3551 GGCCAATGGA CATATCAAAT TTATCAAGAG CCATTTAAAA ATCTGAAAAC 3601 AGGAAAATAT GCAAGAATGA GGGGTGCCCA CACTAATGAT GTAAAACAAT 3651 TAACAGAGGC AGTGCAAAAA ATAACCACAG AAAGCATAGT AATATGGGGA 3701 AAGACTCCTA AATTTAAACT GCCCATACAA AAGGAAACAT GGGAAACATG 3751 GTGGACAGAG TATTGGCAAG CCACCTGGAT TCCTGAGTGG GAGTTTGTTA 3801 ATACCCCTCC CTTAGTGAAA TTATGGTACC AGTTAGAGAA AGAACCCATA 3851 GTAGGAGCAG AAACCTTCTA TGTAGATGGG GCAGCTAACA GGGAGACTAA 3901 ATTAGGAAAA GCAGGATATG TTACTAATAG AGGAAGACAA AAAGTTGTCA 3951 CCCTAACTGA CACAACAAAT CAGAAGACTG AGTTACAAGC AATTTATCTA 4001 GCTTTGCAGG ATTCGGGATT AGAAGTAAAC ATAGTAACAG ACTCACAATA 4051 TGCATTAGGA ATCATTCAAG CACAACCAGA TCAAAGTGAA TCAGAGTTAG 4101 TCAATCAAAT AATAGAGCAG TTAATAAAAA AGGAAAAGGT CTATCTGGCA 4151 TGGGTACCAG CACACAAAGG AATTGGAGGA AATGAACAAG TAGATAAATT 4201 AGTCAGTGCT GGAATCAGGA AAGTACTATT TTTAGATGGA ATAGATAAGG 4251 CCCAAGATGA ACATGAGAAA TATCACAGTA ATTGGAGAGC AATGGCTAGT 4301 GATTTTAACC TGCCACCTGT AGTAGCAAAA GAAATAGTAG CCAGCTGTGA 4351 TAAATGTCAG CTAAAAGGAG AAGCCATGCA TGGACAAGTA GACTGTAGTC 4401 CAGGAATATG GCAACTAGAT TGTACACATT TAGAAGGAAA AGTTATCCTG 4451 GTAGCAGTTC ATGTAGCCAG TGGATATATA GAAGCAGAAG TTATTCCAGC 4501 AGAAACAGGG CAGGAAACAG CATATTTTCT TTTAAAATTA GCAGGAAGAT 4551 GGCCAGTAAA AACAATACAT ACTGACAATG GCAGCAATTT CACCGGTGCT 4601 ACGGTTAGGG CCGCCTGTTG GTGGGCGGGA ATCAAGCAGG AATTTGGAAT 4651 TCCCTACAAT CCCCAAAGTC AAGGAGTAGT AGAATCTATG AATAAAGAAT 4701 TAAAGAAAAT TATAGGACAG GTAAGAGATC AGGCTGAACA TCTTAAGACA 4751 GCAGTACAAA TGGCAGTATT CATCCACAAT TTTAAAAGAA AAGGGGGGAT 4801 TGGGGGGTAC AGTGCAGGGG AAAGAATAGT AGACATAATA GCAACAGACA 4851 TACAAACTAA AGAATTACAA AAACAAATTA CAAAAATTCA AAATTTTCGG 4901 GTTTATTACA GGGACAGCAG AAATTCACTT TGGAAAGGAC CAGCAAAGCT 4951 CCTCTGGAAA GGTGAAGGGG CAGTAGTAAT ACAAGATAAT AGTGACATAA 5001 AAGTAGTGCC AAGAAGAAAA GCAAAGATCA TTAGGGATTA TGGAAAACAG 5051 ATGGCAGGTG ATGATTGTGT GGCAAGTAGA CAGGATGAGG ATTAGAACAT 5101 GGAAAAGTTT AGTAAAACAC CATATGTATG TTTCAGGGAA AGCTAGGGGA 5151 TGGTTTTATA GACATCACTA TGAAAGCCCT CATCCAAGAA TAAGTTCAGA 5201 AGTACACATC CCACTAGGGG ATGCTAGATT GGTAATAACA ACATATTGGG 5251 GTCTGCATAC AGGAGAAAGA GACTGGCATT TGGGTCAGGG AGTCTCCATA 5301 GAATGGAGGA AAAAGAGATA TAGCACACAA GTAGACCCTG AACTAGCAGA 5351 CCAACTAATT CATCTGTATT ACTTTGACTG TTTTTCAGAC TCTGCTATAA 5401 GAAAGGCCTT ATTAGGACAC ATAGTTAGCC CTAGGTGTGA ATATCAAGCA 5451 GGACATAACA AGGTAGGATC TCTACAATAC TTGGCACTAG CAGCATTAAT 5501 AACACCAAAA AAGATAAAGC CACCTTTGCC TAGTGTTACG AAACTGACAG 5551 AGGATAGATG GAACAAGCCC CAGAAGACCA AGGGCCACAG AGGGAGCCAC 5601 ACAATGAATG GACACTAGAG CTTTTAGAGG AGCTTAAGAA TGAAGCTGTT 5651 AGACATTTTC CTAGGATTTG GCTCCATGGC TTAGGGCAAC ATATCTATGA 5701 AACTTATGGG GATACTTGGG CAGGAGTGGA AGCCATAATA AGAATTCTGC 5751 AACAACTGCT GTTTATCCAT TTTCAGAATT GGGTGTCGAC ATAGCAGAAT 5801 AGGCGTTACT CGACAGAGGA GAGCAAGAAA TGGAGCCAGT AGATCCTAGA 5851 CTAGAGCCCT GGAAGCATCC AGGAAGTCAG CCTAAAACTG CTTGTACCAA 5901 TTGCTATTGT AAAAAGTGTT GCTTTCATTG CCAAGTTTGT TTCATAACAA 5951 AAGCCTTAGG CATCTCCTAT GGCAGGAAGA AGCGGAGACA GCGACGAAGA 6001 GCTCATCAGA ACAGTCAGAC TCATCAAGCT TCTCTATCAA AGCAGTAAGT 6051 AGTACATGTA ACGCAACCTA TACCAATAGT AGCAATAGTA GCATTAGTAG 6101 TAGCAATAAT AATAGCAATA GTTGTGTGGT CCATAGTAAT CATAGAATAT 6151 AGGAAAATAT TAAGACAAAG AAAAATAGAC AGGTTAATTG ATAGACTAAT 6201 AGAAAGAGCA GAAGACAGTG GCAATGAGAG TGAAGGAGAA ATATCAGCAC 6251 TTGTGGAGAT GGGGGTGGAG ATGGGGCACC ATGCTCCTTG GGATGTTGAT 6301 GATCTGTAGT GCTACAGAAA AATTGTGGGT CACAGTCTAT TATGGGGTAC 6351 CTGTGTGGAA GGAAGCAACC ACCACTCTAT TTTGTGCATC AGATGCTAAA 6401 GCATATGATA CAGAGGTACA TAATGTTTGG GCCACACATG CCTGTGTACC 6451 CACAGACCCC AACCCACAAG AAGTAGTATT GGTAAATGTG ACAGAAAATT 6501 TTGACATGTG GAAAAATGAC ATGGTAGAAC AGATGCATGA GGATATAATC 6551 AGTTTATGGG ATCAAAGCCT AAAGCCATGT GTAAAATTAA CCCCACTCTG 6601 TGTTAGTTTA AAGTGCACTG ATTTGAAGAA TGATACTAAT ACCAATAGTA 6651 GTAGCGGGAG AATGATAATG GAGAAAGGAG AGATAAAAAA CTGCTCTTTC 6701 AATATCAGCA CAAGCATAAG AGGTAAGGTG CAGAAAGAAT ATGCATTTTT 6751 TTATAAACTT GATATAATAC CAATAGATAA TGATACTACC AGCTATAGCT 6801 TGACAAGTTG TAACACCTCA GTCATTACAC AGGCCTGTCC AAAGGTATCC 6851 TTTGAGCCAA TTCCCATACA TTATTGTGCC CCGGCTGGTT TTGCGATTCT 6901 AAAATGTAAT AATAAGACGT TCAATGGAAC AGGACCATGT ACAAATGTCA 6951 GCACAGTACA ATGTACACAT GGAATTAGGC CAGTAGTATC AACTCAACTG 7001 CTGTTAAATG GCAGTCTAGC AGAAGAAGAG GTAGTAATTA GATCTGTCAA 7051 TTTCACGGAC AATGCTAAAA CCATAATAGT ACAGCTGAAC ACATCTGTAG 7101 AAATTAATTG TACAAGACCC AACAACAATA CAAGAAAAAG AATCCGTATC 7151 CAGAGAGGAC CAGGGAGAGC ATTTGTTACA ATAGGAAAAA TAGGAAATAT 7201 GAGACAAGCA CATTGTAACA TTAGTAGAGC AAAATGGAAT AACACTTTAA 7251 AACAGATAGA TAGCAAATTA AGAGAACAAT TCGGAAATAA TAAAACAATA 7301 ATCTTTAAGC AATCCTCAGG AGGGGACCCA GAAATTGTAA CGCACAGTTT 7351 TAATTGTGGA GGGGAATTTT TCTACTGTAA TTCAACACAA CTGTTTAATA 7401 GTACTTGGTT TAATAGTACT TGGAGTACTG AAGGGTCAAA TAACACTGAA 7451 GGAAGTGACA CAATCACCCT CCCATGCAGA ATAAAACAAA TTATAAACAT 7501 GTGGCAGAAA GTAGGAAAAG CAATGTATGC CCCTCCCATC AGTGGACAAA 7551 TTAGATGTTC ATCAAATATT ACAGGGCTGC TATTAACAAG AGATGGTGGT 7601 AATAGCAACA ATGAGTCCGA GATCTTCAGA CTTGGAGGAG GAGATATGAG 7651 GGACAATTGG AGAAGTGAAT TATATAAATA TAAAGTAGTA AAAATTGAAC 7701 CATTAGGAGT AGCACCCACC AAGGCAAAGA GAAGAGTGGT GCAGAGAGAA 7751 AAAAGAGCAG TGGGAATAGG AGCTTTGTTC CTTGGGTTCT TGGGAGCAGC 7801 AGGAAGCACT ATGGGCGCAG CCTCAATGAC GCTGACGGTA CAGGCCAGAC 7851 AATTATTGTC TGGTATAGTG CAGCAGCAGA ACAATTTGCT GAGGGCTATT 7901 GAGGCGCAAC AGCATCTGTT GCAACTCACA GTCTGGGGCA TCAAGCAGCT 7951 CCAAGCAAGA ATCCTAGCTG TGGAAAGATA CCTAAAGGAT CAACAGCTCC 8001 TAGGGATTTG GGGTTGCTCT GGAAAACTCA TTTGCACCAC TGCTGTGCCT 8051 TGGAATGCTA GTTGGAGTAA TAAATCTCTG GAACAGATCT GGAATCACAC 8101 GACCTGGATG GAGTGGGACA GAGAAATTAA CAATTACACA AGCTTAATAC 8151 ACTCCTTAAT TGAAGAATCG CAAAACCAGC AAGAAAAGAA TGAACAAGAA 8201 TTATTGGAAT TAGATAAATG GGCAAGTTTG TGGAATTGGT TTAACATAAC 8251 AAATTGGCTG TGGTATATAA AATTATTCAT AATGATAGTA GGAGGCTTGG 8301 TAGGTTTAAG AATAGTTTTT GCTGTACTTT CTATAGTGAA TAGAGTTAGG 8351 CAGGGATATT CACCATTATC GTTTCAGACC CACCTCCCAA TCCCGAGGGG 8401 ACCCGACAGG CCCGAAGGAA TAGAAGAAGA AGGTGGAGAG AGAGACAGAG 8451 ACAGATCCAT TCGATTAGTG AACGGATCCT TGGCACTTAT CTGGGACGAT 8501 CTGCGGAGCC TGTGCCTCTT CAGCTACCAC CGCTTGAGAG ACTTACTCTT 8551 GATTGTAACG AGGATTGTGG AACTTCTGGG ACGCAGGGGG TGGGAAGCCC 8601 TCAAATATTG GTGGAATCTC CTACAGTATT GGAGTCAGGA ACTAAAGAAT 8651 AGTGCTGTTA GCTTGCTCAA TGCCACAGCC ATAGCAGTAG CTGAGGGGAC 8701 AGATAGGGTT ATAGAAGTAG TACAAGGAGC TTGTAGAGCT ATTCGCCACA 8751 TACCTAGAAG AATAAGACAG GGCTTGGAAA GGATTTTGCT ATAAGATGGG 8801 TGGCAAGTGG TCAAAAAGTA GTGTGATTGG ATGGCTTACT GTAAGGGAAA 8851 GAATGAGACG AGCTGAGCCA GCAGCAGATG GGGTGGGAGC AGCATCTCGA 8901 GACCTGGAAA AACATGGAGC AATCACAAGT AGCAACACAG CAGCTACCAA 8951 TGCTGCTTGT GCCTGGCTAG AAGCACAAGA GGAGGAGGAG GTGGGTTTTC 9001 CAGTCACACC TCAGGTACCT TTAAGACCAA TGACTTACAA GGCAGCTGTA 9051 GATCTTAGCC ACTTTTTAAA AGAAAAGGGG GGACTGGAAG GGCTAATTCA 9101 CTCCCAAAGA AGACAAGATA TCCTTGATCT GTGGATCTAC CACACACAAG 9151 GCTACTTCCC TGATTGACAG AACTACACAC CAGGGCCAGG GGTCAGATAT 9201 CCACTGACCT TTGGATGGTG CTACAAGCTA GTACCAGTTG AGCCAGATAA 9251 GATAGAAGAG GCCAATAAAG GAGAGAACAC CAGCTTGTTA CACCCTGTGA 9301 GCCTGCATGG GATGGATGAC CCGGAGAGAG AAGTGTTAGA GTGGAGGTTT 9351 GACAGCCGCC TAGCATTTCA TCACGTGGCC CGAGAGCTGC ATCCGGAGTA 9401 CTTCAAGAAC TGCTGACATC GAGCTTGCTA CAAGGGACTT TCCGCTGGGG 9451 ACTTTCCAGG GAGGCGTGGC CTGGGCGGGA CTGGGGAGTG GCGAGCCCTC 9501 AGATCCTGCA TATAAGCAGC TGCTTTTTGC CTGTACTGGG TCTCTCTGGT 9551 TAGACCAGAT CTGAGCCTGG GAGCTCTCTG GCTAACTAGG GAACCCACTG 9601 CTTAAGCCTC AATAAAGCTT GCCTTGAGTG CTTCAAGTAG TGTGTGCCCG 9651 TCTGTTGTGT GACTCTGGTA ACTAGAGATC CCTCAGACCC TTTTAGTCAG 9701 TGTGGAAAAT CTCTAGCA squid/Formats/genbank0000640000175000017520000003547610463223377015075 0ustar naolivbiolinuxGBPRI1.SEQ Genetic Sequence Data Bank 15 August 2000 NCBI-GenBank Flat File Release 119.0 Primate Sequences (Part 1) 6395 loci, 170956138 bases, from 6395 reported sequences LOCUS AAB2MCG1 289 bp DNA PRI 06-JUL-1998 DEFINITION Aotus azarai beta-2-microglobulin precursor, gene, exon 1. ACCESSION AF032092 VERSION AF032092.1 GI:3265027 KEYWORDS . SEGMENT 1 of 2 SOURCE Azara's night monkey. ORGANISM Aotus azarai Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus. REFERENCE 1 (bases 1 to 289) AUTHORS Canavez,F.C., Ladasky,J.J., Muniz,J.A.C., Seuanez,H.N., Parham,P. and Cavanez,F.C. TITLE beta2-Microglobulin in neotropical primates (Platyrrhini) JOURNAL Immunogenetics 48 (2), 133-140 (1998) MEDLINE 98298008 REFERENCE 2 (bases 1 to 289) AUTHORS Canavez,F.C., Ladasky,J.J., Seuanez,H.N. and Parham,P. TITLE Direct Submission JOURNAL Submitted (31-OCT-1997) Structural Biology, Stanford University, Fairchild Building Campus West Dr. Room D-100, Stanford, CA 94305-5126, USA FEATURES Location/Qualifiers source 1..289 /organism="Aotus azarai" /db_xref="taxon:30591" exon <134..200 /number=1 sig_peptide 134..193 intron 201..>289 /number=1 BASE COUNT 30 a 99 c 80 g 80 t ORIGIN 1 gtccccgcgg gccttgtcct gattggctgt ccctgcgggc cttgtcctga ttggctgtgc 61 ccgactccgt ataacataaa tagaggcgtc gagtcgcgcg ggcattactg cagcggacta 121 cacttgggtc gagatggctc gcttcgtggt ggtggccctg ctcgtgctac tctctctgtc 181 tggcctggag gctatccagc gtaagtctct cctcccgtcc ggcgctggtc cttcccctcc 241 cgctcccacc ctctgtagcc gtctctgtgc tctctggttt cgttacctc // LOCUS AAB2MCG2 1276 bp DNA PRI 06-JUL-1998 DEFINITION Aotus azarai beta-2-microglobulin precursor, gene, exons 2 and 3 and complete cds. ACCESSION AF032093 AF032094 VERSION AF032093.1 GI:3287308 KEYWORDS . SEGMENT 2 of 2 SOURCE Azara's night monkey. ORGANISM Aotus azarai Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus. REFERENCE 1 (bases 1 to 1276) AUTHORS Canavez,F.C., Ladasky,J.J., Muniz,J.A.C., Seuanez,H.N., Parham,P. and Cavanez,F.C. TITLE beta2-Microglobulin in neotropical primates (Platyrrhini) JOURNAL Immunogenetics 48 (2), 133-140 (1998) MEDLINE 98298008 REFERENCE 2 (bases 1 to 1276) AUTHORS Canavez,F.C., Ladasky,J.J., Seuanez,H.N. and Parham,P. TITLE Direct Submission JOURNAL Submitted (31-OCT-1997) Structural Biology, Stanford University, Fairchild Building Campus West Dr. Room D-100, Stanford, CA 94305-5126, USA COMMENT On Jul 2, 1998 this sequence version replaced gi:3265029 gi:3265028. FEATURES Location/Qualifiers source 1..1276 /organism="Aotus azarai" /db_xref="taxon:30591" mRNA join(AF032092.1:<134..200,66..344,1023..>1050) /product="beta-2-microglobulin precursor" CDS join(AF032092.1:134..200,66..344,1023..1036) /codon_start=1 /product="beta-2-microglobulin precursor" /protein_id="AAC52107.1" /db_xref="GI:3289965" /translation="MARFVVVALLVLLSLSGLEAIQRXPKIQVYSRHPAENGKPNFLN CYVSGFHPSDIEVDLLKNGKKIEKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRV SHVTLSTPKTVKWDRNM" mat_peptide join(AF032092.1:194..200,66..344,1023..1033) /product="beta-2-microglobulin" intron <1..65 /number=1 variation 3 /note="allele 1" /replace="g" exon 66..344 /number=2 intron 345..1022 /number=2 exon 1023..1050 /number=3 intron 1051..>1276 /number=3 BASE COUNT 353 a 253 c 269 g 400 t 1 others ORIGIN 1 caagttatcc gtaattgaaa taccctggta attaatattc atttgtcttt tcctgatttt 61 ttcaggtrct ccaaagattc aggtttactc acgtcatccg gcagagaatg gaaagccaaa 121 ttttctgaat tgctatgtgt ctgggtttca tccgtccgac attgaagttg acttactgaa 181 gaatggaaag aaaattgaaa aagtggagca ttcagacttg tctttcagca aggactggtc 241 tttctatctc ttgtactaca ccgagtttac ccccaatgaa aaagatgagt atgcctgccg 301 tgtgagccat gtgactttat caacacccaa gacagtaaag tggggtaagt cttacgttct 361 tttgtaggct gctgaaagtt gtgtatgggt agtcatgtca taaagctgct ttgatataaa 421 aaaaattcgt ctatggccat actgccctga atgagtccca tcccgtctga taaaaaaaaa 481 tcttcatatt gggattgtca gggaatgtgc ttaaagatca gattagagac aacggctgag 541 agagcgctgc acagcattct tctgaaccag cagtttccct gcagctgagc agggagcagc 601 agcagcagtt gcacaaatac atatgcactc ctaacacttc ttacctactg acttcctcag 661 ctttcgtggc agctttaggt atatttagca ctaatgaaca tcaggaaggt ataggccttt 721 ctttgtaaat ccttctatcc tagcatccta taatcctgga ctcctccagt actctctggc 781 tggattggta tctgaggcta gtaggtgggg cttgttcctg ctgggtagct ccaaacaagg 841 tattcatgga taggaacagc agcctatttt gccagcctta tttcttaata gttttagaaa 901 tctgttagta cgtggtgttt tttgttttgt tttgttttaa cacagtgtaa acaaaaagta 961 catgtatttt aaaagtaaaa cttaatgtct tcctttttct ttctccactg tctttttcat 1021 agatcgaaac atgtaaccag catcatggag gtaagttctt gaccttaatt aaatgttttt 1081 tgtttcactg gggactattt atagacagcc ctaacatgat aaccctcact atgtggagaa 1141 cattgacaga gtagcatttt agcaggcaaa gaggaatcct atagggttac attccctttt 1201 cctgtggagt ggcatgaaaa aggtatgtgg ccccagctgt ggccacatta ctgactctac 1261 agggagggca aaggaa // LOCUS AACCOSIV1 168 bp DNA PRI 26-JAN-1998 DEFINITION Aotus azarai cytochrome c oxidase subunit IV gene, exon 3. ACCESSION AF042765 VERSION AF042765.1 GI:2809514 KEYWORDS . SEGMENT 1 of 3 SOURCE Azara's night monkey. ORGANISM Aotus azarai Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus. REFERENCE 1 (bases 1 to 168) AUTHORS Wu,W., Goodman,M., Lomax,M.I. and Grossman,L.I. TITLE Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates JOURNAL J. Mol. Evol. 44 (5), 477-491 (1997) MEDLINE 97277139 REFERENCE 2 (bases 1 to 168) AUTHORS Wu,W., Goodman,M., Lomax,M.I. and Grossman,L.I. TITLE Direct Submission JOURNAL Submitted (14-JAN-1998) CMMG, Wayne State University, 540 E. Canfield, Detroit, MI 48201, USA FEATURES Location/Qualifiers source 1..168 /organism="Aotus azarai" /db_xref="taxon:30591" exon 1..168 /number=3 BASE COUNT 40 a 42 c 54 g 32 t ORIGIN 1 gaagtgttgt gaagagcgaa gactatgcgc tcccaagtta tgtggatcgg cgtgactatc 61 ccttgcccga cgtggcccat gtcaggcacc tgtcggccag ccagaaggcc ttgaaggaga 121 aggagaaggc ctcctggagc agcctctcca tggatgagaa agtcgagt // LOCUS AACCOSIV2 132 bp DNA PRI 26-JAN-1998 DEFINITION Aotus azarai cytochrome c oxidase subunit IV gene, exon 4. ACCESSION AF042766 VERSION AF042766.1 GI:2809515 KEYWORDS . SEGMENT 2 of 3 SOURCE Azara's night monkey. ORGANISM Aotus azarai Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus. REFERENCE 1 (bases 1 to 132) AUTHORS Wu,W., Goodman,M., Lomax,M.I. and Grossman,L.I. TITLE Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates JOURNAL J. Mol. Evol. 44 (5), 477-491 (1997) MEDLINE 97277139 REFERENCE 2 (bases 1 to 132) AUTHORS Wu,W., Goodman,M., Lomax,M.I. and Grossman,L.I. TITLE Direct Submission JOURNAL Submitted (14-JAN-1998) CMMG, Wayne State University, 540 E. Canfield, Detroit, MI 48201, USA FEATURES Location/Qualifiers source 1..132 /organism="Aotus azarai" /db_xref="taxon:30591" exon 1..132 /number=4 BASE COUNT 30 a 25 c 38 g 39 t ORIGIN 1 tgtatcgtat tcagttcaag gagagctttg ctgagatgaa caggggctcc aatgagtgga 61 agacggttgt gggtgctgcc atgttcttca tcggcttcac agcaattctt atcatcttgg 121 agaagcgcta tg // LOCUS AACCOSIV3 137 bp DNA PRI 26-JAN-1998 DEFINITION Aotus azarai cytochrome c oxidase subunit IV gene, exon 5; and partial cds. ACCESSION AF042767 VERSION AF042767.1 GI:2809516 KEYWORDS . SEGMENT 3 of 3 SOURCE Azara's night monkey. ORGANISM Aotus azarai Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus. REFERENCE 1 (bases 1 to 137) AUTHORS Wu,W., Goodman,M., Lomax,M.I. and Grossman,L.I. TITLE Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates JOURNAL J. Mol. Evol. 44 (5), 477-491 (1997) MEDLINE 97277139 REFERENCE 2 (bases 1 to 137) AUTHORS Wu,W., Goodman,M., Lomax,M.I. and Grossman,L.I. TITLE Direct Submission JOURNAL Submitted (14-JAN-1998) CMMG, Wayne State University, 540 E. Canfield, Detroit, MI 48201, USA FEATURES Location/Qualifiers source 1..137 /organism="Aotus azarai" /db_xref="taxon:30591" mRNA join(AF042765.1:<1..168,AF042766.1:1..132,1..>137) /product="cytochrome c oxidase subunit IV" CDS join(AF042765.1:<1..168,AF042766.1:1..132,1..137) /codon_start=3 /product="cytochrome c oxidase subunit IV" /protein_id="AAB97755.1" /db_xref="GI:2809518" /translation="SVVKSEDYALPSYVDRRDYPLPDVAHVRHLSASQKALKEKEKAS WSSLSMDEKVELYRIQFKESFAEMNRGSNEWKTVVGAAMFFIGFTAILIILEKRYVYG PLPHTFDKEWVAMQTKRMLDLKVNPVDGLASKWDYDKKEWKK" exon 1..137 /number=5 BASE COUNT 36 a 36 c 43 g 22 t ORIGIN 1 tgtacggccc cctcccgcac acctttgaca aagagtgggt ggccatgcag accaagagga 61 tgctggacct gaaggtgaac cctgtcgatg gcctcgcctc caagtgggac tacgacaaga 121 aggagtggaa gaagtga // LOCUS AAU18601 1771 bp DNA PRI 17-JAN-1997 DEFINITION Aotus azarae interphotoreceptor retinoid-binding protein (IRBP) gene, intron 1, complete sequence. ACCESSION U18601 VERSION U18601.1 GI:624187 KEYWORDS . SOURCE Azara's night monkey. ORGANISM Aotus azarai Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus. REFERENCE 1 (bases 1 to 1771) AUTHORS Harada,M.L., Schneider,H., Schneider,M.P., Sampaio,I., Czelusniak,J. and Goodman,M. TITLE DNA evidence on the phylogenetic systematics of New World monkeys: support for the sister-grouping of Cebus and Saimiri from two unlinked nuclear genes JOURNAL Mol. Phylogenet. Evol. 4 (3), 331-349 (1995) MEDLINE 96111507 REFERENCE 2 (bases 1 to 1771) AUTHORS Harada,M.L. TITLE Direct Submission JOURNAL Submitted (13-DEC-1994) Universidade Federal do Para, Departamento de Genetica, Campus Universitario do Guama, Belem, Para, 66075-900, Brazil FEATURES Location/Qualifiers source 1..1771 /organism="Aotus azarai" /db_xref="taxon:30591" /tissue_type="lymphocytes" /dev_stage="adult" gene 1..1771 /gene="IRBP" intron 1..1771 /gene="IRBP" /note="interphotoreceptor retinoid-binding protein" /number=1 BASE COUNT 384 a 443 c 533 g 411 t ORIGIN 1 gtgagaccca agggagacct ggccgggccc agtcctggga gtgagttgac ctgtcgtttg 61 cacatgcagg gctctgtgca caatgcgtga caatggcttt tagatttgtt ctcatgctta 121 agttgtggcc agttgagtcc tttcctcttt ccatccactg ttccatccac tctctgggac 181 cctggtgctg ctgtagaacc tccgtagaac attcatgtta ggttggtgtg aaagtacttt 241 taattgcaaa acccacaatt acttttgcat caacctcacg ggaagccagt ttggaagcct 301 cgggatagac agagtttcag ccttggctgg gtggaaggtg agcgttggcg gggcttctca 361 tcgtcagtgt gggagaagag gccaacatgt ggcagaggtg gcggtgggct tcaccgcgtg 421 ccccaccgca ggccgagagc tccgcccggg cagcactcac tccacgctgt tctcctacct 481 gtggctttgc tgcattgtca cagttgggca gggcagcatg tgtcatgaat cccttgcaag 541 gagggtctga gactggggtt gggtgcaggc agtttgtctg ggaggtggtt gctgaagcag 601 gtgtgaagga gggagcaggg agagtgagat aggaaggtga caggcaggtc cctcaaagct 661 gttctgctga agccaggacg ctgacaagtg tggggatgct cccaggcaca gttctctgcg 721 ggcgggcccc agggctcctg tcccgctttg gccaagagtt gccctgagga cataactcgg 781 ggtggggcag gctcccctct cttggagaag gcctgagctg agggtggaaa gacaggatgg 841 tgctgtggga gagcctgtca gtggggccag gtgcagctga aatcagaggg ggctgagagt 901 gccaacggca tctgttacag aattctcatc cccattttgc ataactgagg cccagagagg 961 tgcagagggg agtggcctgg agccagagag ctgtgactga aggcagggca gggcctggag 1021 ggcagtgtct ctgtcagcac aggctccttg ccccagtcca gctcaccaag tcctgccgcc 1081 ctcccgcagc cttagagagg gaggaagagg tgcatccaca tggaagtagc ctgtgctagg 1141 ctttcagaat acccagtttc caaattaatt gcttcttcct ttctggtata gccaaggttc 1201 acaatttgga gtcagatgtg gattcagatg ctggctccac cacttattga ctgtgtaacc 1261 tgggactagt tacttaatct cactgtgctt cagtttttcc gtggaaaaga tggggaccat 1321 gttatctcct gtacaggtgg ctgtgaggat gacgataagc tctgcaaagt gcttagtaca 1381 gggccaggca cctgttaaag gtaactaaca tcttccaatc ctgccccagt ggaggggaag 1441 ataagcttag agatgttggg aagtatctgg cgaggttgga cgaatcagag aggagaccat 1501 tcctgggcct tccagctctg aacaccagag cagacaggag catcctctgc aaggaggctt 1561 cccatggatc acacatgtcc cagtggcatg tcacatccca gacatgccac tgggaaagtc 1621 ccaggtgcct actgactcct tcagaaatgt cagttcctgt cccatgccct taatatttcc 1681 catgacataa aggcgatcca tggcacctgc tttcctgggc tcgaaaaccg gctgccctcc 1741 tgacactgag caggacctcc aactcttgca g // squid/Formats/msf0000640000175000017520000003752310463223377014250 0ustar naolivbiolinux MSF: 171 Type: P Check: 4694 .. Name: GLB2_MORMR oo Len: 171 Check: 6522 Weight: 2.7687 Name: GLBZ_CHITH oo Len: 171 Check: 6733 Weight: 2.9329 Name: HBA2_BOSMU oo Len: 171 Check: 5006 Weight: 0.6394 Name: HBA2_GALCR oo Len: 171 Check: 6652 Weight: 0.5183 Name: HBA4_SALIR oo Len: 171 Check: 5434 Weight: 1.9511 Name: HBAD_CHLME oo Len: 171 Check: 6621 Weight: 1.2927 Name: HBAD_PASMO oo Len: 171 Check: 8118 Weight: 1.2927 Name: HBAZ_HORSE oo Len: 171 Check: 8382 Weight: 1.6223 Name: HBA_AILME oo Len: 171 Check: 5402 Weight: 0.4145 Name: HBA_ANSSE oo Len: 171 Check: 3688 Weight: 0.8315 Name: HBA_COLLI oo Len: 171 Check: 4420 Weight: 0.8557 Name: HBA_ERIEU oo Len: 171 Check: 5528 Weight: 0.8390 Name: HBA_FRAPO oo Len: 171 Check: 4136 Weight: 0.5014 Name: HBA_MACFA oo Len: 171 Check: 5986 Weight: 0.2233 Name: HBA_MACSI oo Len: 171 Check: 6064 Weight: 0.2233 Name: HBA_MESAU oo Len: 171 Check: 5499 Weight: 0.6722 Name: HBA_PAGLA oo Len: 171 Check: 6189 Weight: 0.5388 Name: HBA_PHACO oo Len: 171 Check: 5129 Weight: 0.5014 Name: HBA_PONPY oo Len: 171 Check: 5894 Weight: 0.3907 Name: HBA_PROLO oo Len: 171 Check: 5810 Weight: 0.4145 Name: HBA_TRIOC oo Len: 171 Check: 6427 Weight: 0.6883 Name: HBB1_VAREX oo Len: 171 Check: 7239 Weight: 1.1252 Name: HBB2_TRICR oo Len: 171 Check: 7790 Weight: 1.9629 Name: HBB2_XENTR oo Len: 171 Check: 9537 Weight: 1.4685 Name: HBBL_RANCA oo Len: 171 Check: 7490 Weight: 1.4685 Name: HBB_CALAR oo Len: 171 Check: 6568 Weight: 0.4226 Name: HBB_COLLI oo Len: 171 Check: 5043 Weight: 0.7672 Name: HBB_EQUHE oo Len: 171 Check: 6101 Weight: 0.6734 Name: HBB_LARRI oo Len: 171 Check: 5673 Weight: 0.7672 Name: HBB_MANSP oo Len: 171 Check: 7148 Weight: 0.4226 Name: HBB_ORNAN oo Len: 171 Check: 6249 Weight: 0.6615 Name: HBB_RABIT oo Len: 171 Check: 7043 Weight: 0.5259 Name: HBB_SPECI oo Len: 171 Check: 3680 Weight: 0.5422 Name: HBB_SPETO oo Len: 171 Check: 4246 Weight: 0.5422 Name: HBB_SUNMU oo Len: 171 Check: 5601 Weight: 0.6734 Name: HBB_TACAC oo Len: 171 Check: 7133 Weight: 0.6615 Name: HBB_TRIIN oo Len: 171 Check: 4009 Weight: 0.8445 Name: HBB_TUPGL oo Len: 171 Check: 7197 Weight: 0.7375 Name: HBB_URSMA oo Len: 171 Check: 7200 Weight: 0.4695 Name: HBE_PONPY oo Len: 171 Check: 5902 Weight: 1.0101 Name: HBF1_URECA oo Len: 171 Check: 6462 Weight: 2.9329 Name: LGB1_PEA oo Len: 171 Check: 4791 Weight: 2.0005 Name: LGB1_VICFA oo Len: 171 Check: 7426 Weight: 2.0005 Name: MYG_ESCGI oo Len: 171 Check: 9170 Weight: 0.7432 Name: MYG_HORSE oo Len: 171 Check: 1290 Weight: 0.7432 Name: MYG_LYCPI oo Len: 171 Check: 1107 Weight: 0.8773 Name: MYG_MOUSE oo Len: 171 Check: 1320 Weight: 1.0018 Name: MYG_MUSAN oo Len: 171 Check: 5461 Weight: 2.3158 Name: MYG_PROGU oo Len: 171 Check: 1450 Weight: 0.7629 Name: MYG_SAISC oo Len: 171 Check: 1728 Weight: 0.7629 // GLB2_MORMR ...PIVD..S GSVSPLSDAE KNKIRAAW.D IVYKNYEKNG VDILVKFFTG GLBZ_CHITH MKFIILALCV AAASALSGDQ IGLVQST.YG KVKG....DS VGILYAVFKA HBA2_BOSMU ...V...... .....LSAAD KGNVKAAW.G KVGGHAAEYG AEALERMFLS HBA2_GALCR ...V...... .....LSPTD KSNVKAAW.E KVGAHAGDYG AEALERMFLS HBA4_SALIR ...S...... .....LSAKD KANVKAIW.G KILPKSDEIG EQALSRMLVV HBAD_CHLME ...M...... .....LTADD KKLLTQLW.E KVAGHQEEFG SEALQRMFLT HBAD_PASMO ...M...... .....LTAED KKLIQQIW.G KLGGAEEEIG ADALWRMFHS HBAZ_HORSE ...S...... .....LTKAE RTMVVSIW.G KISMQADAVG TEALQRLFSS HBA_AILME ...V...... .....LSPAD KTNVKATW.D KIGGHAGEYG GEALERTFAS HBA_ANSSE ...V...... .....LSAAD KGNVKTVF.G KIGGHAEEYG AETLQRMFQT HBA_COLLI ...V...... .....LSAND KSNVKAVF.A KIGGQAGDLG GEALERLFIT HBA_ERIEU ...V...... .....LSATD KANVKTFW.G KLGGHGGEYG GEALDRMFQA HBA_FRAPO ...V...... .....LSAAD KNNVKGIF.G KISSHAEDYG AEALERMFIT HBA_MACFA ...V...... .....LSPAD KTNVKAAW.G KVGGHAGEYG AEALERMFLS HBA_MACSI ...V...... .....LSPAD KTNVKDAW.G KVGGHAGEYG AEALERMFLS HBA_MESAU ...V...... .....LSAKD KTNISEAW.G KIGGHAGEYG AEALERMFFV HBA_PAGLA ...V...... .....LSSAD KNNIKATW.D KIGSHAGEYG AEALERTFIS HBA_PHACO ...V...... .....LSAAD KNNVKGIF.T KIAGHAEEYG AEALERMFIT HBA_PONPY ...V...... .....LSPAD KTNVKTAW.G KVGAHAGDYG AEALERMFLS HBA_PROLO ...V...... .....LSPAD KANIKATW.D KIGGHAGEYG GEALERTFAS HBA_TRIOC ...V...... .....LSAND KTNVKTVF.T KITGHAEDYG AETLERMFIT HBB1_VAREX ...V...... ....HWTAEE KQLICSLW.G KI..DVGLIG GETLAGLLVI HBB2_TRICR ...V...... ....HLTAED RKEIAAIL.G KV..NVDSLG GQCLARLIVV HBB2_XENTR ...V...... ....HWTAEE KATIASVW.G KV..DIEQDG HDALSRLLVV HBBL_RANCA ...V...... ....HWTAEE KAVINSVW.Q KV..DVEQDG HEALTRLFIV HBB_CALAR ...V...... ....HLTGEE KSAVTALW.G KV..NVDEVG GEALGRLLVV HBB_COLLI ...V...... ....HWSAEE KQLITSIW.G KV..NVADCG AEALARLLIV HBB_EQUHE ...V...... ....QLSGEE KAAVLALW.D KV..NEEEVG GEALGRLLVV HBB_LARRI ...V...... ....HWSAEE KQLITGLW.G KV..NVADCG AEALARLLIV HBB_MANSP ...V...... ....HLTPEE KTAVTTLW.G KV..NVDEVG GEALGRLLVV HBB_ORNAN ...V...... ....HLSGGE KSAVTNLW.G KV..NINELG GEALGRLLVV HBB_RABIT ...V...... ....HLSSEE KSAVTALW.G KV..NVEEVG GEALGRLLVV HBB_SPECI ...V...... ....HLSDGE KNAISTAW.G KV..HAAEVG AEALGRLLVV HBB_SPETO ...V...... ....HLTDGE KNAISTAW.G KV..NAAEIG AEALGRLLVV HBB_SUNMU ...V...... ....HLSGEE KACVTGLW.G KV..NEDEVG AEALGRLLVV HBB_TACAC ...V...... ....HLSGSE KTAVTNLW.G HV..NVNELG GEALGRLLVV HBB_TRIIN ...V...... ....HLTPEE KALVIGLW.A KV..NVKEYG GEALGRLLVV HBB_TUPGL ...V...... ....HLSGEE KAAVTGLW.G KV..DLEKVG GQSLGSLLIV HBB_URSMA ...V...... ....HLTGEE KSLVTGLW.G KV..NVDEVG GEALGRLLVV HBE_PONPY ...V...... ....HFTAEE KAAVTSLW.S KM..NVEEAG GEALGRLLVV HBF1_URECA .......... ....GLTTAQ IKAIQDHWFL NIKGCLQAAA DSIFFKYLTA LGB1_PEA GFTDKQEALV NSSSE.FKQN LPGYSILFYT IVLEKAP..A AKGL...... LGB1_VICFA GFTEKQEALV NSSSQLFKQN PSNYSVLFYT IILQKAP..T AKAM...... MYG_ESCGI ...V...... .....LSDAE WQLVLNIW.A KVEADVAGHG QDILIRLFKG MYG_HORSE ...G...... .....LSDGE WQQVLNVW.G KVEADIAGHG QEVLIRLFTG MYG_LYCPI ...G...... .....LSDGE WQIVLNIW.G KVETDLAGHG QEVLIRLFKN MYG_MOUSE ...G...... .....LSDGE WQLVLNVW.G KVEADLAGHG QEVLIGLFKT MYG_MUSAN .......... ........VD WEKVNSVW.S AVESDLTAIG QNILLRLFEQ MYG_PROGU ...G...... .....LSDGE WQLVLNVW.G KVEGDLSGHG QEVLIRLFKG MYG_SAISC ...G...... .....LSDGE WQLVLNIW.G KVEADIPSHG QEVLISLFKG GLB2_MORMR TPAAQAFFPK FKGLTTADAL KKSSDVRWHA ERIINAVNDA VKSMDDTEKM GLBZ_CHITH DPTIQAAFPQ FVGK.DLDAI KGGAEFSTHA GRIVGFLGGV IDDLP...NI HBA2_BOSMU FPTTKTYFPH FD.LSH.... .GSAQVKGHG AKVAAALTKA VGHLDD...L HBA2_GALCR FPTTKTYFPH FD.LSH.... .GSTQVKGHG KKVADALTNA VLHVDD...M HBA4_SALIR YPQTKAYFSH WASVAP.... .GSAPVKKHG ITIMNQIDDC VGHMDD...L HBAD_CHLME YPQTKTYFPH FD.LHP.... .GSEQVRGHG KKVAAALGNA VKSLDN...L HBAD_PASMO YPSTKTYFPH FD.LSQ.... .GSDQIRGHG KKVVAALSNA IKNLDN...L HBAZ_HORSE YPQTKTYFPH FD.LHE.... .GSPQLRAHG SKVAAAVGDA VKSIDN...V HBA_AILME FPTTKTYFPH FD.LSP.... .GSAQVKAHG KKVADALTTA VGHLDD...L HBA_ANSSE FPQTKTYFPH FD.LQP.... .GSAQIKAHG KKVAAALVEA ANHIDD...I HBA_COLLI YPQTKTYFPH FD.LSH.... .GSAQIKGHG KKVAEALVEA ANHIDD...I HBA_ERIEU HPTTKTYFPH FD.LNP.... .GSAQVKGHG KKVADALTTA VNNLDD...V HBA_FRAPO YPSTKTYFPH FD.LSH.... .GSAQVKGHG KKVVAALIEA ANHIDD...I HBA_MACFA FPTTKTYFPH FD.LSH.... .GSAQVKGHG KKVADALTLA VGHVDD...M HBA_MACSI FPTTKTYFPH FD.LSH.... .GSAQVKGHG KKVADALTLA VGHVDD...M HBA_MESAU YPTTKTYFPH FD.VSH.... .GSAQVKGHG KKVADALTNA VGHLDD...L HBA_PAGLA FPTTKTYFPH FD.LSH.... .GSAQVKAHG KKVADALTLA VGHLED...L HBA_PHACO YPSTKTYFPH FD.LSH.... .GSAQIKGHG KKVVAALIEA VNHIDD...I HBA_PONPY FPTTKTYFPH FD.LSH.... .GSAQVKDHG KKVADALTNA VAHVDD...M HBA_PROLO FPTTKTYFPH FD.LSP.... .GSAQVKAHG KKVADALTLA VGHLDD...L HBA_TRIOC YPPTKTYFPH FD.LHH.... .GSAQIKAHG KKVVGALIEA VNHIDD...I HBB1_VAREX YPWTQRQFSH FGNLSSPTAI AGNPRVKAHG KKVLTSFGDA IKNLDN...I HBB2_TRICR NPWSRRYFHD FGDLSSCDAI CRNPKVLAHG AKVMRSIVEA TKHLDN...L HBB2_XENTR YPWTQRYFSS FGNLSNVSAV SGNVKVKAHG NKVLSAVGSA IQHLDD...V HBBL_RANCA YPWTQRYFST FGDLSSPAAI AGNPKVHAHG KKILGAIDNA IHNLDD...V HBB_CALAR YPWTQRFFES FGDLSTPDAV MNNPKVKAHG KKVLGAFSDG LTHLDN...L HBB_COLLI YPWTQRFFSS FGNLSSATAI SGNPNVKAHG KKVLTSFGDA VKNLDN...I HBB_EQUHE YPWTQRFFDS FGDLSNPAAV MGNPKVKAHG KKVLHSFGEG VHHLDN...L HBB_LARRI YPWTQRFFAS FGNLSSPTAI NGNPMVRAHG KKVLTSFGEA VKNLDN...I HBB_MANSP YPWTQRFFDS FGDLSSPDAV MGNPKVKAHG KKVLGAFSDG LNHLDN...L HBB_ORNAN YPWTQRFFEA FGDLSSAGAV MGNPKVKAHG AKVLTSFGDA LKNLDD...L HBB_RABIT YPWTQRFFES FGDLSSANAV MNNPKVKAHG KKVLAAFSEG LSHLDN...L HBB_SPECI YPWTQRFFDS FGDLSSASAV MGNAKVKAHG KKVIDSFSNG LKHLDN...L HBB_SPETO YPWTQRFFDS FGDLSSASAV MGNAKVKAHG KKVIDSFSNG LKHLDN...L HBB_SUNMU YPWTQRFFDS FGDLSSASAV MGNPKVKAHG KKVLHSLGEG VANLDN...L HBB_TACAC YPWTQRFFES FGDLSSADAV MGNAKVKAHG AKVLTSFGDA LKNLDN...L HBB_TRIIN YPWTQRFFEH FGDLSSASAI MNNPKVKAHG EKVFTSFGDG LKHLED...L HBB_TUPGL YPWTQRFFDS FGDLSSPSAV MSNPKVKAHG KKVLTSFSDG LNHLDN...L HBB_URSMA YPWTQRFFDS FGDLSSADAI MNNPKVKAHG KKVLNSFSDG LKNLDN...L HBE_PONPY YPWTQRFFDS FGNLSSPSAI LGNPKVKAHG KKVLTSFGDA IKNMDN...L HBF1_URECA YPGDLAFFHK FSSV.PLYGL RSNPAYKAQT LTVINYLDKV VDALGG..NA LGB1_PEA .......... FSFLKDTAGV EDSPKLQAHA EQVFGLVRDS AAQLRTKGEV LGB1_VICFA .......... FSFLKDSAGV VDSPKLGAHA EKVFGMVRDS AVQLRATGEV MYG_ESCGI HPETLEKFDK FKHLKTEAEM KASEDLKKHG NTVLTALGGI LKKKGH...H MYG_HORSE HPETLEKFDK FKHLKTEAEM KASEDLKKHG TVVLTALGGI LKKKGH...H MYG_LYCPI HPETLDKFDK FKHLKTEDEM KGSEDLKKHG NTVLTALGGI LKKKGH...H MYG_MOUSE HPETLDKFDK FKNLKSEEDM KGSEDLKKHG CTVLTALGTI LKKKGQ...H MYG_MUSAN YPESQNHFPK FKN.KSLGEL KDTADIKAQA DTVLSALGNI VKKKGS...H MYG_PROGU HPETLEKFDK FKHLKAEDEM RASEELKKHG TTVLTALGGI LKKKGQ...H MYG_SAISC HPETLEKFDK FKHLKSEDEM KASEELKKHG TTVLTALGGI LKKKGQ...H GLB2_MORMR SMKLQELSVK HAQSFYVDRQ YFKVLAGII. ........AD TTAPGDAGFE GLBZ_CHITH GKHVDALVAT H.KPRGVTHA QFNNFRAAFI AYLKGHV..D YTAAVEAAWG HBA2_BOSMU PGALSELSDL HAHKLRVDPV NFKLLSHSLL VTLASHLPSD FTPAVHASLD HBA2_GALCR PSALSALSDL HAHKLRVDPV NFKLLRHCLL VTLACHHPAE FTPAVHASLD HBA4_SALIR FGFLTKLSEL HATKLRVDPT NFKILAHNLI VVIAAYFPAE FTPEIHLSVD HBAD_CHLME SQALSELSNL HAYNLRVDPA NFKLLAQCFQ VVLATHLGKD YSPEMHAAFD HBAD_PASMO SQALSELSNL HAYNLRVDPV NFKFLSQCLQ VSLATRLGKE YSPEVHSAVD HBAZ_HORSE AGALAKLSEL HAYILRVDPV NFKFLSHCLL VTLASRLPAD FTADAHAAWD HBA_AILME PGALSALSDL HAHKLRVDPV NFKLLSHCLL VTLASHHPAE FTPAVHASLD HBA_ANSSE AGALSKLSDL HAQKLRVDPV NFKFLGHCFL VVLAIHHPSL LTPEVHASMD HBA_COLLI AGALSKLSDL HAQKLRVDPV NFKLLGHCFL VVVAVHFPSL LTPEVHASLD HBA_ERIEU PGALSALSDL HAHKLRVDPV NFKLLSHCLL VTLALHHPAD FTPAVHASLD HBA_FRAPO AGTLSKLSDL HAHKLRVDPV NFKLLGQCFL VVVAIHHPSA LTPEVHASLD HBA_MACFA PQALSALSDL HAHKLRVDPV NFKLLSHCLL VTLAAHLPAE FTPAVHASLD HBA_MACSI PQALSALSDL HAHKLRVDPV NFKLLSHCLL VTLAAHLPAE FTPAVHASLD HBA_MESAU PGALSALSDL HAHKLRVDPV NFKLLSHCLL VTLANHHPAD FTPAVHASLD HBA_PAGLA PNALSALSDL HAYKLRVDPV NFKLLSHCLL VTLACHHPAE FTPAVHSALD HBA_PHACO TGTLSKLSDL HAHKLRVDPV NFKLLGQCFL VVVAIHHPSA LTPEVHASLD HBA_PONPY PNALSALSDL HAHKLRVDPV NFKLLSHCLL VTLAAHLPAE FTPAVHASLD HBA_PROLO PGALSALSDL HAYKLRVDPV NFKLLSHCLL VTLACHHPAE FTPAVHASLD HBA_TRIOC AGALSKLSDL HAQKLRVDPV NFKLLGQCFL VVVAIHHPSV LTPEVHASLD HBB1_VAREX KDTFAKLSEL HCDKLHVDPT NFKLLGNVLV IVLADHHGKE FTPAHHAAYQ HBB2_TRICR REYYADLSVT HSLKFYVDPE NFKLFSGIVI VCLALTLQTD FSCHKQLAFE HBB2_XENTR KSHLKGLSKS HAEDLHVDPE NFKRLADVLV IVLAAKLGSA FTPQVQAVWE HBBL_RANCA KGTLHDLSEE HANELHVDPE NFRRLGEVLI VVLGAKLGKA FSPQVQHVWE HBB_CALAR KGTFAHLSEL HCDKLHVDPE NFRLLGNVLV CVLAHHFGKE FTPVVQAAYQ HBB_COLLI KGTFAQLSEL HCDKLHVDPE NFRLLGDILV IILAAHFGKD FTPECQAAWQ HBB_EQUHE KGTFAQLSEL HCDKLHVDPE NFRLLGNVLV VVLARHFGKD FTPELQASYQ HBB_LARRI KNTFAQLSEL HCDKLHVDPE NFRLLGDILI IVLAAHFAKD FTPDSQAAWQ HBB_MANSP KGTFAQLSEL HCDKLHVDPE NFKLLGNVLV CVLAHHFGKE FTPQVQAAYQ HBB_ORNAN KGTFAKLSEL HCDKLHVDPE NFNRLGNVLI VVLARHFSKD FSPEVQAAWQ HBB_RABIT KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV IVLSHHFGKE FTPQVQAAYQ HBB_SPECI KGTFASLSEL HCDKLHVDPE NFKLLGNMIV IVMAHHLGKD FTPEAQAAFQ HBB_SPETO KGTFASLSEL HCDKLHVDPE NFKLLGNMIV IVMAHHLGKD FTPEAQAAFQ HBB_SUNMU KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV VVLASKFGKE FTPPVQAAFQ HBB_TACAC KGTFAKLSEL HCDKLHVDPE NFNRLGNVLV VVLARHFSKE FTPEAQAAWQ HBB_TRIIN KGAFAELSEL HCDKLHVDPE NFRLLGNVLV CVLARHFGKE FSPEAQAAYQ HBB_TUPGL KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV RVLACNFGPE FTPQVQAAFQ HBB_URSMA KGTFAKLSEL HCDKLHVDPE NFKLLGNVLV CVLAHHFGKE FTPQVQAAYQ HBE_PONPY KTTFAKLSEL HCDKLHVDPE NFKLLGNVMV IILATHFGKE FTPEVQAAWQ HBF1_URECA GALMKAKVPS H.DAMGITPK HFGQLLKLVG GVFQEEF..S ADPTTVAAWG LGB1_PEA VLGNATLGAI HVQKGVTNP. HFVVVKEALL QTIKKASGNN WSEELNTAWE LGB1_VICFA VLDGKD.GSI HIQKGVLDP. HFVVVKEALL KTIKEASGDK WSEELSAAWE MYG_ESCGI EAELKPLAQS HATKHKIPIK YLEFISDAII HVLHSRHPGD FGADAQAAMN MYG_HORSE EAELKPLAQS HATKHKIPIK YLEFISDAII HVLHSKHPGN FGADAQGAMT MYG_LYCPI EAELKPLAQS HATKHKIPVK YLEFISDAII QVLQNKHSGD FHADTEAAMK MYG_MOUSE AAEIQPLAQS HATKHKIPVK YLEFISEIII EVLKKRHSGD FGADAQGAMS MYG_MUSAN SQPVKALAAT HITTHKIPPH YFTKITTIAV DVLSEMYPSE MNAQVQAAFS MYG_PROGU AAELAPLAQS HATKHKIPVK YLEFISEAII QVLQSKHPGD FGADAQGAMS MYG_SAISC EAELKPLAQS HATKHKIPVK YLELISDAIV HVLQKKHPGD FGADAQGAMK GLB2_MORMR KLMSMICILL SSAY...... . GLBZ_CHITH ATFDAFFGAV FAK....... M HBA2_BOSMU KFLANVSTVL TSKYR..... . HBA2_GALCR KFMASVSTVL TSKYR..... . HBA4_SALIR KFLQQLALAL AEKYR..... . HBAD_CHLME KFLSAVAAVL AEKYR..... . HBAD_PASMO KFMSAVASVL AEKYR..... . HBAZ_HORSE KFLSIVSSVL TEKYR..... . HBA_AILME KFFSAVSTVL TSKYR..... . HBA_ANSSE KFLCAVATVL TAKYR..... . HBA_COLLI KFVLAVGTVL TAKYR..... . HBA_ERIEU KFLATVATVL TSKYR..... . HBA_FRAPO KFLCAVGNVL TAKYR..... . HBA_MACFA KFLASVSTVL TSKYR..... . HBA_MACSI KFLASVSTVL TSKYR..... . HBA_MESAU KFFASVSTVL TSKYR..... . HBA_PAGLA KFFSAVSTVL TSKYR..... . HBA_PHACO KFLCAVGTVL TAKYR..... . HBA_PONPY KFLASVSTVL TSKYR..... . HBA_PROLO KFFTSVSTVL TSKYR..... . HBA_TRIOC KFLCAVGNVL SAKYR..... . HBB1_VAREX KLVNVVSHSL ARRYH..... . HBB2_TRICR KLMKGVSHAL GHGY...... . HBB2_XENTR KLNATLVAAL SHGYF..... . HBBL_RANCA KFIAVLVDAL SHSYH..... . HBB_CALAR KVVAGVANAL AHKYH..... . HBB_COLLI KLVRVVAHAL ARKYH..... . HBB_EQUHE KVVAGVANAL AHKYH..... . HBB_LARRI KLVRVVAHAL ARKYH..... . HBB_MANSP KVVAGVANAL AHKYH..... . HBB_ORNAN KLVSGVAHAL GHKYH..... . HBB_RABIT KVVAGVANAL AHKYH..... . HBB_SPECI KVVAGVANAL AHKYH..... . HBB_SPETO KVVAGVANAL SHKYH..... . HBB_SUNMU KVVAGVANAL AHKYH..... . HBB_TACAC KLVSGVSHAL AHKYH..... . HBB_TRIIN KVVAGVANAL AHKYH..... . HBB_TUPGL KVVAGVANAL AHKYH..... . HBB_URSMA KVVAGVANAL AHKYH..... . HBE_PONPY KLVSAVAIAL AHKYH..... . HBF1_URECA DAAGVLVAAM .......... K LGB1_PEA VAYDGLATAI KKAMKT.... A LGB1_VICFA VAYDGLATAI K....A.... A MYG_ESCGI KALELFRKDI AAKYKELGFQ G MYG_HORSE KALELFRNDI AAKYKELGFQ G MYG_LYCPI KALELFRNDI AAKYKELGFQ G MYG_MOUSE KALELFRNDI AAKYKELGFQ G MYG_MUSAN GAFKIICSDI EKEYKAANFQ G MYG_PROGU KALELFRNDI AAKYKELGFQ G MYG_SAISC KALELFRNDM AAKYKELGFQ G squid/Formats/phylip0000640000175000017520000002214010463223377014755 0ustar naolivbiolinux 50 171 GLB2_MORMR---PIVD--SGSVSPLSDAEKNKIR AAW-DIVYKNYEKNGVDILVKFFTG GLBZ_CHITHMKFIILALCVAAASALSGDQIGLVQ ST-YGKVKG----DSVGILYAVFKA HBA2_BOSMU---V-----------LSAADKGNVK AAW-GKVGGHAAEYGAEALERMFLS HBA2_GALCR---V-----------LSPTDKSNVK AAW-EKVGAHAGDYGAEALERMFLS HBA4_SALIR---S-----------LSAKDKANVK AIW-GKILPKSDEIGEQALSRMLVV HBAD_CHLME---M-----------LTADDKKLLT QLW-EKVAGHQEEFGSEALQRMFLT HBAD_PASMO---M-----------LTAEDKKLIQ QIW-GKLGGAEEEIGADALWRMFHS HBAZ_HORSE---S-----------LTKAERTMVV SIW-GKISMQADAVGTEALQRLFSS HBA_AILME ---V-----------LSPADKTNVK ATW-DKIGGHAGEYGGEALERTFAS HBA_ANSSE ---V-----------LSAADKGNVK TVF-GKIGGHAEEYGAETLQRMFQT HBA_COLLI ---V-----------LSANDKSNVK AVF-AKIGGQAGDLGGEALERLFIT HBA_ERIEU ---V-----------LSATDKANVK TFW-GKLGGHGGEYGGEALDRMFQA HBA_FRAPO ---V-----------LSAADKNNVK GIF-GKISSHAEDYGAEALERMFIT HBA_MACFA ---V-----------LSPADKTNVK AAW-GKVGGHAGEYGAEALERMFLS HBA_MACSI ---V-----------LSPADKTNVK DAW-GKVGGHAGEYGAEALERMFLS HBA_MESAU ---V-----------LSAKDKTNIS EAW-GKIGGHAGEYGAEALERMFFV HBA_PAGLA ---V-----------LSSADKNNIK ATW-DKIGSHAGEYGAEALERTFIS HBA_PHACO ---V-----------LSAADKNNVK GIF-TKIAGHAEEYGAEALERMFIT HBA_PONPY ---V-----------LSPADKTNVK TAW-GKVGAHAGDYGAEALERMFLS HBA_PROLO ---V-----------LSPADKANIK ATW-DKIGGHAGEYGGEALERTFAS HBA_TRIOC ---V-----------LSANDKTNVK TVF-TKITGHAEDYGAETLERMFIT HBB1_VAREX---V----------HWTAEEKQLIC SLW-GKI--DVGLIGGETLAGLLVI HBB2_TRICR---V----------HLTAEDRKEIA AIL-GKV--NVDSLGGQCLARLIVV HBB2_XENTR---V----------HWTAEEKATIA SVW-GKV--DIEQDGHDALSRLLVV HBBL_RANCA---V----------HWTAEEKAVIN SVW-QKV--DVEQDGHEALTRLFIV HBB_CALAR ---V----------HLTGEEKSAVT ALW-GKV--NVDEVGGEALGRLLVV HBB_COLLI ---V----------HWSAEEKQLIT SIW-GKV--NVADCGAEALARLLIV HBB_EQUHE ---V----------QLSGEEKAAVL ALW-DKV--NEEEVGGEALGRLLVV HBB_LARRI ---V----------HWSAEEKQLIT GLW-GKV--NVADCGAEALARLLIV HBB_MANSP ---V----------HLTPEEKTAVT TLW-GKV--NVDEVGGEALGRLLVV HBB_ORNAN ---V----------HLSGGEKSAVT NLW-GKV--NINELGGEALGRLLVV HBB_RABIT ---V----------HLSSEEKSAVT ALW-GKV--NVEEVGGEALGRLLVV HBB_SPECI ---V----------HLSDGEKNAIS TAW-GKV--HAAEVGAEALGRLLVV HBB_SPETO ---V----------HLTDGEKNAIS TAW-GKV--NAAEIGAEALGRLLVV HBB_SUNMU ---V----------HLSGEEKACVT GLW-GKV--NEDEVGAEALGRLLVV HBB_TACAC ---V----------HLSGSEKTAVT NLW-GHV--NVNELGGEALGRLLVV HBB_TRIIN ---V----------HLTPEEKALVI GLW-AKV--NVKEYGGEALGRLLVV HBB_TUPGL ---V----------HLSGEEKAAVT GLW-GKV--DLEKVGGQSLGSLLIV HBB_URSMA ---V----------HLTGEEKSLVT GLW-GKV--NVDEVGGEALGRLLVV HBE_PONPY ---V----------HFTAEEKAAVT SLW-SKM--NVEEAGGEALGRLLVV HBF1_URECA--------------GLTTAQIKAIQ DHWFLNIKGCLQAAADSIFFKYLTA LGB1_PEA GFTDKQEALVNSSSE-FKQNLPGYS ILFYTIVLEKAP--AAKGL------ LGB1_VICFAGFTEKQEALVNSSSQLFKQNPSNYS VLFYTIILQKAP--TAKAM------ MYG_ESCGI ---V-----------LSDAEWQLVL NIW-AKVEADVAGHGQDILIRLFKG MYG_HORSE ---G-----------LSDGEWQQVL NVW-GKVEADIAGHGQEVLIRLFTG MYG_LYCPI ---G-----------LSDGEWQIVL NIW-GKVETDLAGHGQEVLIRLFKN MYG_MOUSE ---G-----------LSDGEWQLVL NVW-GKVEADLAGHGQEVLIGLFKT MYG_MUSAN ------------------VDWEKVN SVW-SAVESDLTAIGQNILLRLFEQ MYG_PROGU ---G-----------LSDGEWQLVL NVW-GKVEGDLSGHGQEVLIRLFKG MYG_SAISC ---G-----------LSDGEWQLVL NIW-GKVEADIPSHGQEVLISLFKG TPAAQAFFPKFKGLTTADALKKSSDVRWHAERIINAVNDAVKSMDDTEKM DPTIQAAFPQFVGK-DLDAIKGGAEFSTHAGRIVGFLGGVIDDLP---NI FPTTKTYFPHFD-LSH-----GSAQVKGHGAKVAAALTKAVGHLDD---L FPTTKTYFPHFD-LSH-----GSTQVKGHGKKVADALTNAVLHVDD---M YPQTKAYFSHWASVAP-----GSAPVKKHGITIMNQIDDCVGHMDD---L YPQTKTYFPHFD-LHP-----GSEQVRGHGKKVAAALGNAVKSLDN---L YPSTKTYFPHFD-LSQ-----GSDQIRGHGKKVVAALSNAIKNLDN---L YPQTKTYFPHFD-LHE-----GSPQLRAHGSKVAAAVGDAVKSIDN---V FPTTKTYFPHFD-LSP-----GSAQVKAHGKKVADALTTAVGHLDD---L FPQTKTYFPHFD-LQP-----GSAQIKAHGKKVAAALVEAANHIDD---I YPQTKTYFPHFD-LSH-----GSAQIKGHGKKVAEALVEAANHIDD---I HPTTKTYFPHFD-LNP-----GSAQVKGHGKKVADALTTAVNNLDD---V YPSTKTYFPHFD-LSH-----GSAQVKGHGKKVVAALIEAANHIDD---I FPTTKTYFPHFD-LSH-----GSAQVKGHGKKVADALTLAVGHVDD---M FPTTKTYFPHFD-LSH-----GSAQVKGHGKKVADALTLAVGHVDD---M YPTTKTYFPHFD-VSH-----GSAQVKGHGKKVADALTNAVGHLDD---L FPTTKTYFPHFD-LSH-----GSAQVKAHGKKVADALTLAVGHLED---L YPSTKTYFPHFD-LSH-----GSAQIKGHGKKVVAALIEAVNHIDD---I FPTTKTYFPHFD-LSH-----GSAQVKDHGKKVADALTNAVAHVDD---M FPTTKTYFPHFD-LSP-----GSAQVKAHGKKVADALTLAVGHLDD---L YPPTKTYFPHFD-LHH-----GSAQIKAHGKKVVGALIEAVNHIDD---I YPWTQRQFSHFGNLSSPTAIAGNPRVKAHGKKVLTSFGDAIKNLDN---I NPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLDN---L YPWTQRYFSSFGNLSNVSAVSGNVKVKAHGNKVLSAVGSAIQHLDD---V YPWTQRYFSTFGDLSSPAAIAGNPKVHAHGKKILGAIDNAIHNLDD---V YPWTQRFFESFGDLSTPDAVMNNPKVKAHGKKVLGAFSDGLTHLDN---L YPWTQRFFSSFGNLSSATAISGNPNVKAHGKKVLTSFGDAVKNLDN---I YPWTQRFFDSFGDLSNPAAVMGNPKVKAHGKKVLHSFGEGVHHLDN---L YPWTQRFFASFGNLSSPTAINGNPMVRAHGKKVLTSFGEAVKNLDN---I YPWTQRFFDSFGDLSSPDAVMGNPKVKAHGKKVLGAFSDGLNHLDN---L YPWTQRFFEAFGDLSSAGAVMGNPKVKAHGAKVLTSFGDALKNLDD---L YPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDN---L YPWTQRFFDSFGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLDN---L YPWTQRFFDSFGDLSSASAVMGNAKVKAHGKKVIDSFSNGLKHLDN---L YPWTQRFFDSFGDLSSASAVMGNPKVKAHGKKVLHSLGEGVANLDN---L YPWTQRFFESFGDLSSADAVMGNAKVKAHGAKVLTSFGDALKNLDN---L YPWTQRFFEHFGDLSSASAIMNNPKVKAHGEKVFTSFGDGLKHLED---L YPWTQRFFDSFGDLSSPSAVMSNPKVKAHGKKVLTSFSDGLNHLDN---L YPWTQRFFDSFGDLSSADAIMNNPKVKAHGKKVLNSFSDGLKNLDN---L YPWTQRFFDSFGNLSSPSAILGNPKVKAHGKKVLTSFGDAIKNMDN---L YPGDLAFFHKFSSV-PLYGLRSNPAYKAQTLTVINYLDKVVDALGG--NA ----------FSFLKDTAGVEDSPKLQAHAEQVFGLVRDSAAQLRTKGEV ----------FSFLKDSAGVVDSPKLGAHAEKVFGMVRDSAVQLRATGEV HPETLEKFDKFKHLKTEAEMKASEDLKKHGNTVLTALGGILKKKGH---H HPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGH---H HPETLDKFDKFKHLKTEDEMKGSEDLKKHGNTVLTALGGILKKKGH---H HPETLDKFDKFKNLKSEEDMKGSEDLKKHGCTVLTALGTILKKKGQ---H YPESQNHFPKFKN-KSLGELKDTADIKAQADTVLSALGNIVKKKGS---H HPETLEKFDKFKHLKAEDEMRASEELKKHGTTVLTALGGILKKKGQ---H HPETLEKFDKFKHLKSEDEMKASEELKKHGTTVLTALGGILKKKGQ---H SMKLQELSVKHAQSFYVDRQYFKVLAGII---------ADTTAPGDAGFE GKHVDALVATH-KPRGVTHAQFNNFRAAFIAYLKGHV--DYTAAVEAAWG PGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLD PSALSALSDLHAHKLRVDPVNFKLLRHCLLVTLACHHPAEFTPAVHASLD FGFLTKLSELHATKLRVDPTNFKILAHNLIVVIAAYFPAEFTPEIHLSVD SQALSELSNLHAYNLRVDPANFKLLAQCFQVVLATHLGKDYSPEMHAAFD SQALSELSNLHAYNLRVDPVNFKFLSQCLQVSLATRLGKEYSPEVHSAVD AGALAKLSELHAYILRVDPVNFKFLSHCLLVTLASRLPADFTADAHAAWD PGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPAEFTPAVHASLD AGALSKLSDLHAQKLRVDPVNFKFLGHCFLVVLAIHHPSLLTPEVHASMD AGALSKLSDLHAQKLRVDPVNFKLLGHCFLVVVAVHFPSLLTPEVHASLD PGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLALHHPADFTPAVHASLD AGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPSALTPEVHASLD PQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLD PQALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLD PGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPADFTPAVHASLD PNALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHSALD TGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPSALTPEVHASLD PNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLD PGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPAEFTPAVHASLD AGALSKLSDLHAQKLRVDPVNFKLLGQCFLVVVAIHHPSVLTPEVHASLD KDTFAKLSELHCDKLHVDPTNFKLLGNVLVIVLADHHGKEFTPAHHAAYQ REYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFE KSHLKGLSKSHAEDLHVDPENFKRLADVLVIVLAAKLGSAFTPQVQAVWE KGTLHDLSEEHANELHVDPENFRRLGEVLIVVLGAKLGKAFSPQVQHVWE KGTFAHLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPVVQAAYQ KGTFAQLSELHCDKLHVDPENFRLLGDILVIILAAHFGKDFTPECQAAWQ KGTFAQLSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQ KNTFAQLSELHCDKLHVDPENFRLLGDILIIVLAAHFAKDFTPDSQAAWQ KGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQ KGTFAKLSELHCDKLHVDPENFNRLGNVLIVVLARHFSKDFSPEVQAAWQ KGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQ KGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQ KGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPEAQAAFQ KGTFAKLSELHCDKLHVDPENFRLLGNVLVVVLASKFGKEFTPPVQAAFQ KGTFAKLSELHCDKLHVDPENFNRLGNVLVVVLARHFSKEFTPEAQAAWQ KGAFAELSELHCDKLHVDPENFRLLGNVLVCVLARHFGKEFSPEAQAAYQ KGTFAKLSELHCDKLHVDPENFRLLGNVLVRVLACNFGPEFTPQVQAAFQ KGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQ KTTFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFGKEFTPEVQAAWQ GALMKAKVPSH-DAMGITPKHFGQLLKLVGGVFQEEF--SADPTTVAAWG VLGNATLGAIHVQKGVTNP-HFVVVKEALLQTIKKASGNNWSEELNTAWE VLDGKD-GSIHIQKGVLDP-HFVVVKEALLKTIKEASGDKWSEELSAAWE EAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGADAQAAMN EAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGNFGADAQGAMT EAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQNKHSGDFHADTEAAMK AAEIQPLAQSHATKHKIPVKYLEFISEIIIEVLKKRHSGDFGADAQGAMS SQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFS AAELAPLAQSHATKHKIPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMS EAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKHPGDFGADAQGAMK KLMSMICILLSSAY------- ATFDAFFGAVFAK-------M KFLANVSTVLTSKYR------ KFMASVSTVLTSKYR------ KFLQQLALALAEKYR------ KFLSAVAAVLAEKYR------ KFMSAVASVLAEKYR------ KFLSIVSSVLTEKYR------ KFFSAVSTVLTSKYR------ KFLCAVATVLTAKYR------ KFVLAVGTVLTAKYR------ KFLATVATVLTSKYR------ KFLCAVGNVLTAKYR------ KFLASVSTVLTSKYR------ KFLASVSTVLTSKYR------ KFFASVSTVLTSKYR------ KFFSAVSTVLTSKYR------ KFLCAVGTVLTAKYR------ KFLASVSTVLTSKYR------ KFFTSVSTVLTSKYR------ KFLCAVGNVLSAKYR------ KLVNVVSHSLARRYH------ KLMKGVSHALGHGY------- KLNATLVAALSHGYF------ KFIAVLVDALSHSYH------ KVVAGVANALAHKYH------ KLVRVVAHALARKYH------ KVVAGVANALAHKYH------ KLVRVVAHALARKYH------ KVVAGVANALAHKYH------ KLVSGVAHALGHKYH------ KVVAGVANALAHKYH------ KVVAGVANALAHKYH------ KVVAGVANALSHKYH------ KVVAGVANALAHKYH------ KLVSGVSHALAHKYH------ KVVAGVANALAHKYH------ KVVAGVANALAHKYH------ KVVAGVANALAHKYH------ KLVSAVAIALAHKYH------ DAAGVLVAAM----------K VAYDGLATAIKKAMKT----A VAYDGLATAIK----A----A KALELFRKDIAAKYKELGFQG KALELFRNDIAAKYKELGFQG KALELFRNDIAAKYKELGFQG KALELFRNDIAAKYKELGFQG GAFKIICSDIEKEYKAANFQG KALELFRNDIAAKYKELGFQG KALELFRNDMAAKYKELGFQG squid/Formats/pir0000640000175000017520000002757710463223377014265 0ustar naolivbiolinux P R O T E I N S E Q U E N C E D A T A B A S E of PIR-International Section 1. Fully Classified Entries Release 63.00, December 30, 1999 20032 sequences, 7820966 residues Protein Information Resource (PIR)* National Biomedical Research Foundation 3900 Reservoir Road, N.W., Washington, DC 20007, USA International Protein Information Munich Information Center for Database in Japan (JIPID) Protein Sequences (MIPS) Science University of Tokyo GSF-Forschungszentrum f. Umwelt und Gesundheit 2669 Yamazaki, Noda 278, Japan am Max-Planck-Instut f. Biochemie Am Klopferspitz 18, D-82152 Martinsried, FRG This database may be redistributed without prior consent, provided that this notice be given to each user and that the words "Derived from" shall precede this notice if the database has been altered by the redistributor. *PIR is a registered mark of NBRF. \\\ ENTRY CCHU #type complete TITLE cytochrome c - human ORGANISM #formal_name Homo sapiens #common_name man DATE 24-Apr-1984 #sequence_revision 30-Sep-1991 #text_change 28-Jun-1999 ACCESSIONS A31764; A05676; I55192; A00001 REFERENCE A31764 #authors Evans, M.J.; Scarpulla, R.C. #journal Proc. Natl. Acad. Sci. U.S.A. (1988) 85:9625-9629 #title The human somatic cytochrome c gene: two classes of processed pseudogenes demarcate a period of rapid molecular evolution. #cross-references MUID:89071748 #accession A31764 ##molecule_type DNA ##residues 1-105 ##label EVA ##cross-references GB:M22877; NID:g181241; PIDN:AAA35732.1; PID:g181242 REFERENCE A05676 #authors Matsubara, H.; Smith, E.L. #journal J. Biol. Chem. (1963) 238:2732-2753 #title Human heart cytochrome c. Chymotryptic peptides, tryptic peptides, and the complete amino acid sequence. #accession A05676 ##molecule_type protein ##residues 2-28;29-46;47-100;101-105 ##label MATS REFERENCE A00001 #authors Matsubara, H.; Smith, E.L. #journal J. Biol. Chem. (1962) 237:3575-3576 #title The amino acid sequence of human heart cytochrome c. #contents annotation #note 66-Leu is found in 10% of the molecules in pooled protein REFERENCE I55192 #authors Tanaka, Y.; Ashikari, T.; Shibano, Y.; Amachi, T.; Yoshizumi, H.; Matsubara, H. #journal J. Biochem. (1988) 103:954-961 #title Construction of a human cytochrome c gene and its functional expression in Saccharomyces cerevisiae. #cross-references MUID:89008207 #accession I55192 ##status translated from GB/EMBL/DDBJ ##molecule_type mRNA ##residues 78-105 ##label RES ##cross-references GB:D00265; NID:g2897691; PIDN:BAA00187.1; PID:d1000635; PID:g219557 GENETICS #introns 57/1 CLASSIFICATION #superfamily cytochrome c; cytochrome c homology KEYWORDS acetylated amino end; chromoprotein; electron transfer; heme; iron; mitochondrion; oxidative phosphorylation; polymorphism; respiratory chain FEATURE 2-105 #product cytochrome c #status experimental #label MAT\ 5-99 #domain cytochrome c homology #label CYC\ 2 #modified_site acetylated amino end (Gly) (in mature form) #status experimental\ 15,18 #binding_site heme (Cys) (covalent) #status experimental\ 19,81 #binding_site heme iron (His, Met) (axial ligands) #status predicted SUMMARY #length 105 #molecular-weight 11749 #checksum 3247 SEQUENCE 5 10 15 20 25 30 1 M G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G 31 P N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I I W 61 G E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E 91 E R A D L I A Y L K K A T N E /// ENTRY CCCZ #type complete TITLE cytochrome c - chimpanzee (tentative sequence) ORGANISM #formal_name Pan troglodytes #common_name chimpanzee DATE 17-Mar-1987 #sequence_revision 17-Mar-1987 #text_change 25-Apr-1997 ACCESSIONS A00002 REFERENCE A94601 #authors Needleman, S.B. #submission submitted to the Atlas, October 1968 #accession A00002 ##molecule_type protein ##residues 1-104 ##label NEE REFERENCE A94455 #authors Needleman, S.B.; Margoliash, E. #citation unpublished results, 1966, cited by Margoliash, E., and Fitch, W.M., Ann. N.Y. Acad. Sci. 151, 359-381, 1968 #contents annotation; compositions of chymotryptic peptides CLASSIFICATION #superfamily cytochrome c; cytochrome c homology KEYWORDS acetylated amino end; chromoprotein; electron transfer; heme; iron; mitochondrion; oxidative phosphorylation; respiratory chain FEATURE 4-98 #domain cytochrome c homology #label CYC\ 1 #modified_site acetylated amino end (Gly) #status predicted\ 14,17 #binding_site heme (Cys) (covalent) #status predicted\ 18,80 #binding_site heme iron (His, Met) (axial ligands) #status predicted SUMMARY #length 104 #molecular-weight 11617 #checksum 9501 SEQUENCE 5 10 15 20 25 30 1 G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P 31 N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I I W G 61 E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E E 91 R A D L I A Y L K K A T N E /// ENTRY CCMQR #type complete TITLE cytochrome c - rhesus macaque (tentative sequence) ORGANISM #formal_name Macaca mulatta #common_name rhesus macaque DATE 17-Mar-1987 #sequence_revision 17-Mar-1987 #text_change 25-Apr-1997 ACCESSIONS A00003 REFERENCE A00003 #authors Rothfus, J.A.; Smith, E.L. #journal J. Biol. Chem. (1965) 240:4277-4283 #title Amino acid sequence of rhesus monkey heart cytochrome c. #cross-references MUID:66045191 #contents compositions of chymotryptic peptides; sequences of residues 55-61 and 68-70 #accession A00003 ##molecule_type protein ##residues 1-104 ##label ROT CLASSIFICATION #superfamily cytochrome c; cytochrome c homology KEYWORDS acetylated amino end; chromoprotein; electron transfer; heme; iron; mitochondrion; oxidative phosphorylation; respiratory chain FEATURE 4-98 #domain cytochrome c homology #label CYC\ 1 #modified_site acetylated amino end (Gly) #status experimental\ 14,17 #binding_site heme (Cys) (covalent) #status predicted\ 18,80 #binding_site heme iron (His, Met) (axial ligands) #status predicted SUMMARY #length 104 #molecular-weight 11605 #checksum 9512 SEQUENCE 5 10 15 20 25 30 1 G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P 31 N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I T W G 61 E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E E 91 R A D L I A Y L K K A T N E /// ENTRY CCMKP #type complete TITLE cytochrome c - spider monkey ORGANISM #formal_name Ateles sp. #common_name spider monkey DATE 17-Dec-1982 #sequence_revision 17-Dec-1982 #text_change 25-Apr-1997 ACCESSIONS A00004 REFERENCE A00004 #authors Margoliash, E. #citation unpublished results, cited by Shelnutt, J.A., Rousseau, D.L., Dethmers, J.K., and Margoliash, E., Biochemistry 20, 6485-6497, 1981 #accession A00004 ##molecule_type protein ##residues 1-104 ##label MAR CLASSIFICATION #superfamily cytochrome c; cytochrome c homology KEYWORDS acetylated amino end; chromoprotein; electron transfer; heme; iron; mitochondrion; oxidative phosphorylation; respiratory chain FEATURE 4-98 #domain cytochrome c homology #label CYC\ 1 #modified_site acetylated amino end (Gly) #status predicted\ 14,17 #binding_site heme (Cys) (covalent) #status predicted\ 18,80 #binding_site heme iron (His, Met) (axial ligands) #status predicted SUMMARY #length 104 #molecular-weight 11710 #checksum 9066 SEQUENCE 5 10 15 20 25 30 1 G D V F K G K R I F I M K C S Q C H T V E K G G K H K T G P 31 N L H G L F G R K T G Q A S G F T Y T E A N K N K G I I W G 61 E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E E 91 R A D L I A Y L K K A T N E /// ENTRY CCMS #type complete TITLE cytochrome c - mouse ORGANISM #formal_name Mus musculus #common_name house mouse DATE 31-Dec-1990 #sequence_revision 30-Sep-1991 #text_change 11-Jun-1999 ACCESSIONS A23057; A04604; A00009 REFERENCE A23057 #authors Limbach, K.J.; Wu, R. #journal Nucleic Acids Res. (1985) 13:617-630 #title Characterization of a mouse somatic cytochrome c gene and three cytochrome c pseudogenes. #cross-references MUID:85215501 #accession A23057 ##molecule_type DNA ##residues 1-105 ##label LIM ##cross-references EMBL:X01756; NID:g50618; PIDN:CAA25899.1; PID:g50619 ##experimental_source strain BALB/c REFERENCE A04604 #authors Carlson, S.S.; Mross, G.A.; Wilson, A.C.; Mead, R.T.; Wolin, L.D.; Bowers, S.F.; Foley, N.T.; Muijsers, A.O.; Margoliash, E. #journal Biochemistry (1977) 16:1437-1442 #title Primary structure of mouse, rat, and guinea pig cytochrome c. #cross-references MUID:77134768 #accession A04604 ##molecule_type protein ##residues 2-105 ##label CAR ##experimental_source strain BALB/c GENETICS #introns 57/1 CLASSIFICATION #superfamily cytochrome c; cytochrome c homology KEYWORDS acetylated amino end; chromoprotein; electron transfer; heme; iron; mitochondrion; oxidative phosphorylation; respiratory chain FEATURE 2-105 #product cytochrome c #status experimental #label MAT\ 5-99 #domain cytochrome c homology #label CYC\ 2 #modified_site acetylated amino end (Gly) (in mature form) #status experimental\ 15,18 #binding_site heme (Cys) (covalent) #status experimental\ 19,81 #binding_site heme iron (His, Met) (axial ligands) #status predicted SUMMARY #length 105 #molecular-weight 11605 #checksum 1273 SEQUENCE 5 10 15 20 25 30 1 M G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G 31 P N L H G L F G R K T G Q A A G F S Y T D A N K N K G I T W 61 G E D T L M E Y L E N P K K Y I P G T K M I F A G I K K K G 91 E R A D L I A Y L K K A T N E /// squid/Formats/regression.dat0000640000175000017520000000173110463223377016402 0ustar naolivbiolinux# filename format type nseq nres short long autodetect? alignment? singleseq? # -------- -------- ------- ---- ---- ----- ---- ---------- ---------- ---------- fasta fasta Protein 3 1730 356 949 yes no no genbank genbank DNA 6 3773 132 1771 yes no no embl embl DNA 2 1868 233 1635 yes no no swissprot embl Protein 6 2779 75 924 yes no no gcg gcg DNA 1 9718 9718 9718 yes no yes gcgdata.1 gcgdata Protein 20 7100 29 1299 yes no no gcgdata.2 gcgdata DNA 7 5867 105 2886 yes no no pir pir Protein 5 522 104 105 yes no no stockholm.1 stockholm Protein 7 266 38 38 yes yes no stockholm.2 stockholm Protein 16 3769 227 239 yes yes no msf msf Protein 50 7251 141 153 yes yes no clustal clustal DNA 20 1518 75 80 yes yes no selex.1 selex RNA 11 201 11 29 yes yes no selex.2 selex RNA 11 201 11 29 yes yes no phylip phylip Protein 50 7251 141 153 yes yes no a2m a2m Protein 50 7251 141 153 no yes no squid/Formats/swissprot0000640000175000017520000004042710463223377015535 0ustar naolivbiolinuxID 100K_RAT STANDARD; PRT; 889 AA. AC Q62671; DT 01-NOV-1997 (Rel. 35, Created) DT 01-NOV-1997 (Rel. 35, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE 100 KD PROTEIN (EC 6.3.2.-). OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. RN [1] RP SEQUENCE FROM N.A. RC STRAIN=WISTAR; TISSUE=TESTIS; RX MEDLINE; 92253337. RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.; RT "Molecular characterization of a novel rat protein structurally RT related to poly(A) binding proteins and the 70K protein of the U1 RT small nuclear ribonucleoprotein particle (snRNP)."; RL Nucleic Acids Res. 20:1471-1475(1992). RN [2] RP ERRATUM. RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.; RL Nucleic Acids Res. 20:2624-2624(1992). CC -!- FUNCTION: E3 UBIQUITIN-PROTEIN LIGASE WHICH ACCEPTS UBIQUITIN FROM CC AN E2 UBIQUITIN-CONJUGATING ENZYME IN THE FORM OF A THIOESTER AND CC THEN DIRECTLY TRANSFERS THE UBIQUITIN TO TARGETED SUBSTRATES (BY CC SIMILARITY). THIS PROTEIN MAY BE INVOLVED IN MATURATION AND/OR CC POST-TRANSCRIPTIONAL REGULATION OF MRNA. CC -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT CC IN LIVER, KIDNEY, LUNG AND BRAIN. CC -!- DEVELOPMENTAL STAGE: IN EARLY POST-NATAL LIFE, EXPRESSION IN CC THE TESTIS INCREASES TO REACH A MAXIMUM AROUND DAY 28. CC -!- MISCELLANEOUS: A CYSTEINE RESIDUE IS REQUIRED FOR CC UBIQUITIN-THIOLESTER FORMATION. CC -!- SIMILARITY: CONTAINS AN HECT-TYPE E3 UBIQUITIN-PROTEIN LIGASE CC DOMAIN. CC -!- SIMILARITY: A CENTRAL REGION (AA 485-514) IS SIMILAR TO THE CC C-TERMINAL DOMAINS OF MAMMALIAN AND YEAST POLY (A) RNA BINDING CC PROTEINS (PABP). CC -!- SIMILARITY: THE C-TERMINAL HALF SHOWS HIGH SIMILARITY TO CC DROSOPHILA HYPERPLASMIC DISC PROTEIN AND SOME, TO HUMAN E6-AP. CC -!- SIMILARITY: CONTAINS MIXED-CHARGE DOMAINS SIMILAR TO RNA-BINDING CC PROTEINS. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X64411; CAA45756.1; -. DR PFAM; PF00632; HECT; 1. DR PFAM; PF00658; PABP; 1. KW Ubiquitin conjugation; Ligase. FT DOMAIN 77 88 ASP/GLU-RICH (ACIDIC). FT DOMAIN 127 150 PRO-RICH. FT DOMAIN 420 439 ARG/GLU-RICH (MIXED CHARGE). FT DOMAIN 448 457 ARG/ASP-RICH (MIXED CHARGE). FT DOMAIN 485 514 PABP-LIKE. FT DOMAIN 579 590 ASP/GLU-RICH (ACIDIC). FT DOMAIN 786 889 HECT DOMAIN. FT DOMAIN 827 847 PRO-RICH. FT BINDING 858 858 UBIQUITIN (BY SIMILARITY). SQ SEQUENCE 889 AA; 100368 MW; DD7E6C7A CRC32; MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA GSGKCLVEVT MDRNCLEVLP TKMSYAANLK NVMNMQNRQK KAGEDQSMLA EEADSSKPGP SAHDVAAQLK SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLDCIQNAN KGTHTSLMQR LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPDP LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVEEAMELI VAHGRENGAD SILDLGLLDS SEKVQENRKR HGSSRSVVDM DLDDTDDGDD NAPLFYQPGK RGFYTPRPGK NTEARLNCFR NIGRILGLCL LQNELCPITL NRHVIKVLLG RKVNWHDFAF FDPVMYESLR QLILASQSSD ADAVFSAMDL AFAVDLCKEE GGGQVELIPN GVNIPVTPQN VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV // ID 104K_THEPA STANDARD; PRT; 924 AA. AC P15711; DT 01-APR-1990 (Rel. 14, Created) DT 01-APR-1990 (Rel. 14, Last sequence update) DT 01-AUG-1992 (Rel. 23, Last annotation update) DE 104 KD MICRONEME-RHOPTRY ANTIGEN. OS Theileria parva. OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; OC Theileria. RN [1] RP SEQUENCE FROM N.A. RC STRAIN=MUGUGA; RX MEDLINE; 90158697. RA IAMS K.P., YOUNG J.R., NENE V., DESAI J., WEBSTER P., RA OLE-MOIYOI O.K., MUSOKE A.J.; RT "Characterisation of the gene encoding a 104-kilodalton microneme- RT rhoptry protein of Theileria parva."; RL Mol. Biochem. Parasitol. 39:47-60(1990). CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES. CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; M29954; AAA18217.1; -. DR PIR; A44945; A44945. KW Antigen; Sporozoite; Repeat. FT DOMAIN 1 19 HYDROPHOBIC. FT DOMAIN 905 924 HYDROPHOBIC. SQ SEQUENCE 924 AA; 103625 MW; 4563AAA0 CRC32; MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP KKPDSAYIPS ILAILVVSLI VGIL // ID 108_LYCES STANDARD; PRT; 102 AA. AC Q43495; DT 15-JUL-1999 (Rel. 38, Created) DT 15-JUL-1999 (Rel. 38, Last sequence update) DT 15-JUL-1999 (Rel. 38, Last annotation update) DE PROTEIN 108 PRECURSOR. OS Lycopersicon esculentum (Tomato). OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; OC core eudicots; Asteridae; euasterids I; Solanales; Solanaceae; OC Solanum. RN [1] RP SEQUENCE FROM N.A. RC STRAIN=CV. VF36; TISSUE=ANTHER; RX MEDLINE; 94143497. RA CHEN R., SMITH A.G.; RT "Nucleotide sequence of a stamen- and tapetum-specific gene from RT Lycopersicon esculentum."; RL Plant Physiol. 101:1413-1413(1993). CC -!- TISSUE SPECIFICITY: STAMEN- AND TAPETUM-SPECIFIC. CC -!- SIMILARITY: BELONGS TO THE A9 / FIL1 FAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; Z14088; CAA78466.1; -. DR MENDEL; 8853; LYCes;1133;1. KW Signal. FT SIGNAL 1 30 POTENTIAL. FT CHAIN 31 102 PROTEIN 108. FT DISULFID 41 77 BY SIMILARITY. FT DISULFID 51 66 BY SIMILARITY. FT DISULFID 67 92 BY SIMILARITY. FT DISULFID 79 99 BY SIMILARITY. SQ SEQUENCE 102 AA; 10576 MW; AFA4875A CRC32; MASVKSSSSS SSSSFISLLL LILLVIVLQS QVIECQPQQS CTASLTGLNV CAPFLVPGSP TASTECCNAV QSINHDCMCN TMRIAAQIPA QCNLPPLSCS AN // ID 10KD_VIGUN STANDARD; PRT; 75 AA. AC P18646; DT 01-NOV-1990 (Rel. 16, Created) DT 01-NOV-1990 (Rel. 16, Last sequence update) DT 01-FEB-1995 (Rel. 31, Last annotation update) DE 10 KD PROTEIN PRECURSOR (CLONE PSAS10). OS Vigna unguiculata (Cowpea). OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; OC core eudicots; Rosidae; eurosids I; Fabales; Fabaceae; Papilionoideae; OC Vigna. RN [1] RP SEQUENCE FROM N.A. RC TISSUE=COTYLEDON; RX MEDLINE; 91355865. RA ISHIBASHI N., YAMAUCHI D., MINIAMIKAWA T.; RT "Stored mRNA in cotyledons of Vigna unguiculata seeds: nucleotide RT sequence of cloned cDNA for a stored mRNA and induction of its RT synthesis by precocious germination."; RL Plant Mol. Biol. 15:59-64(1990). CC -!- FUNCTION: THIS PROTEIN IS REQUIRED FOR GERMINATION. CC -!- SIMILARITY: BELONGS TO THE GAMMA-PUROTHIONIN FAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X16877; CAA34760.1; -. DR PIR; S11156; S11156. DR HSSP; P45639; 1CHL. DR PFAM; PF00304; Gamma-thionin; 1. DR PROSITE; PS00940; GAMMA_THIONIN; 1. KW Germination; Signal. FT SIGNAL 1 ? POTENTIAL. FT CHAIN ? 75 10 KD PROTEIN. FT DISULFID 31 75 BY SIMILARITY. FT DISULFID 42 63 BY SIMILARITY. FT DISULFID 48 69 BY SIMILARITY. FT DISULFID 52 71 BY SIMILARITY. SQ SEQUENCE 75 AA; 8523 MW; AFF911AB CRC32; MEKKSIAGLC FLFLVLFVAQ EVVVQSEAKT CENLVDTYRG PCFTTGSCDD HCKNKEHLLS GRCRDDVRCW CTRNC // ID 110K_PLAKN STANDARD; PRT; 296 AA. AC P13813; DT 01-JAN-1990 (Rel. 13, Created) DT 01-JAN-1990 (Rel. 13, Last sequence update) DT 01-FEB-1994 (Rel. 28, Last annotation update) DE 110 KD ANTIGEN (PK110) (FRAGMENT). OS Plasmodium knowlesi. OC Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 88039002. RA PERLER F.B., MOON A.M., QIANG B.Q., MEDA M., DALTON M., CARD C., RA SCHMIDT-ULLRICH R., WALLACH D., LYNCH J., DONELSON J.E.; RT "Cloning and characterization of an abundant Plasmodium knowlesi RT antigen which cross reacts with Gambian sera."; RL Mol. Biochem. Parasitol. 25:185-193(1987). CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; M19152; AAA29471.1; -. DR PIR; A54527; A54527. KW Malaria; Antigen; Repeat. FT NON_TER 1 1 FT DOMAIN 131 296 13.5 X 12 AA TANDEM REPEATS OF E-E-T-Q-K- FT T-V-E-P-E-Q-T. SQ SEQUENCE 296 AA; 34077 MW; 666F88DF CRC32; FNSNMLRGSV CEEDVSLMTS IDNMIEEIDF YEKEIYKGSH SGGVIKGMDY DLEDDENDED EMTEQMVEEV ADHITQDMID EVAHHVLDNI THDMAHMEEI VHGLSGDVTQ IKEIVQKVNV AVEKVKHIVE TEETQKTVEP EQIEETQNTV EPEQTEETQK TVEPEQTEET QNTVEPEQIE ETQKTVEPEQ TEEAQKTVEP EQTEETQKTV EPEQTEETQK TVEPEQTEET QKTVEPEQTE ETQKTVEPEQ TEETQKTVEP EQTEETQKTV EPEQTEETQN TVEPEPTQET QNTVEP // ID 11S3_HELAN STANDARD; PRT; 493 AA. AC P19084; DT 01-NOV-1990 (Rel. 16, Created) DT 01-NOV-1990 (Rel. 16, Last sequence update) DT 01-FEB-1994 (Rel. 28, Last annotation update) DE 11S GLOBULIN SEED STORAGE PROTEIN G3 PRECURSOR (HELIANTHININ G3). GN HAG3. OS Helianthus annuus (Common sunflower). OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; OC core eudicots; Asteridae; euasterids II; Asterales; Asteraceae; OC Helianthus. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 89232734. RA VONDER HARR R.A., ALLEN R.D., COHEN E.A., NESSLER C.L., THOMAS T.L.; RT "Organization of the sunflower 11S storage protein gene family."; RL Gene 74:433-443(1988). CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN. CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND A CC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY A CC DISULFIDE BOND. CC -!- SIMILARITY: BELONGS TO THE 11S SEED STORAGE PROTEINS (GLOBULINS) CC FAMILY. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; M28832; AAA33374.1; -. DR PIR; JA0089; JA0089. DR PFAM; PF00190; Seedstore_11s; 1. DR PROSITE; PS00305; 11S_SEED_STORAGE; 1. KW Seed storage protein; Multigene family; Signal. FT SIGNAL 1 20 FT CHAIN 21 305 ACIDIC CHAIN. FT CHAIN 306 493 BASIC CHAIN. FT DISULFID 103 312 INTERCHAIN (ACIDIC-BASIC) (POTENTIAL). FT DOMAIN 23 35 GLN-RICH. FT DOMAIN 111 127 GLN/GLY-RICH. FT DOMAIN 191 297 GLN-RICH. SQ SEQUENCE 493 AA; 55687 MW; E79DEAAE CRC32; MASKATLLLA FTLLFATCIA RHQQRQQQQN QCQLQNIEAL EPIEVIQAEA GVTEIWDAYD QQFQCAWSIL FDTGFNLVAF SCLPTSTPLF WPSSREGVIL PGCRRTYEYS QEQQFSGEGG RRGGGEGTFR TVIRKLENLK EGDVVAIPTG TAHWLHNDGN TELVVVFLDT QNHENQLDEN QRRFFLAGNP QAQAQSQQQQ QRQPRQQSPQ RQRQRQRQGQ GQNAGNIFNG FTPELIAQSF NVDQETAQKL QGQNDQRGHI VNVGQDLQIV RPPQDRRSPR QQQEQATSPR QQQEQQQGRR GGWSNGVEET ICSMKFKVNI DNPSQADFVN PQAGSIANLN SFKFPILEHL RLSVERGELR PNAIQSPHWT INAHNLLYVT EGALRVQIVD NQGNSVFDNE LREGQVVVIP QNFAVIKRAN EQGSRWVSFK TNDNAMIANL AGRVSASAAS PLTLWANRYQ LSREEAQQLK FSQRETVLFA PSFSRGQGIR ASR // squid/Formats/gcgdata.10000640000175000017520000002225610463223377015211 0ustar naolivbiolinux>>>>104K_THEPA 8/92 ASCII Len: 924 P15711 theileria parva. 104 kd microneme-rhoptry antigen. 8/92 MKFLILLFNILCLFPVLAADNHGVGPQGASGVDPITFDINSNQTGPAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIWENASTPLYTGAIVTNNDGPYMAYVEVLGDPNLQFFIKSGDAWVTLSEHEYLAKLQEIRQAVHIESVFSLNMAFQLENNKYEVETHAKNGANMVTFIPRNGHICKMVYHKNVRIYKATGNDTVTSVVGFFRGLRLLLINVFSIDDNGMMSNRYFQHVDDKYVPISQKNYETGIVKLKDYKHAYHPVDLDIKDIDYTMFHLADATYHEPCFKIIPNTGFCITKLFDGDQVLYESFNPLIHCINEVHIYDRNNGSIICLHLNYSPPSYKAYLVLKDTGWEATTHPLLEEKIEELQDQRACELDVNFISDKDLYVAALTNADLNYTMVTPRPHRDVIRVSDGSEVLWYYEGLDNFLVCAWIYVSDGVASLVHLRIKDRIPANNDIYVLKGDLYWTRITKIQFTQEIKRLVKKSKKKLAPITEEDSDKHDEPPEGPGASGLPPKAPGDKEGSEGHKGPSKGSDSSKEGKKPGSGKKPGPAREHKPSKIPTLSKKPSGPKDPKHPRDPKEPRKSKSPRTASPTRRPSPKLPQLSKLPKSTSPRSPPPPTRPSSPERPEGTKIIKTSKPPSPKPPFDPSFKEKFYDDYSKAASRSKETKTTVVLDESFESILKETLPETPGTPFTTPRPVPPKRPRTPESPFEPPKDPDSPSTSPSEFFTPPESKRTRFHETPADTPLPDVTAELFKEPDVTAETKSPDEAMKRPRSPSEYEDTSPGDYPSLPMKRHRLERLRLTTTEMETDPGRMAKDASGKPVKLKRSKSFDDLTTVELAPEPKASRIVVDDEGTEADDEETHPPEERQKTEVRRRRPPKKPSKSPRPSKPKKPKKPDSAYIPSILAILVVSLIVGIL >>>>10KD_VIGUN 2/95 ASCII Len: 75 P18646 vigna unguiculata (cowpea). 10 kd protein precursor (clone psas10). 2/95 MEKKSIAGLCFLFLVLFVAQEVVVQSEAKTCENLVDTYRGPCFTTGSCDDHCKNKEHLLSGRCRDDVRCWCTRNC >>>>110K_PLAKN 2/94 ASCII Len: 296 P13813 plasmodium knowlesi. 110 kd antigen (pk110) (fragment). 2/94 FNSNMLRGSVCEEDVSLMTSIDNMIEEIDFYEKEIYKGSHSGGVIKGMDYDLEDDENDEDEMTEQMVEEVADHITQDMIDEVAHHVLDNITHDMAHMEEIVHGLSGDVTQIKEIVQKVNVAVEKVKHIVETEETQKTVEPEQIEETQNTVEPEQTEETQKTVEPEQTEETQNTVEPEQIEETQKTVEPEQTEEAQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQNTVEPEPTQETQNTVEP >>>>11S3_HELAN 2/94 ASCII Len: 493 P19084 helianthus annuus (common sunflower). 11s globulin seed storage protein g3 precursor (helianthinin g3). 2/94 MASKATLLLAFTLLFATCIARHQQRQQQQNQCQLQNIEALEPIEVIQAEAGVTEIWDAYDQQFQCAWSILFDTGFNLVAFSCLPTSTPLFWPSSREGVILPGCRRTYEYSQEQQFSGEGGRRGGGEGTFRTVIRKLENLKEGDVVAIPTGTAHWLHNDGNTELVVVFLDTQNHENQLDENQRRFFLAGNPQAQAQSQQQQQRQPRQQSPQRQRQRQRQGQGQNAGNIFNGFTPELIAQSFNVDQETAQKLQGQNDQRGHIVNVGQDLQIVRPPQDRRSPRQQQEQATSPRQQQEQQQGRRGGWSNGVEETICSMKFKVNIDNPSQADFVNPQAGSIANLNSFKFPILEHLRLSVERGELRPNAIQSPHWTINAHNLLYVTEGALRVQIVDNQGNSVFDNELREGQVVVIPQNFAVIKRANEQGSRWVSFKTNDNAMIANLAGRVSASAASPLTLWANRYQLSREEAQQLKFSQRETVLFAPSFSRGQGIRASR >>>>11SB_CUCMA 11/90 ASCII Len: 480 P13744 cucurbita maxima (pumpkin) (winter squash). 11s globulin beta subunit precursor. 11/90 MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGSEVWQQHRYQSPRACRLENLRAQDPVRRAEAEAIFTEVWDQDNDEFQCAGVNMIRHTIRPKGLLLPGFSNAPKLIFVAQGFGIRGIAIPGCAETYQTDLRRSQSAGSAFKDQHQKIRPFREGDLLVVPAGVSHWMYNRGQSDLVLIVFADTRNVANQIDPYLRKFYLAGRPEQVERGVEEWERSSRKGSSGEKSGNIFSGFADEFLEEAFQIDGGLVRKLKGEDDERDRIVQVDEDFEVLLPEKDEEERSRGRYIESESESENGLEETICTLRLKQNIGRSVRADVFNPRGGRISTANYHTLPILRQVRLSAERGVLYSNAMVAPHYTVNSHSVMYATRGNARVQVVDNFGQSVFDGEVREGQVLMIPQNFVVIKRASDRGFEWIAFKTNDNAITNLLAGRVSQMRMLPLGVLSNMYRISREEAQRLKYGQQEMRVLSPGRSQGRRE >>>>120K_RICRI 10/94 ASCII Len: 1299 P14914 rickettsia rickettsii. 120 kd surface-exposed protein. 10/94 MVIQSANATGQVNFRHIVDVGADGTTAFKTAASKVTITQDSNFGNTDFGNLAAQIKVPNAITLTGNFTGDASNPGNTAGVITFDANGTLESASADANVAVTNNITAIEASGAGVVQLSGTHAAELRLGNAGSIFKLADGTVINGKVNQTALVGGALAAGTITLDGSATITGDIGNAGGAAALQRITLANDAKKTLTLGGANIIGAGGGTIDLQANGGTIKLTSTQNNIVVDFDLAIATDQTGVVDASSLTNAQTLTINGKIGTIGANNKTLGQFNIGSSKTVLSNGNVAINELVIGNDGAVQFAHDTYLITRTTNAAGQGKIIFNPVVNNGTTLAAGTNLGSATNPLAEINFGSKGVNVDTVLNVGEGVNLYATNITTTDANVGSFVFNAGGTNIVSGTVGGQQGNKFNTVALENGTTVKFLGNATFNGNTTIAANSTLQIGGNYTADCVASADGTGIVEFVNTGPITVTLNKEAAPVNALKQITVSGPGNVVINEIGNAGNHHGAVTDTIAFENSSLGAVVFLPRGIPFNDAGNTMPLTIKSTVGNKTAKGFDVPSVVVLGVDSVIADGQVIVDQNNIVGLGLGSDNGIIVNATTLYAGISTLNNNQGTVTLSGGVPNTPGTVYGLGTGIGASKFKQVTFTTDYNNLGNIIATNATINDGVTVTTGGIAGIGFDGKITLGSVNGNGNVRFADGILSNSTSMIGTTKANNGTVTYLGNAFVGNIGDSDTPVASVRFTGSDSGAGLQGNIYSQVIDFGTYNLGIVNSNIILGGGTTAINGKIDLVTNTLTFASGTSTWGNNTSIETTLTLANGNIGHIVILEGAQVNTTTTGTTTIKVQDNANANFSGTQTYTLIQGGARFNGTLGSPNFAVTGSNRFVNYSLIRAANQDYVITRTNNAENVVTNDIANSPFGGAPGVDQNVTTFVNATNTAAYNNLLLAKNSANSANFVGAIVTDTSAAITNVQLDLAKDIQAQLGNRLGALRYLGTPETAEMADLKLEHIGSVAAGDEAIDNVAYGIWAKPFYTDAHQSKKGGLAGYKAKTTGVVIGLDTLANDNLMIGAAIGITKTDIKHQDYKKGDKTDVNGFSFSLYGAQQLVKNFFAQGSAIFSLNQVKNKSQRYFFDANGNMSKQIAAGHYDNMTFGGNLTVGYDYNAMQGVLVTPMAGLSYLKSSDENYKETGTTVANKQVNSKFSDRTDLIVGAKVAGSTMNRTDLAVYPEVHAFVVHKVTGRLSKTQSVLDGQVTPCINQPDRTTKTSYNLGLSASIRSDAKMEYGIGYDAQISSKYTAHQGTLKVRVNF >>>>128U_DROME 2/94 ASCII Len: 368 P32234 drosophila melanogaster (fruit fly). gtp-binding protein 128up. 2/94 MITILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELISPKGGGGGTGEAGFEVAKTGDARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFMVLDCLKPLGHKKLLEHELEGFGIRLNKKPPNIYYKRKDKGGINLNSMVPQSELDTDLVKTILSEYKIHNADITLRYDATSDDLIDVIEGNRIYIPCIYLLNKIDQISIEELDVIYKIPHCVPISAHHHWNFDDLLELMWEYLRLQRIYTKPKGQLPDYNSPVVLHNERTSIEDFCNKLHRSIAKEFKYALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKKV >>>>12AH_CLOS4 8/91 ASCII Len: 29 P21215 clostridium sp. (strain c 48-50). 12-alpha-hydroxysteroid dehydrogenase (ec 1.1.1.176) (fragment). 8/91 MIFDGKVAIITGGGKAKSIGYGIAVAYAK >>>>12KD_MYCLE 2/95 ASCII Len: 156 P15878 mycobacterium leprae. 12 kd protein. 2/95 MNDIIALKFHISLNATTWIGRIGMVILPLLVYFITYRWCIGLQRSDRAVLEHGIETGIIKRLPHGAYIELHQPLGPVDDHGHPIPLEYQGTAVPKRMNKLGSAGSPSSGSFLFADPVSEDAALREATHVAEQRALTALREHQDSIASSPNGERGKH >>>>12S1_ARATH 4/90 ASCII Len: 472 P15455 arabidopsis thaliana (mouse-ear cress). 12s seed storage protein. 4/90 MARVSSLLSFCLTLLILFHGYAAQQGQQGQQFPNECQLDQLNALEPSHVLKSEAGRIEVWDHHAPQLRCSGVSFARYIIESKGLYLPSFFNTAKLSFVAKGRGLMGKVIPGCAETFQDSSEFQPRFEGQGQSQRFRDMHQKVEHIRSGDTIATTPGVAQWFYNDGQQPLVIVSVFDLASHQNQLDRNPRPFYLAGNNPQGQVWLQGREQQPQKNIFNGFGPEVIAQALKIDLQTAQQLQNQDDNRGNIVRVQGPFGVIRPPLRGQRPQEEEEEEGRHGRHGNGLEETICSARCTDNLDDPSRADVYKPQLGYISTLNSYDLPILRFIRLSALRGSIRQNAMVLPQWNANANAILYETDGEAQIQIVNDNGNRVFDGQVSQGQLIAVPQGFSVVKRATSNRFQWVEFKTNANAQINTLAGRTSVLRGLPLEVITNGFQISPEEARRVKFNTLETTLTHSSGPASYGRPRVAAA >>>>12S2_ARATH 4/90 ASCII Len: 455 P15456 arabidopsis thaliana (mouse-ear cress). 12s seed storage protein. 4/90 MGRVSSIISFSLTLLILFNGYTAQQWPNECQLDQLNALEPSQIIKSEGGRIEVWDHHAPQLRCSGFAFERFVIEPQGLFLPTFLNAGKLTFVVHGRGLMGRVIPGCAETFMESPVFGEGQGQGQSQGFRDMHQKVEHLRCGDTIATPSGVAQWFYNNGNEPLILVAAADLASNQNQLDRNLRPFLIAGNNPQGQEWLQGRKQQKQNNIFNGFAPEILAQAFKINVETAQQLQNQQDNRGNIVKVNGPFGVIRPPLRRGEGGQQPHEIANGLEETLCTMRCTENLDDPSDADVYKPSLGYISTLNSYNLPILRLLRLSALRGSIRKNAMVLPQWNVNANAALYVTNGKAHIQMVNDNGERVFDQEISSGQLLVVPQGFSVMKHRIGEQFEWIEFKTNENAQVNTLAGRTSVMRGLPLEVITNGYQISPEEAKRVKFSTIETTLTHSSPMSYGRPRA >>>>1433_DROME 12/92 ASCII Len: 248 P29310 drosophila melanogaster (fruit fly). 14-3-3-like protein. 12/92 MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN >>>>1433_HORVU 2/94 ASCII Len: 262 P29305 hordeum vulgare (barley). 14-3-3-like protein. 2/94 MSTAEATREENVYMAKLAEQAERYEEMVEFMEKVAKTADVGELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNEAYVASIKEYRTRIETELSKICDGILKLLDSHLVPSATAAESKVFYLKMKGDYHRYLAEFKAGAERKEAAENTLVAYKSAQDIALADLPTTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDSLGEESYKDSTLIMQLLRDNLTLWTSDNAEEGGDEIKEAASKPEGEGHS >>>>1433_MAIZE 6/94 ASCII Len: 61 P29306 zea mays (maize). 14-3-3-like protein (fragment). 6/94 ILNSPDRACNLAKQAFDEAISELDSLGEESYKDSTLIMQLLXDNLTLWTSDTNEDGGDEIK >>>>1433_OENHO 12/92 ASCII Len: 260 P29307 oenothera hookeri (hooker's evening primrose). 14-3-3-like protein. 12/92 MATAPSPREENVYLAKLAEQAERYEEMVEFMEKVCAAADSEELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNDDHVSTIRDYRSKIETELSNICGGILKLLDSRLIPSAASGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLSAYKAAQDIANAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLANEAFDEAIAELDTLEEESYKDSTLIMQLLRDNLTLWTSDNQDDGGDEIKEAAPKPDEQY >>>>1433_ORYSA 6/94 ASCII Len: 260 Q06967 oryza sativa (rice). 14-3-3-like protein s94. 6/94 MSPAEASREENVYMAKLAEQAERYEEMVEFMEKVAKTTDVGELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNEAYVASIKEYRSRIETELSKICDGILKLLDSHLVPSATAAESNVFYLKMKGDYHRYLAEFKSGAERKEAAENTLVAYKSAQDIALADLPTTHPIRLGLALNLSVFYYEILNSPDRACNLAKQAFDDAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDNAEDGGDEIKEAAKPEGEGH >>>>1433_SPIOL 12/92 ASCII Len: 220 P29308 spinacia oleracea (spinach). 14-3-3-like protein (fragment). 12/92 RNLLSVAYKNVVGARRASWRIISSIEQKEESRGNEDHVSVIRDYRSRIEKELSDNCDGILKLLDTKLVPAASSGDSKVFYLKMKGDYHRYLAEFKTGAQRKEAAESTLTAYKAAQDIANAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFVEAIAELDTLGEDSYKDSTLIMQLLRDNLTLWTSDMQDEAADEITEEAAKQQKAVNNNKIAY >>>>1433_XENLA 12/92 ASCII Len: 235 P29309 xenopus laevis (african clawed frog). 14-3-3-like protein (fragment). 12/92 AKLSEQAERYDDMAASMKAVTELGAELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEGNDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNATPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEEADNVEGDN >>>>1434_ARATH 2/94 ASCII Len: 259 Q01525 arabidopsis thaliana (mouse-ear cress). 14-3-3-like protein gf14. 2/94 MASGREELVYMAKLAEQAERYEEMVEFMEKVSAAVDGDELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRGNDDHVTAIREYRSKIETELSGICDGILKLLDSRLIPAAASGDSKVFYLKMKGDYHRYLAEFKTGQERKDAAEHTLAAYKSAQDIANAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDAADEIKEAAAPKPTEEQQ >>>>1434_MAIZE 6/94 ASCII Len: 248 Q01526 zea mays (maize). 14-3-3-like protein gf14-12. 6/94 MAKLAEQAERYEEMVEFMEKVAKTVDSEELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEEGRGNEDRVTLIKDYRGKIETELTKICDGILKLLESHLVPSSTAPESKVFYLKMKGDYYRYLAEFKTGAERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACSLAKQAFDEAISELDTLSEESYKDSTLIMQLLHDNLTLWTSDISEDPAEEIREAPKHDLSEGQ squid/Formats/selex.10000640000175000017520000000261010463223377014727 0ustar naolivbiolinux#=ID r17 #=AC PF99999 #=DE Test of extended SELEX format #=AU SRE, Tue Dec 1 19:17:48 1998 #=GA -1.0 -2.0 #=TC -3.0 -4.0 #=NC -5.0 -6.0 # Derived from r17.slx #tag name weight source src acc # from,to,olen description #=SQ 28 1.0000 IDENT: ACCESSION 1..29::29 Sequence one #=SQ longname 102.0000 SWISS NUMBER; 3..19::100 A long name #=SQ 2 2.0000 OR OR 0..0::0 two #=SQ 3 3.0000 PIR - 0..0::0 three #=SQ 4 4.0000 OR FOR 0..0::0 - means no data #=SQ 5 5.0000 WHATEVER MISSING 0..0::0 - #=SQ 6 6.0000 - DATA 0..0::0 foo #=SQ 7 7 - - 0..0::0 bar #=SQ 8 8.0000 - - 0..0::0 baz #=SQ 9 9.0000 - - 0..0::0 a description of several words. #=SQ 10 10.0000 - - 0..0::0 - #=RF xxxxxxx xxxx xxxxxx #=CS >>>>+>> ^^^^ <<<<<< 28 gGAGUAAGAUAGC AUCA GCAUCUUGUUCC #=SS +++++>>>>>+>> ^^^^ <<<<<<<+++++ longname GUUCACC AUCA GGGGAc #=SS >>>>+>> ^^^^ <<<<<< 2 AUGGAUGCGCACC AUCA GGGCGUaucuau 3 GAUCACC AUCA GGGauc 4 GGUCACC AUCA GGGauc 5 GGACACC AUCA GGGucu 6 CACC AUCA GGG 7 GAUCACC AUCA GGGauc 8 CUCACC AUCA GGGGG 9 AUGCACC AUCA GGGCAU 10 CUCACC AUCA GGGGG squid/Formats/stockholm.10000640000175000017520000000630710463223377015621 0ustar naolivbiolinux# STOCKHOLM 1.0 # # This is an example of a Stockholm multiple sequence alignment # file. It is deliberately designed to be weird, to exercise many of the # features of Stockholm format, in order to test a parser. # #=GF ID 14-3-3 #=GF AC PF00244 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 8.80 8.80 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF SQ 119 #=GS 1431_ENTHI/4-239 WT 0.42 #=GS seq1 WT 0.40 #=GS seq2 WT 0.41 #=GS seq3 WT 0.43 #=GS seq4 WT 0.44 #=GS seq5 WT 0.45 #=GS seq6 WT 0.46 #=GS seq4 AC PF00001 #=GS seq4 DE A description of seq4. #=GS seq1 NEWTAG foo #=GS seq2 NEWTAG bar #=GS seq3 NEWTAG baz #=GS seq3 TAG2 foo2 #=GS seq4 TAG2 foo3 #=GS seq5 TAG2 foo4 #=GC SS_cons xxxxxxxxxxxxxxxxxxx #=GC SA_cons xxxxxxxxxxxxxxxxxxx #=GC New_long_tag_thingie xxxxxxxxxxxxxxxxxxx 1431_ENTHI/4-239 ACDEFGHKLMNPQRSTVWY #=GR seq1 SS ................... #=GR seq1 SA 0000000000000000000 seq1 ACDEFGHKLMNPQRSTVWY seq2 ACDEFGHKLMNPQRSTVWY seq3 ACDEFGHKLMNPQRSTVWY seq4 ACDEFGHKLMNPQRSTVWY seq5 ACDEFGHKLMNPQRSTVWY seq6 ACDEFGHKLMNPQRSTVWY #=GR seq6 SS ................... #=GR seq6 SA 9999999999999999999 #=GR seq6 Invented_tag ******************* #=GR seq6 Another_tag ------------------- #=GC SS_cons xxxxxxxxxxxxxxxxxxx #=GC SA_cons xxxxxxxxxxxxxxxxxxx #=GC New_long_tag_thingie xxxxxxxxxxxxxxxxxxx 1431_ENTHI/4-239 ACDEFGHKLMNPQRSTVWY #=GR seq1 SS ................... #=GR seq1 SA 0000000000000000000 seq1 ACDEFGHKLMNPQRSTVWY seq2 ACDEFGHKLMNPQRSTVWY seq3 ACDEFGHKLMNPQRSTVWY seq4 ACDEFGHKLMNPQRSTVWY seq5 ACDEFGHKLMNPQRSTVWY seq6 ACDEFGHKLMNPQRSTVWY #=GR seq6 SS ................... #=GR seq6 SA 9999999999999999999 #=GR seq6 Invented_tag ******************* #=GR seq6 Another_tag ------------------- # # And here's some trailing comments, just to # try to confuse a parser. # //squid/Formats/gcgdata.20000640000175000017520000000422010463223377015201 0ustar naolivbiolinux>>>>ACRP3R654 1/95 2BIT Len: 2886 X80661 Actinophage RP3 of S.rimosus R6-554 DNA sequence. 1/95 LàEmÈìM ·ß~ó =7ÏüÁAÝ óòñ'÷Ÿ<ôò ,Ï,gÂøTÁ<þ19/Tì»Û õìžÆ̼¼I{ŸçÎpÖôH„º¶Í3 (¬ÈTwÕÁüÃìýÄšüÈÈüHW(/ó#ÚÅ«ËÒ»Âä\’/'ž÷ ù;‡ð¬;ÃsÈÀúÐ˱ë/žÇà ÷£K ÂNÌó„®¹ "2 ÂL0!OŸà““¼â?~ì‚ìÒØ0,£ýðK0:à@Å2J³ÌL8ð14ç 4“1À‹¾<ã¾ççÓI4?ó¯ÿÍ{,S¯Îq˳âë+<Àºû̪ó· ºA¬«ñìäw}{e(Íc¯pÃa>È¿ø=ÏÓ­¤³XœøÝÍÚÈÀŒÜv$®ä‚óí6É÷’ ÞX@=ñôL?k¾òÝñc.ë?K"¿,¯È÷óô=Šÿ |xºCÕCŽºàÄNüÎËìÒä¯$~NCïìŽ<áL ‰ËLóë3Ããƒè ƒÇî‚$3ìˆOÞ$õ8Ó„_,¸'çNùÒÃÿ!Ít#’xóÃ~3®½#Ö€ÇSÃÏ2ú9Ç̼2ëУ8óì¾3Aðèñ<-ýÇ‚ ”Ãà þ¿ÁÈ3Š#}Ì0°ÿ?»Sw’C$Ó¾ØöKìÎ;#Ê+¯ö$ñ{Î:èãËc?ã~7 5̱Ç1,áðò€O‘W# K óLþ‡ß27yøÎû¿3?Í2 þ3°åÇâsóüÇ#ˆç->äózû |Ôï<ÿ ÓÃþJÏ%’ë<óœÌ;8~þ¾æQúüŸ:7ütã]ÿÍÑK¯3ìÍ*D@©äa?ž#À;º^B샬ýÓ/S¤?ò !‚ßXŠü ÒìµGÁ=Dœa\Ey`Çá“ >>>>AL3CSA 6/88 2BIT Len: 105 M10631 Bacteriophage alpha-3 cleavage site for phage phi-X174 gene A protein. 6/88 íáÀQúà™òSëw šm¢¸ Ø_œ >>>>AL3HP 6/91 2BIT Len: 1786 M25640 Bacteriophage alpha-3 H protein gene, complete cds. 6/91 ôÝåö 1Žõ”ž˜+AK Zš¯2=npp-Ûòàì6>暆ú7ëÍl0Pq¬ «íbÎu½Ã]}ò\Álm÷ S©e~ñÍûTuœ²½Ã´pùxhóÏ0•ù§‚½”´q”¯§PAÇÒÅ´K¡uŸqö‰Å6œ~­Åãèe/Qæ­k+!eæµåûÚyÆ®ú¼ 3–Ç<±( þÇì}Åpýn‘Gé,º»œzç)~i.®eÊ©ËŸš)\¹qöRÑÂM*˜ëåYÀº{œRÙ¤£{L¼Œ×4d !àHᨼ`'©'¾|€ÜKîK%xhD¹gÅ~ê¯Frê_ª”’¹„ª1ŸlD­aÃêçXéžX9ýÅ_ÕË~”ÔV¾}­ =•i‚êš]x” {„\RŽ£­¾ÑUg¨,I0FIq}EõÕ­À5gSYíI#Ó–½MÇSx4²×— Aª—ã]%ǹxÖGH_g•zÇ®ÙÇ·yCÈgì]uD½©GÎõ”Ä‘ëÕ×yæ~Ÿž¥Ï¶´Ÿ¨u“ê•—ñ—\Eœv~—W”ûÕ êe[WÛž‰g˜¯•r >>>>AL3ORI 6/88 2BIT Len: 419 J02444 Bacteriophage alpha3 origin of DNA replication. 6/88 MÞ_`“á/YIé‚´°Å©ªñÃ!ÖçÝ¿.Ãcî`9¨o£~¼ÖÃÀª¾Ö,ç[Ü5×ß%Á,ÆßpÅ:–Wï,ßµGYË+Ü;G—†<ó QŸšx+ÙKGJñ:u}, >>>>AL3ORIAA 9/91 2BIT Len: 213 X62058 Bacteriophage alpha3 origin of cDNA synthesis (oriAA). 9/91 Ø$Æ8KÖRz`­,1jj¬rÈ@õ¹ÁÀ·o˃°Øû˜jè߯5°Á@AÆ°*¯µ‹9Ö÷ uÀ >>>>AL3ORIGA 9/91 2BIT Len: 213 X62059 Bacteriophage alpha3 origin of cDNA synthesis (oriGA). 9/91 Ø$Æ8KÖRz`­,1jj¼rÈ@õ¹ÁÀ·o˃°Øû˜jè߯5°Á@AÆ°*¯µ‹9Ö÷ uÀ >>>>APINVREP 4/94 2BIT Len: 245 X77530 Actinophage phic31 genomic DNA conserved inverted repeat. 4/94 ¼³CÅ‚x”9'Ì\(Ñí„í½³ÿÊ@À ñT' ê>ÌÕ{DʽwOLëý%ú( ºÙ0@ squid/Formats/selex.20000640000175000017520000000054710463223377014737 0ustar naolivbiolinux28 gGAGUAAGAUAGC AUCA GCAUCUUGUUCC longname GUUCACC AUCA GGGGAc 2 AUGGAUGCGCACC AUCA GGGCGUaucuau 3 GAUCACC AUCA GGGauc 4 GGUCACC AUCA GGGauc 5 GGACACC AUCA GGGucu 6 CACC AUCA GGG 7 GAUCACC AUCA GGGauc 8 CUCACC AUCA GGGGG 9 AUGCACC AUCA GGGCAU 10 CUCACC AUCA GGGGG squid/Formats/stockholm.20000640000175000017520000005210410463223377015616 0ustar naolivbiolinux# STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00244 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 8.80 8.80 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken A, #=GF RA Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated by #=GF RT the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, Omata #=GF RA S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF SQ 16 1431_ENTHI/4-239 REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE #=GS 1431_ENTHI/4-239 AC P42648 1432_ENTHI/4-238 REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE #=GS 1432_ENTHI/4-238 AC P42649 1433_CAEEL/5-237 VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED #=GS 1433_CAEEL/5-237 AC P41932 1433_LYCES/9-246 REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG #=GS 1433_LYCES/9-246 AC P93209 1433_XENLA/1-227 .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE #=GS 1433_XENLA/1-227 AC P29309 1434_LYCES/6-243 REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV #=GS 1434_LYCES/6-243 AC P42652 143B_VICFA/7-242 RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG #=GS 143B_VICFA/7-242 AC P42654 143E_HUMAN/4-239 REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG #=GS 143E_HUMAN/4-239 AC P42655 143F_MOUSE/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE #=GS 143F_MOUSE/3-240 AC P11576 143R_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD #=GS 143R_ARATH/7-245 AC P42647 143S_HUMAN/3-238 RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE #=GS 143S_HUMAN/3-238 AC P31947 143T_HUMAN/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE #=GS 143T_HUMAN/3-236 AC P27348 143Z_DROME/6-239 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE #=GS 143Z_DROME/6-239 AC P29310 BMH1_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG #=GS BMH1_YEAST/4-240 AC P29311 RA24_SCHPO/6-241 REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA #=GS RA24_SCHPO/6-241 AC P42656 RA25_SCHPO/5-240 RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ #=GS RA25_SCHPO/5-240 AC P42657 // # STOCKHOLM 1.0 #=GF ID rrm #=GF AC PF00076 #=GF DE RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) #=GF GA 14.6 0.0 #=GF TC 14.5 14.5 #=GF TC 14.6 0.1 ARP2_PLAFA/364-438 VEVTYLF....STYLVNGQTL..IYS.....N.ISVV....LVILY.... CABA_MOUSE/77-147 MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD... GR10_BRANA/8-79 CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND... NSR1_YEAST/170-241 IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE... RT19_ARATH/33-104 LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN... RO28_NICSY/99-170 LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN... RO33_NICSY/116-187 LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD... RO33_NICSY/219-290 LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD... GBP2_YEAST/221-291 VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD... HUD_HUMAN/48-119 LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD... SXLF_DROME/127-198 LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD... PABP_DROME/4-75 LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD... NAM8_YEAST/165-237 IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD... PUB1_YEAST/163-234 LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD... TIA1_HUMAN/108-179 VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD... PES4_YEAST/93-164 LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD... NOP4_YEAST/28-98 LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD... CST2_HUMAN/18-89 VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD... RN15_YEAST/20-91 VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD... YIS1_YEAST/66-136 IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD... IF4B_HUMAN/98-168 AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR.... NSR1_YEAST/269-340 LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH... GBP2_YEAST/124-193 IFVRNL......TFDCTPEDLKELFG.....T.VGEV..VEADIIT.... NOP3_YEAST/127-190 LFVRPF......PLDVQESELNEIFG.....P.FGPM..KEVKILN.... U2AF_HUMAN/261-332 LFIGGL......PNYLNDDQVKELLT.....S.FGPL..KAFNLVKD... U2AF_SCHPO/312-383 IYISNL......PLNLGEDQVVELLK.....P.FGDL..LSFQLIKN... ELAV_DROME/250-322 LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN... SXLF_DROME/213-285 LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD... ELAV_DROME/404-475 IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD... MSSP_HUMAN/31-102 LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD... NONA_DROME/304-369 LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD... PABP_DROME/92-162 VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD... PABP_DROME/183-254 VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS.... PABP_SCHPO/263-333 VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD... PUB1_YEAST/342-407 AYIGNI......PHFATEADLIPLFQ.....N.FGFI..LDFKHYPE... PUB1_YEAST/76-146 LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID... TIA1_HUMAN/9-78 LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD... TIA1_HUMAN/216-281 VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD... EWS_HUMAN/363-442 IYVQGL......NDSVTLDDLADFFK.....Q.CGVV..K.MNKRTG... PTB_HUMAN/186-253 IIVENL......FYPVTLDVLHQIFS.....K.FGTV....LKIIT.... ROC_HUMAN/18-82 VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK.... YIS5_YEAST/33-104 IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD... RU1A_HUMAN/12-84 IYINNLNE..KIKKDELKKSLYAIFS.....Q.FGQI..LDILVSR.... RU2B_HUMAN/9-81 IYINNMND..KIKKEELKRSLYALFS.....Q.FGHV..VDIVALK.... CABA_MOUSE/161-231 IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID... ROA1_BOVIN/106-176 IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD... SQD_DROME/138-208 IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD... RB97_DROME/34-104 LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD... SQD_DROME/58-128 LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD... ROG_HUMAN/10-81 LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD... SFR2_CHICK/16-87 LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD... SFR1_HUMAN/17-85 IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR... SR55_DROME/5-68 VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN.... SFR3_HUMAN/12-78 VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN... TRA2_DROME/99-170 IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID... RU17_DROME/104-175 LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD... GBP2_YEAST/351-421 IYCSNL......PFSTARSDLFDLFG.....P.IGKI..NNAELKP.... RNP1_YEAST/37-109 LYVGNL......PKNCRKQDLRDLFE.....PNYGKI..TINMLKKK... PES4_YEAST/305-374 IFIKNL......PTITTRDDILNFFS.....E.VGPI..KSIYLSN.... YHH5_YEAST/315-384 ILVKNL......PSDTTQEEVLDYFS.....T.IGPI..KSVFISEK... YHC4_YEAST/348-415 IFVGQL......DKETTREELNRRFS.....T.HGKI..QDINLIFK... IF39_YEAST/79-157 IVVNGAPVIPSAKVPVLKKALTSLFS.....K.AGKV..VNMEFPID... MEI2_SCHPO/197-265 LFVTNL......PRIVPYATLLELFS.....K.LGDV..KGIDTSSL... NOP4_YEAST/292-363 VFVRNV......PYDATEESLAPHFS.....K.FGSV..KYALPVID... MODU_DROME/260-326 VVVGLI......GPNITKDDLKTFFE.....K.VAPV..EAVTISSN... ROF_HUMAN/113-183 VRLRGL......PFGCTKEEIVQFFS.....G.LEIV.PNGITLPVD... MODU_DROME/342-410 LVVENVG....KHESYSSDALEKIFK.....K.FGDV..EEIDVVC.... NUCL_CHICK/283-352 LFVKNL......TPTKDYEELRTAIK.....EFFGKK...NLQVSEV... NONA_DROME/378-448 LRVSNL......TPFVSNELLYKSFE.....I.FGPI..ERASITVD... PSF_HUMAN/373-443 LSVRNL......SPYVSNELLEEAFS.....Q.FGPI..ERAVVIVD... NOP3_YEAST/202-270 ITMKNL......PEGCSWQDLKDLAR.....E.NSLE..TTFSSVN.... SFR1_HUMAN/122-186 VVVSGL......PPSGSWQDLKDHMR.....E.AGDV..CYADVYRD... CPO_DROME/453-526 LFVSGL......PMDAKPRELYLLFR.....A.YEGY..EGSLLKV.... WHI3_YEAST/540-614 LYVGNL......PSDATEQELRQLFS.....G.QEGF..RRLSFRNK... RU1A_HUMAN/210-276 LFLTNL......PEETNELMLSMLFN.....Q.FPGF..KEVRLVPG... RU2B_HUMAN/153-220 LFLNNL......PEETNEMMLSMLFN.....Q.FPGF..KEVRLVPG... RU1A_YEAST/229-293 LLIQNL......PSGTTEQLLSQILG.....N.EALV...EIRLVSV... MODU_DROME/177-246 VFVTNL......PNEYLHKDLVALFA.....K.FGRL..SALQRFTN... PR24_YEAST/43-111 VLVKNL......PKSYNQNKVYKYFK.....H.CGPI..IHVDVAD.... MODU_DROME/422-484 ILVTNL......TSDATEADLRKVFN.....D.SGEI..ESIIMLG.... PR24_YEAST/212-284 IMIRNL.....STELLDENLLRESFE.....G.FGSI..EKINIPAG... SSB1_YEAST/39-114 IFIGNV......AHECTEDDLKQLFV.....EEFGDE..VSVEIPIK... PTB_HUMAN/61-128 IHIRKL......PIDVTEGEVISLGL.....P.FGKV..TNLLMLKG... RN12_YEAST/200-267 IVIKFQ......GPALTEEEIYSLFR.....R.YGTI....IDIFP.... D111_ARATH/281-360 LLLRNMVG.PGQVDDELEDEVGGECA.....K.YGTV..TRVLIFE.... U2AG_HUMAN/67-142 CAVSDVEM..QEHYDEFFEEVFTEME.....EKYGEV..EEMNVCDN... IF39_SCHPO/41-124 VVIEGAP....VVEEAKQQDFFRFLSSKVLAK.IGKVKENGFYMPFE... LA_DROME/151-225 AYAKGF......PLDSQISELLDFTA.....N.YDKV..VNLTMRNS... LA_HUMAN/113-182 VYIKGF......PTDATLDDIKEWLE.....D.KGQV..LNIQMRR.... PR24_YEAST/119-190 LWMTNF......PPSYTQRNIRDLLQ.....D.INVV.ALSIRLPSL... ARP2_PLAFA/364-438 ....HQKFKETVLGRNSGFGFVSYDNVISAQHAIQFMNG.Y...FVNNKY CABA_MOUSE/77-147 ..........PNTGRSRGFGFILFKDSSSVEKVLD.QKE.H...RLDGRV GR10_BRANA/8-79 ..........RETGRSRGFGFVTFKDEKSMKDAIDEMNG.K...ELDGRT NSR1_YEAST/170-241 ..........RGTDRSRGYGYVDFENKSYAEKAIQEMQG.K...EIDGRP RT19_ARATH/33-104 ..........KVTGRSRGYGFVNFISEDSANSAISAMNG.Q...ELNGFN RO28_NICSY/99-170 ..........RETDRSRGFGFVTMSTVEEADKAVELYSQ.Y...DLNGRL RO33_NICSY/116-187 ..........RVTDRSRGFAFVTMGSVEEAKEAIRLFDG.S...QVGGRT RO33_NICSY/219-290 ..........RSSGRSRGFGFITFSSAEAMNSALDTMNE.V...ELEGRP GBP2_YEAST/221-291 ...........FNGFSRGFGSVIYPTEDEMIRAIDTFNG.M...EVEGRV HUD_HUMAN/48-119 ..........KITGQSLGYGFVNYIDPKDAEKAINTLNG.L...RLQTKT SXLF_DROME/127-198 ..........YKTGYSFGYAFVDFTSEMDSQRAIKVLNG.I...TVRNKR PABP_DROME/4-75 ..........VITRRSLGYAYVNFQQPADAERALDTMNF.D...LVRNKP NAM8_YEAST/165-237 ..........QVTGMSKGYGFVKFTNSDEQQLALSEMQG.V...FLNGRA PUB1_YEAST/163-234 ..........MQTGSSRGYGFVSFTSQDDAQNAMDSMQG.Q...DLNGRP TIA1_HUMAN/108-179 ..........MATGKSKGYGFVSFFNKWDAENAIQQMGG.Q...WLGGRQ PES4_YEAST/93-164 ..........SVTKKSLGHGYLNFEDKEEAEKAMEELNY.T...KVNGKE NOP4_YEAST/28-98 ...........TNKRSRGFGFVSFAVEDDTKEALAKARK.T...KFNGHI CST2_HUMAN/18-89 ..........RETGKPKGYGFCEYQDQETALSAMRNLNG.R...EFSGRA RN15_YEAST/20-91 ..........PQTGRSKGYAFIEFRDLESSASAVRNLNG.Y...QLGSRF YIS1_YEAST/66-136 ..........RNTGTPKGYGYIEFESPAYREKALQ.LNG.G...ELKGKK IF4B_HUMAN/98-168 ........EPSNPERLKGFGYAEFEDLDSLLSALS.LNE.E...SLGNRR NSR1_YEAST/269-340 ..........PETEQPKGFGYVQFSNMEDAKKALDALQG.E...YIDNRP GBP2_YEAST/124-193 ...........SKGHHRGMGTVEFTKNESVQDAISKFDG.A...LFMDRK NOP3_YEAST/127-190 .................GFAFVEFEEAESAAKAIEEVHG.K...SFANQP U2AF_HUMAN/261-332 ..........SATGLSKGYAFCEYVDINVTDQAIAGLNG.M...QLGDKK U2AF_SCHPO/312-383 ..........IADGSSKGFCFCEFKNPSDAEVAISGLDG.K...DTYGNK ELAV_DROME/250-322 .........AGNDTQTKGVGFIRFDKREEATRAIIALNG.T...TPSSCT SXLF_DROME/213-285 ..........KLTGRPRGVAFVRYNKREEAQEAISALNNVI...PEGGSQ ELAV_DROME/404-475 ..........PTTNQCKGYGFVSMTNYDEAAMAIRALNG.Y...TMGNRV MSSP_HUMAN/31-102 ..........KTTNKCKGYGFVDFDSPAAAQKAVSALKA.S...GVQAQK NONA_DROME/304-369 ................KNFTFLKVDYHPNAEKAKRALDG.S...MRKGRQ PABP_DROME/92-162 ...........EKGNSKGYGFVHFETEEAANTSIDKVNG.M...LLNGKK PABP_DROME/183-254 ..........KEDGKSKGFGFVAFETTEAAEAAVQALNGKD...MGEGKS PABP_SCHPO/263-333 ...........QNDKPRGFGFVNYANHECAQKAVDELND.K...EYKGKK PUB1_YEAST/342-407 ................KGCCFIKYDTHEQAAVCIVALAN.F...PFQGRN PUB1_YEAST/76-146 ...........KNNKNVNYAFVEYHQSHDANIALQTLNG.K...QIENNI TIA1_HUMAN/9-78 ............TAGNDPYCFVEFHEHRHAAAALAAMNG.R...KIMGKE TIA1_HUMAN/216-281 ................KGYSFVRFNSHESAAHAIVSVNG.T...TIEGHV EWS_HUMAN/363-442 .QPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG.K...DFQGSK PTB_HUMAN/186-253 ...........FTKNNQFQALLQYADPVSAQHAKLSLDG.Q...NIYNAC ROC_HUMAN/18-82 .................GFAFVQYVNERNARAAVAGEDG.R...MIAGQV YIS5_YEAST/33-104 ..........ENTGESQGFAYLKYEDQRSTILAVDNLNG.F...KIGGRA RU1A_HUMAN/12-84 ............SLKMRGQAFVIFKEVSSATNALRSMQG.F...PFYDKP RU2B_HUMAN/9-81 ............TMKMRGQAFVIFKELGSSTNALRQLQG.F...PFYGKP CABA_MOUSE/161-231 ..........PKLNKRRGFVFITFKEEDPVKKVLE.KKF.H...TVSGSK ROA1_BOVIN/106-176 ..........RGSGKKRGFAFVTFDDHDSVDKIVI.QKY.H...TVNGHN SQD_DROME/138-208 ..........KQKSQRKGFCFITFDSEQVVTDLLK.TPK.Q...KIAGKE RB97_DROME/34-104 ..........AATKRSRGFGFITYTKSLMVDRAQE..NRPH...IIDGKT SQD_DROME/58-128 ..........PQTGRSRGFAFIVFTNTEAIDKVSA.ADE.H...IINSKK ROG_HUMAN/10-81 ..........RETNKSRGFAFVTFESPADAKDAARDMNG.K...SLDGKA SFR2_CHICK/16-87 ..........RYTKESRGFAFVRFHDKRDAEDAMDAMDG.A...VLDGRE SFR1_HUMAN/17-85 .............RGGPPFAFVEFEDPRDAEDAVYGRDG.Y...DYDGYR SR55_DROME/5-68 .................GYGFVEFEDYRDADDAVYELNG.K...ELLGER SFR3_HUMAN/12-78 ...............PPGFAFVEFEDPRDAADAVRELDG.R...TLCGCR TRA2_DROME/99-170 ..........AQTQRSRGFCFIYFEKLSDARAAKDSCSG.I...EVDGRR RU17_DROME/104-175 ..........QESGKPKGYAFIEYEHERDMHAAYKHADG.K...KIDSKR GBP2_YEAST/351-421 ..........QENGQPTGVAVVEYENLVDADFCIQKLNN.Y...NYGGCS RNP1_YEAST/37-109 ..........PLKKPLKRFAFIEFQEGVNLKKVKEKMNG.K...IFMNEK PES4_YEAST/305-374 ...........ATKVKYLWAFVTYKNSSDSEKAIKRYNN.F...YFRGKK YHH5_YEAST/315-384 ............QANTPHKAFVTYKNEEESKKAQKCLNK.T...IFKNHT YHC4_YEAST/348-415 ..............PTNIFAFIKYETEEAAAAALESENH.A...IFLNKT IF39_YEAST/79-157 ..........EATGKTKGFLFVECGSMNDAKKIIKSFHGKR...LDLKHR MEI2_SCHPO/197-265 ..............STDGICIVAFFDIRQAIQAAKSLRSQR...FFNDRL NOP4_YEAST/292-363 ..........KSTGLAKGTAFVAFKDQYTYNECIKNAPA.A...GSTSLL MODU_DROME/260-326 ..............RLMPRAFVRLASVDDIPKALK.LHS.T...ELFSRF ROF_HUMAN/113-183 ...........PEGKITGEAFVQFASQELAEKALG.KHK.E...RIGHRY MODU_DROME/342-410 ..............SKAVLAFVTFKQSDAATKALAQLDG.K...TVNKFE NUCL_CHICK/283-352 ...........RIGSSKRFGYVDFLSAEDMDKALQ.LNG.K...KLMGLE NONA_DROME/378-448 ...........DRGKHMGEGIVEFAKKSSASACLRMCNE.K...CFFLTA PSF_HUMAN/373-443 ...........DRGRSTGKGIVEFASKPAARKAFERCSE.G...VFLLTT NOP3_YEAST/202-270 ............TRDFDGTGALEFPSEEILVEALERLNN.I...EFRGSV SFR1_HUMAN/122-186 .................GTGVVEFVRKEDMTYAVRKLDN.T...KFRSHE CPO_DROME/453-526 ........TSKNGKTASPVGFVTFHTRAGAEAAKQDLQGVR...FDPDMP WHI3_YEAST/540-614 .......NTTSNGHSHGPMCFVEFDDVSFATRALAELYG.R...QLPRST RU1A_HUMAN/210-276 ...............RHDIAFVEFDNEVQAGAARDALQG.F...KITQNN RU2B_HUMAN/153-220 ...............RHDIAFVEFENDGQAGAARDALQGFK...ITPSHA RU1A_YEAST/229-293 ................RNLAFVEYETVADATKIKNQLGS.T...YKLQNN MODU_DROME/177-246 .............LNGNKSVLIAFDTSTGAEAVLQAKPKAL...TLGDNV PR24_YEAST/43-111 ...........SLKKNFRFARIEFARYDGALAAIT.KTH.K...VVGQNE MODU_DROME/422-484 .................QKAVVKFKDDEGFCKSFL.ANE.S...IVNNAP PR24_YEAST/212-284 .........QKEHSFNNCCAFMVFENKDSAERALQ.MNR.S...LLGNRE SSB1_YEAST/39-114 .......EHTDGHIPASKHALVKFPTKIDFDNIKENYDT.K...VVKDRE PTB_HUMAN/61-128 ................KNQAFIEMNTEEAANTMVN.YYT.SVTPVLRGQP RN12_YEAST/200-267 ...........PTAANNNVAKVRYRSFRGAISAKNCVSG.I...EIHNTV D111_ARATH/281-360 ......ITEPNFPVHEAVRIFVQFSRPEETTKALVDLDG.R...YFGGRT U2AG_HUMAN/67-142 ...........LGDHLVGNVYVKFRREEDAEKAVIDLNN.R...WFNGQP IF39_SCHPO/41-124 ......EKNGK..KMSLGLVFADFENVDGADLCVQELDGKQ...ILKNHT LA_DROME/151-225 ......YDKPTKSYKFKGSIFLTFETKDQAKAFLE.QEK.I...VYKERE LA_HUMAN/113-182 ..........TLHKAFKGSIFVVFDSIESAKKFVE.TPG.Q...KYKETD PR24_YEAST/119-190 ...........RFNTSRRFAYIDVTSKEDARYCVEKLNG.L...KIEGYT ARP2_PLAFA/364-438 LKV CABA_MOUSE/77-147 IDP GR10_BRANA/8-79 ITV NSR1_YEAST/170-241 INC RT19_ARATH/33-104 ISV RO28_NICSY/99-170 LTV RO33_NICSY/116-187 VKV RO33_NICSY/219-290 LRL GBP2_YEAST/221-291 LEV HUD_HUMAN/48-119 IKV SXLF_DROME/127-198 LKV PABP_DROME/4-75 IRI NAM8_YEAST/165-237 IKV PUB1_YEAST/163-234 LRI TIA1_HUMAN/108-179 IRT PES4_YEAST/93-164 IRI NOP4_YEAST/28-98 LRV CST2_HUMAN/18-89 LRV RN15_YEAST/20-91 LKC YIS1_YEAST/66-136 IAV IF4B_HUMAN/98-168 IRV NSR1_YEAST/269-340 VRL GBP2_YEAST/124-193 LMV NOP3_YEAST/127-190 LEV U2AF_HUMAN/261-332 LLV U2AF_SCHPO/312-383 LHA ELAV_DROME/250-322 DPI SXLF_DROME/213-285 PLS ELAV_DROME/404-475 LQV MSSP_HUMAN/31-102 AKQ NONA_DROME/304-369 LRV PABP_DROME/92-162 VYV PABP_DROME/183-254 LYV PABP_SCHPO/263-333 LYV PUB1_YEAST/342-407 LRT PUB1_YEAST/76-146 VKI TIA1_HUMAN/9-78 VKV TIA1_HUMAN/216-281 VKC EWS_HUMAN/363-442 LKV PTB_HUMAN/186-253 CTL ROC_HUMAN/18-82 LDI YIS5_YEAST/33-104 LKI RU1A_HUMAN/12-84 MRI RU2B_HUMAN/9-81 MRI CABA_MOUSE/161-231 CEI ROA1_BOVIN/106-176 CEV SQD_DROME/138-208 VDV RB97_DROME/34-104 VEA SQD_DROME/58-128 VDP ROG_HUMAN/10-81 IKV SFR2_CHICK/16-87 LRV SFR1_HUMAN/17-85 LRV SR55_DROME/5-68 VVV SFR3_HUMAN/12-78 VRV TRA2_DROME/99-170 IRV RU17_DROME/104-175 VLV GBP2_YEAST/351-421 LQI RNP1_YEAST/37-109 IVI PES4_YEAST/305-374 LLV YHH5_YEAST/315-384 IWV YHC4_YEAST/348-415 MHV IF39_YEAST/79-157 LFL MEI2_SCHPO/197-265 LYF NOP4_YEAST/292-363 IGD MODU_DROME/260-326 ITV ROF_HUMAN/113-183 IEV MODU_DROME/342-410 WKL NUCL_CHICK/283-352 IKL NONA_DROME/378-448 SLR PSF_HUMAN/373-443 TPR NOP3_YEAST/202-270 ITV SFR1_HUMAN/122-186 GET CPO_DROME/453-526 QTI WHI3_YEAST/540-614 VSS RU1A_HUMAN/210-276 AMK RU2B_HUMAN/153-220 MKI RU1A_YEAST/229-293 DVT MODU_DROME/177-246 LSV PR24_YEAST/43-111 IIV MODU_DROME/422-484 IFI PR24_YEAST/212-284 ISV SSB1_YEAST/39-114 IHI PTB_HUMAN/61-128 IYI RN12_YEAST/200-267 LHI D111_ARATH/281-360 VRA U2AG_HUMAN/67-142 IHA IF39_SCHPO/41-124 FVV LA_DROME/151-225 LLR LA_HUMAN/113-182 LLI PR24_YEAST/119-190 LVT // squid/INSTALL0000640000175000017520000000624310463223377013151 0ustar naolivbiolinuxBrief installation instructions for squid SRE, Tue Jul 25 08:52:03 2000 $CVS Id$ ________________________________________________________________ Quick start --------------- For a source distribution (example: squid.tar.gz), on a UNIX system: gunzip squid.tar.gz Uncompresses the archive. tar xf squid.tar Unpacks the archive. (makes a new directory, squid) cd squid Moves into the distribution toplevel directory. ./configure Configures the software for your system. make Builds the binaries. make check (optional) Runs the testsuite. make install (optional) Installs the software. (You may need to be root to install.) make clean (optional) Cleans up. make deinstall Deletes SQUID from your system... assuming you haven't changed the Makefile since you installed. (may need to be root.) Note that the software doesn't have to be "installed" to run. After the "make", it's sitting in the squid directory and you can test it out there, or copy any of the executables anywhere you want by hand. Any failure to install on a UNIX system is a bug. Please report it. Man pages are provided for some programs; see Man/ subdirectory. ---------------------------------------- More fancy configuration instructions: ---------------------------------------- The only command you should want to putz around with is the ./configure; for instance, you may want to change where SQUID is going to be installed. The default is to install into /usr/local/bin and other /usr/local subdirectories as follows: executables in /usr/local/bin man pages in /usr/local/man/man1 header files in /usr/local/include libsquid.a in /usr/local/lib scripts in /usr/local/bin To install in bin, man/man1, include, and lib subdirectories of some other directory, reset the prefix in the configuration like this: % ./configure prefix=/usr/mylocal For heterogenous computing environments, also set the exec_prefix, which gives you some flexibility for installing architecture dependent files (e.g. the programs). For example, the St. Louis installation sets prefix=/usr/seshare/ exec_prefix=/usr/seshare/`uname`, and for Linux (for example), this results in: executables in /usr/seshare/Linux/bin man pages in /usr/seshare/man header files in /usr/seshare/include libsquid.a in /usr/seshare/Linux/lib scripts in /usr/seshare/Linux/bin The configure script has a few other options that may be useful; ./configure --help lists them. An important one is --enable-lfs, which turns on optional support for LFS, the Large File Summit, which enables squid to deal with >2 GB files if your system is capable of it. This is highly recommended, because sequence files can easily exceed standard 2 GB filesystem limitations these days FYI, the configuration incantation here in StL is: % env CFLAGS="-O3" ./configure --enable-lfs prefix=/usr/seshare/ exec_prefix=/usr/seshare/`uname` squid/LOG0000640000175000017520000003333110463223377012462 0ustar naolivbiolinux Cambridge Mon Jul 14 03:52:51 1997 - new functions: AllocAlignment() [alignio.c] BlosumWeights() [weight.c] RandomString() [sre_string.c] PrintNewHampshireTree() [cluster.c] PrintPhylo() [cluster.c] - renamed functions: SonnhammerWeights() to GSCWeights() [weight.c] - deleted functions: FlushAlignment() [msf.c] - interfaces changed: MingapAlignment() FreeAlignment() ReadInterleaved() ReadAlignment() ReadMSF() - structures changed: sequence weights moved out of SQINFO, into AINFO - Strparse() simplified and made more Perl-y, with sqd_parse[] globals. - PairwiseIdentity(), MakeDiffMx() simplified. - kXPearson format deleted. 1.5l SRE, Tue Dec 17 11:10:04 1996 - added OWL database to getseq's options - New functions: DAdd(), FAdd(), DCopy(), FCopy(), DDot(), FDot(). SeqfileRewind(), WeightedLinefit(), FMX2Alloc(), FMX2Free(), DMX2Alloc(), DMX2Free(), FMX2Multiply() IncompleteGamma(): Sat Jun 14 14:55:43 1997 - ReadSeq() now reentrant for alignments. aseqs, ainfo in SQINFO structure. - BUGFIX: sqio.c readLoop(): seqs from files not ending in "\n" truncated - PORT: SunOS: interleaved.c needs to deal w/ missing SEEK_SET 1.5k SRE, Mon Dec 2 09:21:43 1996 - frozen for a "distribution". 1.5j summer 1996 - GSI indices revised. Network byte ordering. sqd_uint16, sqd_uint32 typedefs which should work on any UNIX, but may fail on other OSs. - Clash resolution w/ NCBI toolkit. Getopt() ARG_* changed to sqdARG_*. - aafq[] updated to SwissProt 34 frequencies - FileExists() added, file.c - BUGFIX in getseq_main.c -- -f without -t wasn't working. - BUGFIX (SERIOUS!): FSet(), DSet() were completely broken. 1.5i - file.c added: new functions FileDirname(), FileConcat(); moved EnvFileOpen() into file.c - Platform independence for GSI indices. (thanks to S. Brenner). Magic number and byteswapping. File formats kept. GSIGetRecord(), Byteswap() added. gsi_int4 typedef. good speedup in fetches, prob. because of keeping format. 1.5h - BUGFIX: serious! sre_random() with seed == zero fails! default now 666. - BUGFIX: small memory leak (sa) fixed in ReadSELEX(). - BUGFIX: useless to set SQERR_MEM and return 0 since I never check return status. Replace malloc's with MallocOrDie(). 1.5g (Cambridge visit + subsequent) - shuffle: shuffle_main.c added; StrShuffle() in sre_string.c - DChoose(), FChoose() added to sre_math.c - getopt.c: Getopt() added - portable and more powerful getopt() - weight.c: FilterAlignment() added from HMM code - compstruct -q (quiet) option added - Numerical Recipes encumbrances obliterated: * Gaussrandom() replaced from RANLIB.c * Linefit() replaced with my own * Gammln() replaced from Spouge's NCBI implementation * sre_random() replaced with my own - PORT: IRIX4 - more const declarations removed, gnuregex.h - BUGFIX: reformat opts -ludr didn't work for inter-alignment conversion. 1.5f Tue Jan 9 23:28:02 1996 - PORT: Maspar: const declarations in gnuregex.c removed. 1.5e Sun Jan 7 10:43:24 1996 - genpept2gsi.pl, swiss2gsi.pl, pir2gsi.pl added to Scripts - added CHOOSE() macro to squid.h - BUGFIX: FASTA format doesn't always allow a space between > and name - PORT: Solaris: gnuregex.c #include problem 1.5d Tue Dec 5 11:27:20 1995 - getseq_main.c: native fetch mode added, bypassing ReadSeq. Full record fetch w/ annotation. >250x speedup on some entries. - SQINFO_FREE field removed, as well as its support in sqio.c 1.5c Mon Dec 4 12:47:20 1995 - getseq_main.c: couldn't fetch by accession number in PIR, because of entries with multiple accessions. General problem with sqio.c for multiple accessions not resolved. 1.5b Sun Dec 3 10:00:55 1995 (Dealing with Berlin 5S rRNA database) - Modified endEMBL() to deal with Berlin "extended" EMBL - SetSeqinfoString() now ignored trailing whitespace too 1.5a Sat Sep 9 10:49:50 1995 - New seq i/o support: Extended FASTA (kXPearson) [not a general standard] GCG datalibrary (kGCGdata) [both ASCII and mixed ASCII/2BIT] Clustal (kClustal) - interleaved.c added, generalized interleaved alignment input (Clustal and MSF support) - ReadMSF(), CompareSeqs() removed. - Strparse(), MakeIdentityMx(), sre_random(), sre_srandom() added - RANDOM_FRAC and friends deleted from squid.h - gnuregex.c and gnuregex.h added, GNU Regex 0.12 -- slightly modified for portability (force -DREGEX_MALLOC) - str*() functions renamed to Str*, so as not to conflict with ANSI reserved namespace - bugfix: GCG Pileup output puts CompCheck: line in, fooling SeqfileFormat() into thinking Pileup MSF alignments are unaligned GCG files. 1.4.3 Fri Aug 25 11:03:32 1995 - portability and lint happiness, while porting to DEC OSF/1 (sable). Minor changes. 1.4.2 Sun Jun 25 10:28:01 1995 - genpept names are > 31 char. Increase length limits to 63 in squid.h, using new SQINFO_NAMELEN and SQINFO_DESCLEN macros 1.4.1 Thu Apr 20 16:50:23 1995 - translate added, adapted from orfer. - serious bugfix in PairwiseIdentity(), infinite loop when both gaps 1.4 Sat Feb 11 13:53:41 1995 - SeqfileOpen(), SeqfileFormat() now take optional environment variable (e.g. BLASTDB) - added: EnvFileOpen() - removed: AlignedBases(), AlignmentSimilarity(), refcoords.c - severe bugfix in selex.c, if/if brackets, introduced in 1.3.17 - ParsePAMFile() now deals with newer NCBI matrix format - alistat modified so that low % is for most distant sequence w/ respect to all others, rather than most distant pair. - bugfix: Seqtype() looks now at first 300 *non-gap* characters. - bugfix: ParsePAMMatrix() made more robust for scale factor parsing 1.3.18 Mon Jan 30 14:45:07 1995 - SELEX format supports #=SA side chain % surface accessibility - sre_math.c ansi'fied; FNorm(), FScale(), FSet(), DSum(), FSum(), Gammln() added. - ReadSELEX() fortified against TAB characters in alignments 1.3.17 Thu Jan 26 17:28:02 1995 - compalign_main.c added and heavily revised - aligneval.c revised - CompareMatMultAlignments() and kin removed, they are replaced by a more general CompareRefMultAlignments(). - selex.c now quietly ignores #= machine comments it doesn't recognize 1.3.16 Fri Jan 13 14:21:00 1995 - modified readEMBL() to parse Staden experiment file format had to include a hack (V->dash_equals_n) to read '-' as 'N' in Staden format -- which means that EMBL parsing is affected as well, if anyone were to use EMBL files for aligned (gap-containing) strings. 1.3.15 Tue Jan 10 09:16:53 1995 - allow_ragged added to PairwiseIdentity() 1.3.14 Thu Dec 8 11:14:06 1994 - cleaner PairwiseIdentity() replaces PairSimilarity() (at last!) - Copyleft info attached to all source files. - fflush(NULL) fails in SunOS; replace with fflush(stderr) - SEEK_SET is in unistd.h in SunOS 1.3.13 Mon Dec 5 14:57:33 1994 - GSI format redefined to allow indexing of multifile databases such as GenBank. Modifications to sqio.c, squid.h. - getseq revised to read environment variables like fetch - free text field added to SQINFO; only used in GenBank currently - Scripts/ subdirectory added, and Makefiles 'dist' and 'install' modified 1.3.12 Wed Nov 23 17:32:25 1994 - Solaris portability: random(x) changed to random() 1.3.11 Fri Nov 11 07:40:02 1994 - serious memory bug fixed in FlushAlignment(); affected ReadMSF() - GSIOpen(), GSIGetOffset(), SeqfilePosition() added - getseq now attempts to read a GSI index file - moved IsSELEXFormat() to end of SeqfileFormat() for speed - benchmarks: getseq getting ZK1236, last cosmid in allcmid: 10.318u old getseq 5.889u new getseq .119u new getseq, with GSI indexing of allcmid (100x speedup) 1.3.10 Thu Nov 10 14:06:31 1994 - Die(), Warn() flush output buffers - version info gets hard-coded in iupac.c; distribution packages that bundle squid files now get properly version-stamped 1.3.9 Fri Oct 14 10:16:06 1994 - seqstat output slightly modified - sqio.c SetSeqinfoString now allows appending to description (bugfix to this, Thu Oct 20 18:00:08 1994) 1.3.8 Fri Sep 30 10:04:02 1994 - MallocOrDie(), ReallocOrDie() added. (sre_string.c) - DNorm(), DScale() added. (sre_math.c) - homogenize_gapsym added to selex.c, so RF line can come out unmodified 1.3.7 Sun Sep 25 11:53:26 1994 - bugfix: ReadMSF() didn't deal with files containing coordinate lines. 1.3.6 Mon Sep 19 16:36:15 1994 Modifications as HMM goes to 1.7 version - ParsePAMFile() now returns scale factor as well as matrix - bugfix: SELEX format was requiring #=CS, #=RF lines to be first in block; relaxed - bugfix: Seqtype() returns kOtherSeq for DNA/RNA that doesn't have any T or U. Have it return kDNA instead (though this is a bit permissive) 1.3.5 Wed Aug 31 09:08:12 1994 - bugfix in compstruct - was undercounting false positive pair predictions 1.3.4 Tue Aug 30 11:58:06 1994 - compstruct program written. - ReadSeq() not reentrant -- can't read from multiple files at once. Put sbuffer inside of V; now it's reentrant for all but alignment files. - SQFILE defined now as part of the reentrancy fix. SeqfileOpen() now returns SQFILE * not FILE *. This must be closed with SeqfileClose() not fclose(). 1.3.3 Mon Aug 29 11:58:50 1994 - squid format added for secondary structure annotation to sqio.c and to reformat - kAmbiguous, kNucleic codes removed from Seqtype() - getseq -F option added to extract in different formats. Squid extraction fully functional -- can extract fragments of secondary structure annotation - -l,-u options added to reformat to force upper, lower case 1.3.2 Sun Aug 28 17:29:22 1994 - -r,-d options added to reformat - raw output added to WriteSeq() and reformat 1.3.1 Fri Aug 26 15:17:43 1994 - bugfix: RandomAlignment() needed to create sqinfo array for ainfo. - bugfix: strtok() calls should include \n in sqio for many things 1.3 Thu Aug 11 16:47:34 1994 - Goals of modifications: sqinfo structure for secondary structure, source and source coords ainfo flags for "info not available" PIR-CODATA file reading more stringent format recognition formats for reading now settable by main programs, thru user options utility programs moved to this directory for coherent maintenance improved testing (Formats/ directory) - major modifications to sqio and alignio: sqinfo added (optional per sequence info) and ainfo heavily modified. - listSequences options removed from sqio - readPlain, readFitch, readOlsen, readPhylip removed from sqio - readPIR (PIR-CODATA format) added - IsSELEX() rewritten - added Formats directory for testing all different formats - added programs "seqstat", "reformat", "revcomp", "getseq" - the following functions are affected in ways that are externally visible: SeqfileFormat() must be called before reading sequences now ReadMultipleRseqs() new prototype includes file format, seqinfo ReadAlignment() new prototype includes file format SeqfileOpen() replaces SeqDBopen() ReadSeq() replaces readSeq() WriteSeq() replaces writeSeq() FreeSequence() new SetSeqinfoString() new SeqinfoCopy() new SeqFormatString() new MakeAlignedString() new MakeDealignedString() new 1.2.7 Fri Aug 5 14:45:08 1994 - portability to Sun Solaris 2.3 1.2.6 Fri Jul 29 15:59:13 1994 - bugfix: revcomp() chokes on non-IUPAC symbol and returns NULL; but I often don't check the return value. Insert an N for non-IUPAC instead. 1.2.5 Mon Jul 25 14:02:39 1994 - bugfix: isSeqChar() returns TRUE for 255, because of a known IRIX 4.0 bug in isascii(). Added a workaround. - added ReverseIntStack() to stack.c 1.2.4 Tue Jun 14 11:21:15 1994 - bugfix: sqio.c, ReadMultipleRseqs(): ainfo was uninitialized 1.2.3 Wed May 25 15:42:07 1994 - bugfix: the branch length calculations in Cluster() broke the filtering algorithm in "clust". Added diff field to the tree structure. 1.2.2 Fri May 20 14:07:31 1994 - added VoronoiWeights() to weight.c 1.2.1 Thu Apr 21 16:10:58 1994 - bugfix: major bugs in weight.c which only manifest themselves on large data sets (like 400 globins set) found and killed 1.2 Thu Mar 3 13:33:52 1994 - added cluster.c - difference matrix construction and simple tree construction - added stack.c - simple generic data structure support (intstack) - added weight.c - Erik's weighting rule Sat Feb 19 09:16:02 1994 1.1.1 - ansified all functions used by the cove package, while tracking an IRIX compiler problem Tue Feb 8 13:07:41 1994 1.1 - global "squid_version" added to iupac.c for version control. Arbitarily set to 1.1. Fri Jul 30 11:00:22 1993 New aligneval alignment comparison algorithm in place and tested. Old one was subtly wrong! Wed Aug 25 12:00:39 1993 Removed seqexec.c, idraw.c from the distribution Added Die(), Warn() functions to sqerror.c Thu Oct 7 19:26:05 1993 modified Seqtype to allow blank sequences. It will return kAmino. possibly not the best thing to do - quick hack, anticipating some blank sequences when I hack the ribosomal alignments into small pieces. Tue Oct 12 17:24:47 1993 bugfix: IsSELEXFormat() was opening a file, but not closing it on a failed return. Multiple opens of a non-SELEX formatted file filled the open file table and caused a fatal error. sqio.c is hacked beyond belief, slow, and ugly. Wed Oct 20 09:09:47 1993 WritePairwiseAlignment() added. squid/Licenses/0000755000175000017520000000000010463223377013664 5ustar naolivbiolinuxsquid/Licenses/COPYRIGHT.gnu0000640000175000017520000000375210463223377015752 0ustar naolivbiolinuxSQUID - a library of functions for biological sequence analysis Copyright (C) 1992-2002 Washington University School of Medicine All Rights Reserved This suite of programs is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. In other words, you are free to modify, copy, or redistribute this source code and its documentation in any way you like, but you must distribute all derivative versions as free software under the same terms that I've provided my code to you (i.e. the GNU General Public License). This precludes any use of the code in proprietary or commercial software unless your source code is made freely available. If you wish to use SQUID code under a different Open Source license that's not compatible with the GPL (like the Artistic License, BSD license, or the Netscape Public License), please contact me (eddy@genetics.wustl.edu) for permission. Incorporation into commercial software under non-GPL terms is possible, by arranging a license with the Washington University School of Medicine Center for Technology Management (CTM). For this purpose, the CTM is authorized to negotiate on behalf of the Howard Hughes Medical Institute, the other copyright holder on the code. Certain third party code modules may have to be removed from a non-GPL distribution. Contact Tom Hagerty (HagertyT@otm.wustl.edu) in our Office of Technology Management to arrange non-GPL licensing terms. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this HMMER release, in the file LICENSE; if not, write to the Free Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139 USA. squid/Licenses/LICENSE.gnu0000640000175000017520000004307610463223377015467 0ustar naolivbiolinux GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave, Cambridge, MA 02139, USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS Appendix: How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) 19yy This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) 19yy name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. squid/Licenses/gnu0000640000175000017520000000043110463223377014372 0ustar naolivbiolinuxSQUID - a library of functions for biological sequence analysis Copyright (C) 1992-2002 Washington University School of Medicine This source code is freely distributed under the terms of the GNU General Public License. See the files COPYRIGHT and LICENSE for details. squid/Makefile.in0000640000175000017520000001645010463223377014166 0ustar naolivbiolinux############################################################### # Makefile for SQUID library # CVS $Id: Makefile.in,v 1.57 2004/06/16 14:46:04 eddy Exp $ # # Note: The autoconf variables in this file must be coordinated # with HMMER. HMMER creates a Makefile from this # Makefile.in using its own configure script, not SQUID's. ################################################################# # @LICENSE@ ################################################################# ### Installation points ### prefix = @prefix@ exec_prefix = @exec_prefix@ BINDIR = @bindir@ MANDIR = @mandir@ INCLUDEDIR = @includedir@ LIBDIR = @libdir@ SCRIPTDIR = @bindir@ ## your compiler and compiler flags # CC = @CC@ CFLAGS = @CFLAGS@ CPPFLAGS = @CPPFLAGS@ LDFLAGS = @LDFLAGS@ DEFS = @DEFS@ LIBS = @LIBS@ -lm ## Archiver command # AR = @AR@ rcv RANLIB = @RANLIB@ ## instructions for installing man pages # INSTMAN = cp MANSUFFIX = 1 # Configuration for compiling in optional PVM support # PVMLIBDIR = @PVMLIBDIR@ PVMINCDIR = @PVMINCDIR@ PVMLIBS = @PVMLIBS@ ####### ## You should not need to modify below this line ####### SHELL = /bin/sh BASENAME = @PACKAGE_TARNAME@ PACKAGE = @PACKAGE_NAME@ RELEASE = @PACKAGE_VERSION@ RELCODE = @SQUID_RELCODE@ RELEASEDATE = "@SQUID_DATE@" SEEALSO = "http:\/\/www.genetics.wustl.edu\/eddy\/software\/\#squid" FTPDIR = /nfs/ftp/eddy/software/ LICENSETAG = @SQUID_LICENSETAG@ COMPRESS = gzip PROGS = afetch\ alistat\ compalign\ compstruct\ revcomp\ seqsplit\ seqstat\ sfetch\ shuffle\ sindex\ sreformat\ translate\ weight MANS = afetch\ alistat\ seqstat\ sfetch\ shuffle\ sreformat\ READMES = 00README INSTALL Makefile.in SCRIPTS = PRECONFHDRS = \ squid.h.in\ squidconf.h.in POSTCONFHDRS = \ squid.h\ squidconf.h HDRS = dirichlet.h\ rk.h\ sqfuncs.h\ gki.h\ msa.h\ sre_random.h\ sre_stack.h\ ssi.h\ stopwatch.h\ vectorops.h OBJS = a2m.o\ aligneval.o\ alignio.o\ clustal.o\ cluster.o\ dayhoff.o\ dirichlet.o\ eps.o\ file.o\ getopt.o\ gki.o\ hsregex.o\ iupac.o\ msa.o\ msf.o\ phylip.o\ revcomp.o\ rk.o\ selex.o\ seqencode.o\ shuffle.o\ sqerror.o\ sqio.o\ squidcore.o\ sre_ctype.o\ sre_math.o\ sre_random.o\ sre_stack.o\ sre_string.o\ ssi.o\ stockholm.o\ stopwatch.o\ translate.o\ types.o\ vectorops.o\ weight.o\ wuss.o ################################################################ # Targets that actually build the squid executables all: $(PROGS) libsquid.a $(PROGS): @EXEC_DEPENDENCY@ ${OBJS} ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o $@ $@_main.o ${OBJS} ${PVMLIBS} ${LIBS} .c.o: ${CC} ${CFLAGS} ${CPPFLAGS} ${PVMINCDIR} ${DEFS} -c $< ################################################################ ################################################################ # Targets expected by packages (e.g. HMMER) that # include SQUID as a module. # module: libsquid.a libsquid.a: $(OBJS) $(AR) libsquid.a $(OBJS) $(RANLIB) libsquid.a chmod 644 libsquid.a ################################################################# install: $(PROGS) libsquid.a test -d $(LIBDIR) || mkdir -p $(LIBDIR) test -d $(BINDIR) || mkdir -p $(BINDIR) test -d $(SCRIPTDIR) || mkdir -p $(SCRIPTDIR) test -d $(INCLUDEDIR)|| mkdir -p $(INCLUDEDIR) test -d $(MANDIR)/man$(MANSUFFIX) || mkdir -p $(MANDIR)/man$(MANSUFFIX) cp libsquid.a $(LIBDIR)/ cp $(HDRS) $(INCLUDEDIR)/ cp $(POSTCONFHDRS) $(INCLUDEDIR)/ cp $(PROGS) $(BINDIR)/ # for scriptfile in $(SCRIPTS); do\ # cp Scripts/$$scriptfile $(SCRIPTDIR)/;\ # done @for manpage in $(MANS); do\ $(INSTMAN) Man/$$manpage.man $(MANDIR)/man$(MANSUFFIX)/$$manpage.$(MANSUFFIX);\ done uninstall: rm $(LIBDIR)/libsquid.a for file in $(HDRS); do\ rm $(INCLUDEDIR)/$$file;\ done for file in $(PROGS); do\ rm $(BINDIR)/$$file;\ done # for file in $(SCRIPTS); do\ # rm $(SCRIPTDIR)/$$file;\ # done for file in $(MANS); do\ rm $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ done check: libsquid.a (cd Testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") (cd Testsuite; make check) distclean: -rm -f *.o *~ core TAGS llib-lsquid.ln ccmalloc.log $(PROGS) -rm -f Makefile libsquid.a ${POSTCONFHDRS} -rm -f config.log config.status -rm -rf autom4te.cache (cd Testsuite; make distclean) clean: -rm -f *.o *~ core TAGS llib-lsquid.ln ccmalloc.log $(PROGS) (cd Testsuite; make clean) binclean: (cd Testsuite; make binclean) -rm -f *.o *~ core TAGS llib-lsquid.ln ccmalloc.log -rm -f libsquid.a ${POSTCONFHDRS} -rm -f config.log config.status -rm -rf autom4te.cache # dist: build a new distribution directory in squid-$RELEASE, and make a tarball. # Extracts straight from the CVS repository, so you must first do # a "cvs commit" (it checks to be sure you do, at least for the current # working directory). dist: # Delete old versions of the same release # @if test -d ${BASENAME}-$(RELEASE); then rm -rf ${BASENAME}-$(RELEASE); fi @if test -e ${BASENAME}-$(RELEASE).tar; then rm -f ${BASENAME}-$(RELEASE).tar; fi @if test -e ${BASENAME}-$(RELEASE).tar.Z; then rm -f ${BASENAME}-$(RELEASE).tar.Z; fi @if test -e ${BASENAME}-$(RELEASE).tar.gz; then rm -f ${BASENAME}-$(RELEASE).tar.gz; fi # # CVS tag and extract. -c: make sure we committed; # -F: allow more than one "make dist" per rel # prep: must have done "cvs commit", and CVSROOT must be set # cvs tag -c -F ${RELCODE} cvs export -r ${RELCODE} -d ${BASENAME}-${RELEASE} ${BASENAME} # # Make the configure script from configure.ac # (cd ${BASENAME}-${RELEASE}; autoconf) # # Include the appropriate license files # cp Licenses/LICENSE.${LICENSETAG} ${BASENAME}-${RELEASE}/LICENSE cp Licenses/COPYRIGHT.${LICENSETAG} ${BASENAME}-${RELEASE}/COPYRIGHT # # Put license tags (short licenses) on files that need 'em (replace LICENSE keyword) # for file in $(READMES) *.c ${HDRS} ${PRECONFHDRS}; do\ licenseadd.pl Licenses/$(LICENSETAG) ${BASENAME}-${RELEASE}/$$file;\ done; # # Remove files/directories that aren't supposed to go out in the distro. # Do this last, so other steps (license adding, etc.) have simple loops. # -rm -rf ${BASENAME}-${RELEASE}/Licenses -rm -rf ${BASENAME}-${RELEASE}/Docs -rm ${BASENAME}-${RELEASE}/LOG -rm ${BASENAME}-${RELEASE}/configure.ac -rm ${BASENAME}-${RELEASE}/test_main.c # # Do replacements # (move this to configure) # for file in ${MANS}; do\ # sedition2 @RELEASEDATE@ ${RELEASEDATE} @PACKAGE@ ${PACKAGE} @RELEASE@ ${RELEASE} @COPYRIGHT@ ${COPYRIGHT} @LICENSE@ ${LICENSE} @SEEALSO@ ${SEEALSO} ${BASENAME}-${RELEASE}/Man/$$file.man;\ # done # # Set permissions. # chmod -R ugo+rX ${BASENAME}-${RELEASE} chmod +x ${BASENAME}-${RELEASE}/install-sh chmod +x ${BASENAME}-${RELEASE}/Testsuite/bug-* chmod +x ${BASENAME}-${RELEASE}/Testsuite/x-base-* # # pack it up! # tar cvf ${BASENAME}-${RELEASE}.tar ${BASENAME}-${RELEASE} ${COMPRESS} ${BASENAME}-$(RELEASE).tar ftpdist: cp -f ${BASENAME}-${RELEASE}.tar.gz ${FTPDIR}/ rm -f ${FTPDIR}/${BASENAME}.tar.gz (cd ${FTPDIR}; ln -s ${BASENAME}-${RELEASE}.tar.gz ${BASENAME}.tar.gz ) # implode: # Collapse a distro version of the squid library, removing all StL-specific # development material. # implode: -rm -rf 00CHECKLIST Bugs INSTALL LOG configure.ac -rm -rf Docs Formats Licenses Man TAGS: etags -t *.h *.c Makefile.in squid/Man/0000755000175000017520000000000010463223377012632 5ustar naolivbiolinuxsquid/Man/afetch.man0000640000175000017520000000322210463223377014554 0ustar naolivbiolinux.TH "afetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP afetch - retrieve an alignment from an alignment database .SH SYNOPSIS .B afetch .I [options] .I alignmentdb .I key .PP .B afetch --index .I alignmentdb .SH DESCRIPTION .B afetch retrieves the alignment named .I key from an alignment database in file .I alignmentdb. .PP .I alignmentdb is a "multiple multiple alignment" file in Stockholm (e.g. native Pfam) format. .PP .I key is either the name (ID) of the alignment, or its accession number (AC). .PP The .I alignmentdb file should first be SSI indexed with .B afetch --index for efficient retrieval. An SSI index is not required, but alignment retrieval without one may be painfully slow. .SH OPTIONS .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .SH EXPERT OPTIONS .TP .B --index Instead of retrieving a .I key, the special command .B afetch --index .I alignmentdb produces an SSI index of the names and accessions of the alignments in the file .I alignmentdb. This should be run once on the .I alignmentdb file to prepare it for all future afetch's. .SH SEE ALSO .PP Master man page, with full list of and guide to the individual man pages for SQUID's auxiliary programs: see .B squid(1). .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/alistat.man0000640000175000017520000000655310463223377014775 0ustar naolivbiolinux.TH "alistat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP alistat - show statistics for a multiple alignment file .SH SYNOPSIS .B alistat .I [options] .I alignfile .SH DESCRIPTION .B alistat reads a multiple sequence alignment from the file .I alignfile in any supported format (including SELEX, GCG MSF, and CLUSTAL), and shows a number of simple statistics about it. These statistics include the name of the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, the alignment length (e.g. including gap characters). .PP Also shown are some percent identities. A percent pairwise alignment identity is defined as .I (idents / MIN(len1, len2)) where .I idents is the number of exact identities and .I len1, len2 are the unaligned lengths of the two sequences. The "average percent identity", "most related pair", and "most unrelated pair" of the alignment are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively. The "most distant seq" is calculated by finding the maximum pairwise identity (best relative) for all N sequences, then finding the minimum of these N numbers (hence, the most outlying sequence). .SH OPTIONS .TP .B -a Show additional verbose information: a table with one line per sequence showing name, length, and its highest and lowest pairwise identity. These lines are prefixed with a * character to enable easily .BR grep' ing them out and sorting them. For example, .I alistat -a foo.slx | grep "*" | sort -n +3 gives a ranked list of the most distant sequences in the alignment. Incompatible with the .B -f option. .TP .B -f Fast; use a sampling method to estimate the average %id. When this option is chosen, .B alistat doesn't show the other three pairwise identity numbers. This option is useful for very large alignments, for which the full (N)(N-1) calculation of all pairs would be prohibitive (e.g. Pfam's GP120 alignment, with over 10,000 sequences). Incompatible with the .B -a option. .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .B -q be quiet - suppress the verbose header (program name, release number and date, the parameters and options in effect). .TP .B -B (Babelfish). Autodetect and read a sequence file format other than the default (FASTA). Almost any common sequence file format is recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal alignment formats). See the printed documentation for a complete list of supported formats. .SH EXPERT OPTIONS .TP .BI --informat " " Specify that the sequence file is in format .I , rather than the default FASTA format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option overrides the default format (FASTA) and the .I -B Babelfish autodetection option. .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/compstruct.man0000644000175000017520000000726310463223377015542 0ustar naolivbiolinux.TH "compstruct" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP compstruct - calculate accuracy of RNA secondary structure predictions .SH SYNOPSIS .B compstruct .I [options] .I trusted_file .I test_file .SH DESCRIPTION .I compstruct evaluates the accuracy of RNA secondary structure predictions, at the on a per-base-pair basis. The .I trusted_file contains one or more sequences with trusted (known) RNA secondary structure annotation. The .I test_file contains the same sequences, in the same order, with predicted RNA secondary structure annotation. .I compstruct reads the structures and compares them, and calculates both the sensitivity (the number of true base pairs that are correctly predicted) and the specificity (positive predictive value, the number of predicted base pairs that are true). Results are reported for each individual sequence, and in summary for all sequences together. .PP Both files must contain secondary structure annotation in WUSS notation. Only SELEX and Stockholm formats support structure markup at present. .PP The default definition of a correctly predicted base pair is that a true pair (i,j) must exactly match a predicted pair (i,j). .PP Mathews, Zuker, Turner and colleagues (see: Mathews et al., JMB 288:911-940, 1999) use a more relaxed definition. Mathews defines "correct" as follows: a true pair (i,j) is correctly predicted if any of the following pairs are predicted: (i,j), (i+1,j), (i-1,j), (i,j+1), or (i,j-1). This rule allows for "slipped helices" off by one base. The .B -m option activates this rule for both sensitivity and for specificity. For specificity, the rule is reversed: predicted pair (i,j) is considered to be true if the true structure contains one of the five pairs (i,j), (i+1,j), (i-1,j), (i,j+1), or (i,j-1). .SH OPTIONS .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .B -m Use the Mathews relaxed accuracy rule (see above), instead of requiring exact prediction of base pairs. .TP .B -p Count pseudoknotted base pairs towards the accuracy, in either trusted or predicted structures. By default, pseudoknots are ignored. .IP Normally, only the .I trusted_file would have pseudoknot annotation, since most RNA secondary structure prediction programs do not predict pseudoknots. Using the .B -p option allows you to penalize the prediction program for not predicting known pseudoknots. In a case where both the .I trusted_file and the .I test_file have pseudoknot annotation, the .B -p option lets you count pseudoknots in evaluating the prediction accuracy. Beware, however, the case where you use a pseudoknot-capable prediction program to generate the .I test_file, but the .I trusted_file does not have pseudoknot annotation; in this case, .B -p will penalize any predicted pseudoknots when it calculates specificity, even if they're right, because they don't appear in the trusted annotation; this is probably not what you'd want to do. .SH EXPERT OPTIONS .TP .BI --informat " " Specify that the two sequence files are in format .I . In this case, both files must be in the same format. The default is to autodetect the file formats, in which case they could be different (one SELEX, one Stockholm). .TP .B --quiet Don't print any verbose header information. .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/seqstat.man0000640000175000017520000000417510463223377015016 0ustar naolivbiolinux.TH "seqstat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP seqstat - show statistics and format for a sequence file .SH SYNOPSIS .B seqstat .I [options] .I seqfile .SH DESCRIPTION .B seqstat reads a sequence file .I seqfile and shows a number of simple statistics about it. .pp The printed statistics include the name of the format, the residue type of the first sequence (protein, RNA, or DNA), the number of sequences, the total number of residues, and the average and range of the sequence lengths. .SH OPTIONS .TP .B -a Show additional verbose information: a table with one line per sequence showing name, length, and description line. These lines are prefixed with a * character to enable easily .BR grep' ing them out and sorting them. .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .B -B (Babelfish). Autodetect and read a sequence file format other than the default (FASTA). Almost any common sequence file format is recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal alignment formats). See the printed documentation for a complete list of supported formats. .SH EXPERT OPTIONS .TP .BI --informat " " Specify that the sequence file is in format .I , rather than the default FASTA format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option overrides the default expected format (FASTA) and the .I -B Babelfish autodetection option. .TP .B --quiet Suppress the verbose header (program name, release number and date, the parameters and options in effect). .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/sfetch.man0000640000175000017520000001057110463223377014603 0ustar naolivbiolinux.TH "sfetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP sfetch - get a sequence from a flatfile database. .SH SYNOPSIS .B sfetch .I [options] .I seqname .SH DESCRIPTION .B sfetch retrieves the sequence named .I seqname from a sequence database. .PP Which database is used is controlled by the .B -d and .B -D options, or "little databases" and "big databases". The directory location of "big databases" can be specified by environment variables, such as $SWDIR for Swissprot, and $GBDIR for Genbank (see .B -D for complete list). A complete file path must be specified for "little databases". By default, if neither option is specified and the name looks like a Swissprot identifier (e.g. it has a _ character), the $SWDIR environment variable is used to attempt to retrieve the sequence .I seqname from Swissprot. .PP A variety of other options are available which allow retrieval of subsequences .RI ( -f,-t ); retrieval by accession number instead of by name .RI ( -a ); reformatting the extracted sequence into a variety of other formats .RI ( -F ); etc. .PP If the database has been SSI indexed, sequence retrieval will be extremely efficient; else, retrieval may be painfully slow (the entire database may have to be read into memory to find .IR seqname ). SSI indexing is recommended for all large or permanent databases. The program .B sindex creates SSI indexes for any sequence file. .pp .B sfetch was originally named .B getseq, and was renamed because it clashed with a GCG program of the same name. .SH OPTIONS .TP .B -a Interpret .I seqname as an accession number, not an identifier. .TP .BI -d " " Retrieve the sequence from a sequence file named .I . If a GSI index .I .gsi exists, it is used to speed up the retrieval. .TP .BI -f " " Extract a subsequence starting from position .I , rather than from 1. See .B -t. If .I is greater than .I (as specified by the .B -t option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence). .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .BI -o " " Direct the output to a file named .I . By default, output would go to stdout. .TP .BI -r " " Rename the sequence .I in the output after extraction. By default, the original sequence identifier would be retained. Useful, for instance, if retrieving a sequence fragment; the coordinates of the fragment might be added to the name (this is what Pfam does). .TP .BI -t " " Extract a subsequence that ends at position .I , rather than at the end of the sequence. See .B -f. If .I is less than .I (as specified by the .B -f option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence) .TP .BI -D " " Retrieve the sequence from the main sequence database coded .I . For each code, there is an environment variable that specifies the directory path to that database. Recognized codes and their corresponding environment variables are .I -Dsw (Swissprot, $SWDIR); .I -Dpir (PIR, $PIRDIR); .I -Dem (EMBL, $EMBLDIR); .I -Dgb (Genbank, $GBDIR); .I -Dwp (Wormpep, $WORMDIR); and .I -Dowl (OWL, $OWLDIR). Each database is read in its native flatfile format. .TP .BI -F " " Reformat the extracted sequence into a different format. (By default, the sequence is extracted from the database in the same format as the database.) Available formats are .B embl, fasta, genbank, gcg, strider, zuker, ig, pir, squid, and .B raw. .SH EXPERT OPTIONS .TP .BI --informat " " Specify that the sequence file is in format .I , rather than the default FASTA format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option overrides the default format (FASTA) and the .I -B Babelfish autodetection option. .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/shuffle.man0000640000175000017520000001146710463223377014770 0ustar naolivbiolinux.TH "shuffle" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP shuffle - randomize the sequences in a sequence file .SH SYNOPSIS .B shuffle .I [options] .I seqfile .SH DESCRIPTION .B shuffle reads a sequence file .I seqfile, randomizes each sequence, and prints the randomized sequences in FASTA format on standard output. The sequence names are unchanged; this allows you to track down the source of each randomized sequence if necessary. .pp The default is to simply shuffle each input sequence, preserving monosymbol composition exactly. To shuffle each sequence while preserving both its monosymbol and disymbol composition exactly, use the .I -d option. .pp The .I -0 and .I -1 options allow you to generate sequences with the same Markov properties as each input sequence. With .I -0, for each input sequence, 0th order Markov statistics are collected (e.g. symbol composition), and a new sequence is generated with the same composition. With .I -1, the generated sequence has the same 1st order Markov properties as the input sequence (e.g. the same disymbol frequencies). .pp Note that the default and .I -0, or .I -d and .I -1, are similar; the shuffling algorithms preserve composition exactly, while the Markov algorithms only expect to generate a sequence of similar composition on average. .pp Other shuffling algorithms are also available, as documented below in the options. .SH OPTIONS .TP .B -0 Calculate 0th order Markov frequencies of each input sequence (e.g. residue composition); generate output sequence using the same 0th order Markov frequencies. .TP .B -1 Calculate 1st order Markov frequencies for each input sequence (e.g. diresidue composition); generate output sequence using the same 1st order Markov frequencies. The first residue of the output sequence is always the same as the first residue of the input sequence. .TP .B -d Shuffle the input sequence while preserving both monosymbol and disymbol composition exactly. Uses an algorithm published by S.F. Altschul and B.W. Erickson, Mol. Biol. Evol. 2:526-538, 1985. .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .B -l Look only at the length of each input sequence; generate an i.i.d. output protein sequence of that length, using monoresidue frequencies typical of proteins (taken from Swissprot 35). .TP .BI -n " " Make .I different randomizations of each input sequence in .I seqfile, rather than the default of one. .TP .B -r Generate the output sequence by reversing the input sequence. (Therefore only one "randomization" per input sequence is possible, so it's not worth using .I -n if you use reversal.) .TP .BI -t " " Truncate each input sequence to a fixed length of exactly .I residues. If the input sequence is shorter than .I it is discarded (therefore the output file may contain fewer sequences than the input file). If the input sequence is longer than .I a contiguous subsequence is randomly chosen. .TP .BI -w " " Regionally shuffle each input sequence in window sizes of .I , preserving local residue composition in each window. Probably a better shuffling algorithm for biosequences with nonstationary residue composition (e.g. composition that is varying along the sequence, such as between different isochores in human genome sequence). .TP .B -B (Babelfish). Autodetect and read a sequence file format other than the default (FASTA). Almost any common sequence file format is recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal alignment formats). See the printed documentation for a complete list of supported formats. .SH EXPERT OPTIONS .TP .BI --informat " " Specify that the sequence file is in format .I , rather than the default FASTA format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option overrides the default expected format (FASTA) and the .I -B Babelfish autodetection option. .TP .B --nodesc Do not output any sequence description in the output file, only the sequence names. .TP .BI --seed " " Set the random number seed to .I . If you want reproducible results, use the same seed each time. By default, .B shuffle uses a different seed each time, so does not generate the same output in subsequent runs with the same input. .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/sindex.man0000640000175000017520000000501610463223377014617 0ustar naolivbiolinux.TH "sindex" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP sindex - index a sequence database for sfetch .SH SYNOPSIS .B sindex .I [options] .I seqfile1 [seqfile2...] .SH DESCRIPTION .B sindex indexes one or more .I seqfiles for future sequence retrievals by .B sfetch. An SSI ("squid sequence index") file is created in the same directory with the sequence files. By default, this file is called .I .ssi. .PP If there is more than one sequence file on the command line, the SSI filename will be constructed from the last sequence file name. This may not be what you want; see the .I -o option to specify your own name for the SSI file. .PP .I sindex is capable of indexing large files (>2 GB) if optional LFS support has been enabled at compile-time. See INSTALL instructions that came with @PACKAGE@. .SH OPTIONS .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .BI -o " " Direct the SSI index to a file named .I . By default, the SSI file would go to .I .ssi. .SH EXPERT OPTIONS .TP .B --64 Force the SSI file into 64-bit (large seqfile) mode, even if the seqfile is small. You don't want to do this unless you're debugging. .TP .B --external Force .I sindex to do its record sorting by external (on-disk) sorting. This is only useful for debugging, too. .TP .BI --informat " " Specify that the sequence file is definitely in format .I ; blocks sequence file format autodetection. This is useful in automated pipelines, because it improves robustness (autodetection can occasionally go wrong on a perversely misformed file). Common examples include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip; see the printed documentation for a complete list of accepted format names. .TP .B --pfamseq A hack for Pfam; indexes a FASTA file that is known to have identifier lines in format ">[name] [accession] [optional description]". Normally only the sequence name would be indexed as a primary key in a FASTA SSI file, but this allows indexing both the name (as a primary key) and accession (as a secondary key). .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Man/sreformat.man0000640000175000017520000001526310463223377015334 0ustar naolivbiolinux.TH "sreformat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" .SH NAME .TP sreformat - convert sequence file to different format .SH SYNOPSIS .B sreformat .I [options] .I format .I seqfile .SH DESCRIPTION .B sreformat reads the sequence file .I seqfile in any supported format, reformats it into a new format specified by .I format, then prints the reformatted text. .PP Supported input formats include (but are not limited to) the unaligned formats FASTA, Genbank, EMBL, SWISS-PROT, PIR, and GCG, and the aligned formats Stockholm, Clustal, GCG MSF, and Phylip. .PP Available unaligned output file format codes include .I fasta (FASTA format); .I embl (EMBL/SWISSPROT format); .I genbank (Genbank format); .I gcg (GCG single sequence format); .I gcgdata (GCG flatfile database format); .I pir (PIR/CODATA flatfile format); .I raw (raw sequence, no other information). .pp The available aligned output file format codes include .I stockholm (PFAM/Stockholm format); .I msf (GCG MSF format); .I a2m (an aligned FASTA format); .I PHYLIP (Felsenstein's PHYLIP format); and .I clustal (Clustal V/W/X format); and .I selex (the old SELEX/HMMER/Pfam annotated alignment format); .pp All thee codes are interpreted case-insensitively (e.g. MSF, Msf, or msf all work). .PP Unaligned format files cannot be reformatted to aligned formats. However, aligned formats can be reformatted to unaligned formats -- gap characters are simply stripped out. .PP This program was originally named .B reformat, but that name clashes with a GCG program of the same name. .SH OPTIONS .TP .B -d DNA; convert U's to T's, to make sure a nucleic acid sequence is shown as DNA not RNA. See .B -r. .TP .B -h Print brief help; includes version number and summary of all options, including expert options. .TP .B -l Lowercase; convert all sequence residues to lower case. See .B -u. .TP .B -n For DNA/RNA sequences, converts any character that's not unambiguous RNA/DNA (e.g. ACGTU/acgtu) to an N. Used to convert IUPAC ambiguity codes to N's, for software that can't handle all IUPAC codes (some public RNA folding codes, for example). If the file is an alignment, gap characters are also left unchanged. If sequences are not nucleic acid sequences, this option will corrupt the data in a predictable fashion. .TP .B -r RNA; convert T's to U's, to make sure a nucleic acid sequence is shown as RNA not DNA. See .B -d. .TP .B -u Uppercase; convert all sequence residues to upper case. See .B -l. .TP .B -x For DNA sequences, convert non-IUPAC characters (such as X's) to N's. This is for compatibility with benighted people who insist on using X instead of the IUPAC ambiguity character N. (X is for ambiguity in an amino acid residue). .IP Warning: like the .B -n option, the code doesn't check that you are actually giving it DNA. It simply literally just converts non-IUPAC DNA symbols to N. So if you accidentally give it protein sequence, it will happily convert most every amino acid residue to an N. .SH EXPERT OPTIONS .TP .BI --gapsym " " Convert all gap characters to .I . Used to prepare alignment files for programs with strict requirements for gap symbols. Only makes sense if the input .I seqfile is an alignment. .TP .BI --informat " " Specify that the sequence file is in format .I , rather than allowing the program to autodetect the file format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. .TP .B --mingap If .I seqfile is an alignment, remove any columns that contain 100% gap characters, minimizing the overall length of the alignment. (Often useful if you've extracted a subset of aligned sequences from a larger alignment.) .TP .B --nogap Remove any aligned columns that contain any gap symbols at all. Useful as a prelude to phylogenetic analyses, where you only want to analyze columns containing 100% residues, so you want to strip out any columns with gaps in them. Only makes sense if the file is an alignment file. .TP .B --pfam For SELEX alignment output format only, put the entire alignment in one block (don't wrap into multiple blocks). This is close to the format used internally by Pfam in Stockholm and Cambridge. .TP .B --sam Try to convert gap characters to UC Santa Cruz SAM style, where a . means a gap in an insert column, and a - means a deletion in a consensus/match column. This only works for converting aligned file formats, and only if the alignment already adheres to the SAM convention of upper case for residues in consensus/match columns, and lower case for residues in insert columns. This is true, for instance, of all alignments produced by old versions of HMMER. (HMMER2 produces alignments that adhere to SAM's conventions even in gap character choice.) This option was added to allow Pfam alignments to be reformatted into something more suitable for profile HMM construction using the UCSC SAM software. .TP .BI --samfrac " " Try to convert the alignment gap characters and residue cases to UC Santa Cruz SAM style, where a . means a gap in an insert column and a - means a deletion in a consensus/match column, and upper case means match/consensus residues and lower case means inserted resiudes. This will only work for converting aligned file formats, but unlike the .B --sam option, it will work regardless of whether the file adheres to the upper/lower case residue convention. Instead, any column containing more than a fraction .I of gap characters is interpreted as an insert column, and all other columns are interpreted as match columns. This option was added to allow Pfam alignments to be reformatted into something more suitable for profile HMM construction using the UCSC SAM software. .TP .B --wussify Convert RNA secondary structure annotation strings (both consensus and individual) from old "KHS" format, ><, to the new WUSS notation, <>. If the notation is already in WUSS format, this option will screw it up, without warning. Only SELEX and Stockholm format files have secondary structure markup at present. .TP .B --dewuss Convert RNA secondary structure annotation strings from the new WUSS notation, <>, back to the old KHS format, ><. If the annotation is already in KHS, this option will corrupt it, without warning. Only SELEX and Stockholm format files have secondary structure markup. .SH SEE ALSO .PP @SEEALSO@ .SH AUTHOR @PACKAGE@ and its documentation are @COPYRIGHT@ @LICENSE@ See COPYING in the source code distribution for more details, or contact me. .nf Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu .fi squid/Scripts/0000755000175000017520000000000010463223377013546 5ustar naolivbiolinuxsquid/Shiva/0000755000175000017520000000000010463223377013171 5ustar naolivbiolinuxsquid/Testsuite/0000755000175000017520000000000010463223377014110 5ustar naolivbiolinuxsquid/Testsuite/00README0000640000175000017520000000175010463223377015127 0ustar naolivbiolinuxSRE, Tue Mar 5 13:28:13 2002 x-* : These are scripts (Perl or sh) that exercise the programs. An exercise script returns 0 on success, 1 on failure, so another controlling program can execute all exercise-* programs and count successes and failures. The script is also responsible for printing a message like: x-sindex basic sindex tests ... ok. x-sreformat basic sreformat tests ... ok. x-options-sindex sindex option tests ... FAILED ^^^++++++++++++++++++++^xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx^... ====== (20) (35) (6) Message width: 70. Max script name length: 20. Max description length: 35. Message: "ok." or "FAILED" examples: printf(" %-20s %-35s ... %s\n", $ARGV[0], $desc, $status); echo " x-sindex basic sindex tests ... ok." squid/Testsuite/Makefile.in0000640000175000017520000000344510463223377016157 0ustar naolivbiolinux############################################################### # Makefile for SQUID's testsuite # CVS $Id: Makefile.in,v 1.6 2003/05/23 16:16:42 eddy Exp $ # # Note: The autoconf variables in this file must be coordinated # with HMMER, if you change them, because HMMER will # create a Makefile from this Makefile.in using its own # configure script, not SQUID's. # ########### # @LICENSE@ ########### SHELL = /bin/sh CC = @CC@ CFLAGS = @CFLAGS@ DEFS = @DEFS@ LIBS = -lsquid @LIBS@ -lm TESTPROGS = iospeed rndspeed X-BASE = x-base-afetch\ x-base-alistat\ x-base-seqstat\ x-base-sfetch\ x-base-shuffle\ x-base-sindex\ x-base-sreformat BUGLIST = bug-1-sfetch-paths ################################################################ # Targets for building the test programs. # all: sqdconfig $(TESTPROGS) $(TESTPROGS): @EXEC_DEPENDENCY@ $(CC) $(CFLAGS) -L../ -I../ $(DEFS) -o $@ $@_main.o $(LIBS) sqdconfig: @EXEC_DEPENDENCY@ $(CC) $(CFLAGS) -L../ -I../ $(DEFS) -o $@ $@_main.o $(LIBS) .c.o: $(CC) $(CFLAGS) $(DEFS) -L../ -I../ -c $< ################################################################ ################################################################ # 'make check' actually runs the tests. # check: $(TESTPROGS) sqdconfig @for testprog in $(TESTPROGS); do\ if ./$$testprog; then\ echo $$testprog: ok;\ else\ echo $$testprog: FAILED;\ fi;\ done @for xprog in $(X-BASE); do\ ./$$xprog;\ done @for bugprog in $(BUGLIST); do\ ./$$bugprog;\ done ####### ## Miscellaneous ####### clean: -rm -f *.o *~ Makefile.bak core $(TESTPROGS) TAGS gmon.out sqdconfig distclean: make clean -rm -f Makefile binclean: -rm -f *.o *~ Makefile.bak core TAGS gmon.out sqdconfig TAGS: etags -t *.c *.h Makefile.in squid/Testsuite/bug-1-sfetch-paths0000640000175000017520000000161410463223377017333 0ustar naolivbiolinux#! /usr/bin/perl # Test for bug #1: sfetch/SSI path bug. # sfetch can't follow paths out of current directory if it's using # an SSI index. # Reported by Zhirong. # SRE, Wed Mar 6 21:07:47 2002 use testsuite; testsuite::description("bug-1-sfetch-path", "sfetch/SSI path bug"); $tmp = testsuite::tempname(); $tmpdir = testsuite::tempname(); mkdir $tmpdir, 0700; testsuite::run("../shuffle -i --dna -n 10 -t 100 > $tmp"); testsuite::run("../sindex $tmp > /dev/null"); testsuite::run("../sfetch -d $tmp randseq5 > /dev/null"); testsuite::run("../shuffle -i --dna -n 10 -t 100 > $tmpdir/foo"); testsuite::run("../sindex $tmpdir/foo > /dev/null"); testsuite::run("../sfetch -d $tmpdir/foo randseq5 > /dev/null"); testsuite::run("cp $tmp $tmpdir/"); testsuite::run("cp $tmp.ssi $tmpdir/"); testsuite::run("../sfetch -d $tmpdir/$tmp randseq5 > /dev/null"); system("rm -rf $tmpdir"); testsuite::done(); squid/Testsuite/exercises.sqc0000644000175000017520000000043610463223377016615 0ustar naolivbiolinux# squid's crash exercises, in sqc command format. # SRE, Fri Oct 31 13:13:17 2003 # CVS $Id: exercises.sqc,v 1.1 2003/10/31 19:25:26 eddy Exp $ # # To run: # ~/src/ssdk/sqc 4 exercises.sqc ../ # 1 exercise translate @translate-test.pl@ @shuffle@ @sindex@ @sfetch@ @translate@ squid/Testsuite/testsuite.pm0000640000175000017520000000154110463223377016474 0ustar naolivbiolinuxpackage testsuite; $status = 0; $ntmp = 0; $tmpbase = "sqd_test_out"; sub description { my ($name, $desc) = @_; $| = 1; printf " %-20s %-35s ... ", $name, $desc; 1; } sub getconfig { my ($cfgprog, $flag) = @_; my $output; $output = `./$cfgprog`; if ($output =~ /$flag\s+false/) { return 0; } elsif ($output =~ /$flag\s+true/) { return 1; } else { die "$flag not found in output of $cfgprog"; } 1; } sub done { unlink(<$tmpbase.*>); if ($status == 0) { print "ok.\n"; exit(0); } else { print "FAILED\n"; exit($status); } 1; } sub tempname { my $tmp; $tmp = "$tmpbase.$ntmp"; $ntmp++; return $tmp; } sub run { my ($cmd) = @_; system("$cmd 2>/dev/null"); # stderr directed away if ($? != 0) { $status = 1; &done(); } 1; } 1; squid/Testsuite/translate-test.pl0000755000175000017520000000304410463223377017423 0ustar naolivbiolinux#! /usr/bin/perl # Creates tmp files in current directory: testxxx, testxxx.pep, testxxx.ssi, testxxx.orf # # SRE, Fri Oct 31 12:42:26 2003 # CVS $Id: translate-test.pl,v 1.1 2003/10/31 19:25:26 eddy Exp $ $usage = "translate-test \n"; if ($#ARGV != 3) { die "Wrong argument number.\n$usage"; } $shuffle = shift; $sindex = shift; $sfetch = shift; $translate = shift; $tmp = "testxxx"; system("$shuffle -i -n 5 -t 200 --dna -o $tmp"); if ($? != 0) { print("FAILED (shuffle)\n"); exit(1); } system("$sindex $tmp"); if ($? != 0) { print("FAILED (sindex)\n"); exit(1); } system("$translate -o $tmp.pep -l 10 $tmp"); if ($? != 0) { print("FAILED (translate)\n"); exit(1); } if (! open(TRANSLATIONS,"$tmp.pep")) { print("FAILED (open tmp file)\n"); exit(1); } while () { if (/^>\s*(\S+)\.\d+\s+length (\d+), nt (\d+)\.\.(\d+)/) { $source = $1; $peplength = $2; $start = $3; $end = $4; print("$start..$end\n"); system("$sfetch -d $tmp -f $start -t $end -o $tmp.orf $source"); if ($? != 0) { print("FAILED (sfetch)\n"); exit(1); } $line = `$translate -l10 $tmp.orf | head -2 | tail -1`; if ($? != 0) { print("FAILED (2nd translate)\n"); exit(1); } $ntlength = $peplength * 3; $line =~ /^>\s*\S+\s+length (\d+), nt (\d+)\.\.(\d+)/; if ($1 != $peplength || $2 != 1 || $3 != $ntlength) { print("FAILED (orf match)\n"); exit(1); } } } close TRANSLATIONS; unlink "$tmp.orf"; unlink "$tmp.pep"; unlink "$tmp.ssi"; unlink "$tmp"; print "ok\n"; exit 0; squid/Testsuite/x-base-afetch0000640000175000017520000000054510463223377016442 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-afetch", "basic tests of afetch"); $tmp = testsuite::tempname(); testsuite::run("cp ../Formats/stockholm.2 $tmp"); testsuite::run("../afetch --index $tmp > /dev/null"); testsuite::run("../afetch $tmp rrm > /dev/null"); testsuite::run("../afetch $tmp 14-3-3 > /dev/null"); testsuite::done(); squid/Testsuite/x-base-alistat0000640000175000017520000000120110463223377016637 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-alistat", "basic tests of alistat"); testsuite::run("../alistat ../Formats/a2m > /dev/null"); testsuite::run("../alistat ../Formats/clustal > /dev/null"); testsuite::run("../alistat ../Formats/msf > /dev/null"); testsuite::run("../alistat ../Formats/phylip > /dev/null"); testsuite::run("../alistat ../Formats/selex.1 > /dev/null"); testsuite::run("../alistat ../Formats/selex.2 > /dev/null"); testsuite::run("../alistat ../Formats/stockholm.1 > /dev/null"); testsuite::run("../alistat ../Formats/stockholm.2 > /dev/null"); testsuite::done(); squid/Testsuite/x-base-seqstat0000640000175000017520000000221110463223377016664 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-seqstat", "basic tests of seqstat"); testsuite::run("../seqstat ../Formats/a2m > /dev/null"); testsuite::run("../seqstat ../Formats/clustal > /dev/null"); testsuite::run("../seqstat ../Formats/embl > /dev/null"); testsuite::run("../seqstat ../Formats/fasta > /dev/null"); testsuite::run("../seqstat ../Formats/gcg > /dev/null"); testsuite::run("../seqstat ../Formats/gcgdata.1 > /dev/null"); testsuite::run("../seqstat ../Formats/gcgdata.2 > /dev/null"); testsuite::run("../seqstat ../Formats/genbank > /dev/null"); testsuite::run("../seqstat ../Formats/msf > /dev/null"); testsuite::run("../seqstat ../Formats/phylip > /dev/null"); testsuite::run("../seqstat ../Formats/pir > /dev/null"); testsuite::run("../seqstat ../Formats/selex.1 > /dev/null"); testsuite::run("../seqstat ../Formats/selex.2 > /dev/null"); testsuite::run("../seqstat ../Formats/stockholm.1 > /dev/null"); testsuite::run("../seqstat ../Formats/stockholm.2 > /dev/null"); testsuite::run("../seqstat ../Formats/swissprot > /dev/null"); testsuite::done(); squid/Testsuite/x-base-sfetch0000640000175000017520000000050310463223377016456 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-sfetch", "basic tests of sfetch"); testsuite::run("../sfetch -d ../Formats/fasta AC3.1 > /dev/null"); testsuite::run("../sfetch -d ../Formats/fasta AC3.2 > /dev/null"); testsuite::run("../sfetch -d ../Formats/fasta AC3.3 > /dev/null"); testsuite::done(); squid/Testsuite/x-base-shuffle0000640000175000017520000000027210463223377016641 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-shuffle", "basic tests of shuffle"); testsuite::run("../shuffle ../Formats/fasta > /dev/null"); testsuite::done(); squid/Testsuite/x-base-sindex0000640000175000017520000000102110463223377016470 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-sindex", "basic tests of sindex"); $tmp = testsuite::tempname(); testsuite::run("../shuffle -i --dna -n 10 -t 100 > $tmp"); testsuite::run("../sindex $tmp > /dev/null"); testsuite::run("../sindex --external $tmp > /dev/null"); $largefile = testsuite::getconfig("sqdconfig", "HAS_64BIT_FILE_OFFSETS"); if ($largefile) { testsuite::run("../sindex --64 $tmp > /dev/null"); testsuite::run("../sindex --64 --external $tmp > /dev/null"); } testsuite::done(); squid/Testsuite/x-base-sreformat0000640000175000017520000000121210463223377017202 0ustar naolivbiolinux#! /usr/bin/perl use testsuite; testsuite::description("x-base-sreformat", "basic tests of sreformat"); testsuite::run("../sreformat fasta ../Formats/fasta > /dev/null"); testsuite::run("../sreformat embl ../Formats/fasta > /dev/null"); testsuite::run("../sreformat genbank ../Formats/fasta > /dev/null"); testsuite::run("../sreformat gcg ../Formats/fasta > /dev/null"); testsuite::run("../sreformat gcgdata ../Formats/fasta > /dev/null"); testsuite::run("../sreformat pir ../Formats/fasta > /dev/null"); testsuite::run("../sreformat raw ../Formats/fasta > /dev/null"); testsuite::done(); squid/Testsuite/iospeed_main.c0000640000175000017520000000355210463223377016711 0ustar naolivbiolinux #include #include #include "squid.h" #include "stopwatch.h" #define NSEQ 40000 #define SEQLEN 200 int main(int argc, char **argv) { SQFILE *sqfp; SQINFO sqinfo; FILE *fp; char *testfile; char *buf; int buflen; int format = SQFILE_FASTA; int n = 10; int i; Stopwatch_t *w; w = StopwatchCreate(); /* Create the sequence file. */ testfile = tmpnam(NULL); if ((fp = fopen(testfile, "w")) == NULL) Die("failed to open %s", testfile); for (i = 0; i < NSEQ; i++) { buf = RandomSequence(AMINO_ALPHABET, aafq, 20, SEQLEN); WriteSimpleFASTA(fp, buf, "foo", NULL); free(buf); } fclose(fp); /* Timing test 1: fgets(). */ StopwatchStart(w); for (i = 0; i < n; i++) { if ((fp = fopen(testfile, "r")) == NULL) Die("iospeed failed to open %s", testfile); buf = malloc(sizeof(char) * 256); buflen = 256; while (fgets(buf, buflen, fp) != NULL); free(buf); fclose(fp); } StopwatchStop(w); StopwatchDisplay(stdout, "fgets(): \t", w); /* Timing test 2: sre_fgets() */ StopwatchStart(w); for (i = 0; i < n; i++) { if ((fp = fopen(testfile,"r")) == NULL) Die("iospeed failed to open %s", testfile); buf = NULL; buflen = 0; while (sre_fgets(&buf, &buflen, fp) != NULL); free(buf); fclose(fp); } StopwatchStop(w); StopwatchDisplay(stdout, "sre_fgets(): \t", w); /* Timing test 3: ReadSeq() */ StopwatchStart(w); for (i = 0; i < n; i++) { if ((sqfp = SeqfileOpen(testfile, format, NULL)) == NULL) Die("iospeed failed to open %s", testfile); while (ReadSeq(sqfp, sqfp->format, &buf, &sqinfo)) { FreeSequence(buf, &sqinfo); } SeqfileClose(sqfp); } StopwatchStop(w); StopwatchDisplay(stdout, "ReadSeq(): \t", w); remove(testfile); StopwatchFree(w); return(EXIT_SUCCESS); } squid/Testsuite/rndspeed_main.c0000640000175000017520000000124110463223377017056 0ustar naolivbiolinux #include #include #include "squid.h" #include "stopwatch.h" int main(int argc, char **argv) { int n = 1000000; int r1; float r2; int i; Stopwatch_t *w; w = StopwatchCreate(); /* Timing test 1: Linux/UNIX rand(). */ StopwatchStart(w); for (i = 0; i < n; i++) { r1 = rand(); } StopwatchStop(w); StopwatchDisplay(stdout, "rand(): \t", w); /* Timing test 2: sre_random() */ StopwatchStart(w); for (i = 0; i < n; i++) { r2 = sre_random(); } StopwatchStop(w); StopwatchDisplay(stdout, "sre_random(): \t", w); StopwatchFree(w); return(EXIT_SUCCESS); } squid/Testsuite/sqdconfig_main.c0000640000175000017520000000130610463223377017231 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sqdconfig_main.c * SRE, Tue Mar 5 15:58:27 2002 [St. Louis] * * Small C program designed to print out information on squid's * compile-time configuration options - testsuite scripts can * call this to determine what optional stuff is compiled in. * * CVS $Id: sqdconfig_main.c,v 1.1 2002/03/05 23:11:28 eddy Exp $ */ #include #include #include "squid.h" int main(void) { #ifdef HAS_64BIT_FILE_OFFSETS printf("%-30s true\n", "HAS_64BIT_FILE_OFFSETS"); #else printf("%-30s false\n", "HAS_64BIT_FILE_OFFSETS"); #endif } squid/config.sub0000644000175000017520000006630510463223377014111 0ustar naolivbiolinux#! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001 # Free Software Foundation, Inc. timestamp='2001-06-08' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software # can handle that machine. It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, # Boston, MA 02111-1307, USA. # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit 0 ;; --version | -v ) echo "$version" ; exit 0 ;; --help | --h* | -h ) echo "$usage"; exit 0 ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit 0;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | storm-chaos* | os2-emx* | windows32-*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis) os= basic_machine=$1 ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. tahoe | i860 | ia64 | m32r | m68k | m68000 | m88k | ns32k | arc \ | arm | arme[lb] | arm[bl]e | armv[2345] | armv[345][lb] | strongarm | xscale \ | pyramid | mn10200 | mn10300 | tron | a29k \ | 580 | i960 | h8300 \ | x86 | ppcbe | mipsbe | mipsle | shbe | shle \ | hppa | hppa1.0 | hppa1.1 | hppa2.0 | hppa2.0w | hppa2.0n \ | hppa64 \ | alpha | alphaev[4-8] | alphaev56 | alphapca5[67] \ | alphaev6[78] \ | we32k | ns16k | clipper | i370 | sh | sh[34] \ | powerpc | powerpcle \ | 1750a | dsp16xx | pdp10 | pdp11 \ | mips16 | mips64 | mipsel | mips64el \ | mips64orion | mips64orionel | mipstx39 | mipstx39el \ | mips64vr4300 | mips64vr4300el | mips64vr4100 | mips64vr4100el \ | mips64vr5000 | mips64vr5000el | mcore | s390 | s390x \ | sparc | sparclet | sparclite | sparc64 | sparcv9 | sparcv9b \ | v850 | c4x \ | thumb | d10v | d30v | fr30 | avr | openrisc | tic80 \ | pj | pjl | h8500 | z8k) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. # FIXME: clean up the formatting here. vax-* | tahoe-* | i*86-* | i860-* | ia64-* | m32r-* | m68k-* | m68000-* \ | m88k-* | sparc-* | ns32k-* | fx80-* | arc-* | c[123]* \ | arm-* | armbe-* | armle-* | armv*-* | strongarm-* | xscale-* \ | mips-* | pyramid-* | tron-* | a29k-* | romp-* | rs6000-* \ | power-* | none-* | 580-* | cray2-* | h8300-* | h8500-* | i960-* \ | xmp-* | ymp-* \ | x86-* | ppcbe-* | mipsbe-* | mipsle-* | shbe-* | shle-* \ | hppa-* | hppa1.0-* | hppa1.1-* | hppa2.0-* | hppa2.0w-* \ | hppa2.0n-* | hppa64-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphapca5[67]-* \ | alphaev6[78]-* \ | we32k-* | cydra-* | ns16k-* | pn-* | np1-* | xps100-* \ | clipper-* | orion-* \ | sparclite-* | pdp10-* | pdp11-* | sh-* | sh[34]-* | sh[34]eb-* \ | powerpc-* | powerpcle-* | sparc64-* | sparcv9-* | sparcv9b-* | sparc86x-* \ | mips16-* | mips64-* | mipsel-* \ | mips64el-* | mips64orion-* | mips64orionel-* \ | mips64vr4100-* | mips64vr4100el-* | mips64vr4300-* | mips64vr4300el-* \ | mipstx39-* | mipstx39el-* | mcore-* \ | f30[01]-* | f700-* | s390-* | s390x-* | sv1-* | t3e-* \ | [cjt]90-* \ | m88110-* | m680[01234]0-* | m683?2-* | m68360-* | z8k-* | d10v-* \ | thumb-* | v850-* | d30v-* | tic30-* | tic80-* | c30-* | fr30-* \ | bs2000-* | tic54x-* | c54x-* | x86_64-* | pj-* | pjl-*) ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | ymp) basic_machine=ymp-cray os=-unicos ;; cray2) basic_machine=cray2-cray os=-unicos ;; [cjt]90) basic_machine=${basic_machine}-cray os=-unicos ;; crds | unos) basic_machine=m68k-crds ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. Should this be sysv3.2? i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 ;; i*86v4*) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv4 ;; i*86v) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv ;; i*86sol2) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-solaris2 ;; i386mach) basic_machine=i386-mach os=-mach ;; i386-vsta | vsta) basic_machine=i386-unknown os=-vsta ;; iris | iris4d) basic_machine=mips-sgi case $os in -irix*) ;; *) os=-irix4 ;; esac ;; isi68 | isi) basic_machine=m68k-isi os=-sysv ;; m88k-omron*) basic_machine=m88k-omron ;; magnum | m3230) basic_machine=mips-mips os=-sysv ;; merlin) basic_machine=ns32k-utek os=-sysv ;; mingw32) basic_machine=i386-pc os=-mingw32 ;; miniframe) basic_machine=m68000-convergent ;; *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) basic_machine=m68k-atari os=-mint ;; mipsel*-linux*) basic_machine=mipsel-unknown os=-linux-gnu ;; mips*-linux*) basic_machine=mips-unknown os=-linux-gnu ;; mips3*-*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` ;; mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; mmix*) basic_machine=mmix-knuth os=-mmixware ;; monitor) basic_machine=m68k-rom68k os=-coff ;; msdos) basic_machine=i386-pc os=-msdos ;; mvs) basic_machine=i370-ibm os=-mvs ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pentium | p5 | k5 | k6 | nexgen) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon) basic_machine=i686-pc ;; pentiumii | pentium2) basic_machine=i686-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pn) basic_machine=pn-gould ;; power) basic_machine=power-ibm ;; ppc) basic_machine=powerpc-unknown ;; ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown ;; ppcle-* | powerpclittle-*) basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sparclite-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; sun2) basic_machine=m68000-sun ;; sun2os3) basic_machine=m68000-sun os=-sunos3 ;; sun2os4) basic_machine=m68000-sun os=-sunos4 ;; sun3os3) basic_machine=m68k-sun os=-sunos3 ;; sun3os4) basic_machine=m68k-sun os=-sunos4 ;; sun4os3) basic_machine=sparc-sun os=-sunos3 ;; sun4os4) basic_machine=sparc-sun os=-sunos4 ;; sun4sol2) basic_machine=sparc-sun os=-solaris2 ;; sun3 | sun3-*) basic_machine=m68k-sun ;; sun4) basic_machine=sparc-sun ;; sun386 | sun386i | roadrunner) basic_machine=i386-sun ;; sv1) basic_machine=sv1-cray os=-unicos ;; symmetry) basic_machine=i386-sequent os=-dynix ;; t3e) basic_machine=t3e-cray os=-unicos ;; tic54x | c54x*) basic_machine=tic54x-unknown os=-coff ;; tx39) basic_machine=mipstx39-unknown ;; tx39el) basic_machine=mipstx39el-unknown ;; tower | tower-32) basic_machine=m68k-ncr ;; udi29k) basic_machine=a29k-amd os=-udi ;; ultra3) basic_machine=a29k-nyu os=-sym1 ;; v810 | necv810) basic_machine=v810-nec os=-none ;; vaxv) basic_machine=vax-dec os=-sysv ;; vms) basic_machine=vax-dec os=-vms ;; vpp*|vx|vx-*) basic_machine=f301-fujitsu ;; vxworks960) basic_machine=i960-wrs os=-vxworks ;; vxworks68) basic_machine=m68k-wrs os=-vxworks ;; vxworks29k) basic_machine=a29k-wrs os=-vxworks ;; w65*) basic_machine=w65-wdc os=-none ;; w89k-*) basic_machine=hppa1.1-winbond os=-proelf ;; windows32) basic_machine=i386-pc os=-windows32-msvcrt ;; xmp) basic_machine=xmp-cray os=-unicos ;; xps | xps100) basic_machine=xps100-honeywell ;; z8k-*-coff) basic_machine=z8k-unknown os=-sim ;; none) basic_machine=none-none os=-none ;; # Here we handle the default manufacturer of certain CPU types. It is in # some cases the only manufacturer, in others, it is the most popular. w89k) basic_machine=hppa1.1-winbond ;; op50n) basic_machine=hppa1.1-oki ;; op60c) basic_machine=hppa1.1-oki ;; mips) if [ x$os = x-linux-gnu ]; then basic_machine=mips-unknown else basic_machine=mips-mips fi ;; romp) basic_machine=romp-ibm ;; rs6000) basic_machine=rs6000-ibm ;; vax) basic_machine=vax-dec ;; pdp10) # there are many clones, so DEC is not a safe bet basic_machine=pdp10-unknown ;; pdp11) basic_machine=pdp11-dec ;; we32k) basic_machine=we32k-att ;; sh3 | sh4) basic_machine=sh-unknown ;; sparc | sparcv9 | sparcv9b) basic_machine=sparc-sun ;; cydra) basic_machine=cydra-cydrome ;; orion) basic_machine=orion-highlevel ;; orion105) basic_machine=clipper-highlevel ;; mac | mpw | mac-mpw) basic_machine=m68k-apple ;; pmac | pmac-mpw) basic_machine=powerpc-apple ;; c4x*) basic_machine=c4x-none os=-coff ;; *-unknown) # Make sure to match an already-canonicalized machine name. ;; *) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; esac # Here we canonicalize certain aliases for manufacturers. case $basic_machine in *-digital*) basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` ;; *-commodore*) basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` ;; *) ;; esac # Decode manufacturer-specific aliases for certain operating systems. if [ x"$os" != x"" ] then case $os in # First match some system type aliases # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` ;; -solaris) os=-solaris2 ;; -svr4*) os=-sysv4 ;; -unixware*) os=-sysv4.2uw ;; -gnu/linux*) os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'` ;; # First accept the basic system types. # The portable systems comes first. # Each alternative MUST END IN A *, to match a version number. # -sysv* is not here because it comes later, after sysvr4. -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ | -aos* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -netbsd* | -openbsd* | -freebsd* | -riscix* \ | -lynxos* | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ | -chorusos* | -chorusrdb* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -uxpv* | -beos* | -mpeix* | -udk* \ | -interix* | -uwin* | -rhapsody* | -darwin* | -opened* \ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* | -os2*) # Remember, each alternative MUST END IN *, to match a version number. ;; -qnx*) case $basic_machine in x86-* | i*86-*) ;; *) os=-nto$os ;; esac ;; -nto*) os=-nto-qnx ;; -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \ | -windows* | -osx | -abug | -netware* | -os9* | -beos* \ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*) ;; -mac*) os=`echo $os | sed -e 's|mac|macos|'` ;; -linux*) os=`echo $os | sed -e 's|linux|linux-gnu|'` ;; -sunos5*) os=`echo $os | sed -e 's|sunos5|solaris2|'` ;; -sunos6*) os=`echo $os | sed -e 's|sunos6|solaris3|'` ;; -opened*) os=-openedition ;; -wince*) os=-wince ;; -osfrose*) os=-osfrose ;; -osf*) os=-osf ;; -utek*) os=-bsd ;; -dynix*) os=-bsd ;; -acis*) os=-aos ;; -386bsd) os=-bsd ;; -ctix* | -uts*) os=-sysv ;; -ns2 ) os=-nextstep2 ;; -nsk*) os=-nsk ;; # Preserve the version number of sinix5. -sinix5.*) os=`echo $os | sed -e 's|sinix|sysv|'` ;; -sinix*) os=-sysv4 ;; -triton*) os=-sysv3 ;; -oss*) os=-sysv3 ;; -svr4) os=-sysv4 ;; -svr3) os=-sysv3 ;; -sysvr4) os=-sysv4 ;; # This must come after -sysvr4. -sysv*) ;; -ose*) os=-ose ;; -es1800*) os=-ose ;; -xenix) os=-xenix ;; -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) os=-mint ;; -none) ;; *) # Get rid of the `-' at the beginning of $os. os=`echo $os | sed 's/[^-]*-//'` echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2 exit 1 ;; esac else # Here we handle the default operating systems that come with various machines. # The value should be what the vendor currently ships out the door with their # machine or put another way, the most popular os provided with the machine. # Note that if you're going to try to match "-MANUFACTURER" here (say, # "-sun"), then you have to tell the case statement up towards the top # that MANUFACTURER isn't an operating system. Otherwise, code above # will signal an error saying that MANUFACTURER isn't an operating # system, and we'll never get to this point. case $basic_machine in *-acorn) os=-riscix1.2 ;; arm*-rebel) os=-linux ;; arm*-semi) os=-aout ;; pdp10-*) os=-tops20 ;; pdp11-*) os=-none ;; *-dec | vax-*) os=-ultrix4.2 ;; m68*-apollo) os=-domain ;; i386-sun) os=-sunos4.0.2 ;; m68000-sun) os=-sunos3 # This also exists in the configure program, but was not the # default. # os=-sunos4 ;; m68*-cisco) os=-aout ;; mips*-cisco) os=-elf ;; mips*-*) os=-elf ;; *-tti) # must be before sparc entry or we get the wrong os. os=-sysv3 ;; sparc-* | *-sun) os=-sunos4.1.1 ;; *-be) os=-beos ;; *-ibm) os=-aix ;; *-wec) os=-proelf ;; *-winbond) os=-proelf ;; *-oki) os=-proelf ;; *-hp) os=-hpux ;; *-hitachi) os=-hiux ;; i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent) os=-sysv ;; *-cbm) os=-amigaos ;; *-dg) os=-dgux ;; *-dolphin) os=-sysv3 ;; m68k-ccur) os=-rtu ;; m88k-omron*) os=-luna ;; *-next ) os=-nextstep ;; *-sequent) os=-ptx ;; *-crds) os=-unos ;; *-ns) os=-genix ;; i370-*) os=-mvs ;; *-next) os=-nextstep3 ;; *-gould) os=-sysv ;; *-highlevel) os=-bsd ;; *-encore) os=-bsd ;; *-sgi) os=-irix ;; *-siemens) os=-sysv4 ;; *-masscomp) os=-rtu ;; f30[01]-fujitsu | f700-fujitsu) os=-uxpv ;; *-rom68k) os=-coff ;; *-*bug) os=-coff ;; *-apple) os=-macos ;; *-atari*) os=-mint ;; *) os=-none ;; esac fi # Here we handle the case where we know the os, and the CPU type, but not the # manufacturer. We pick the logical manufacturer. vendor=unknown case $basic_machine in *-unknown) case $os in -riscix*) vendor=acorn ;; -sunos*) vendor=sun ;; -aix*) vendor=ibm ;; -beos*) vendor=be ;; -hpux*) vendor=hp ;; -mpeix*) vendor=hp ;; -hiux*) vendor=hitachi ;; -unos*) vendor=crds ;; -dgux*) vendor=dg ;; -luna*) vendor=omron ;; -genix*) vendor=ns ;; -mvs* | -opened*) vendor=ibm ;; -ptx*) vendor=sequent ;; -vxsim* | -vxworks*) vendor=wrs ;; -aux*) vendor=apple ;; -hms*) vendor=hitachi ;; -mpw* | -macos*) vendor=apple ;; -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) vendor=atari ;; esac basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"` ;; esac echo $basic_machine$os exit 0 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: squid/configure.ac0000644000175000017520000002463110463223377014413 0ustar naolivbiolinux# Process this file with autoconf to produce a configure script. # SRE, Wed Jul 19 11:57:36 2000 # CVS $Id: configure.ac,v 1.4 2003/06/13 20:05:31 eddy Exp $ # # Hint: See autoconf macro archive at # http://www.gnu.org/software/ac-archive/ # AC_INIT information. # # The four AC_INIT args set the following output variables and preprocessor symbols: # PACKAGE_NAME e.g. "SQUID" # PACKAGE_VERSION e.g. "1.9a" # PACKAGE_BUGREPORT e.g. "eddy@genetics.wustl.edu" # PACKAGE_TARNAME e.g. "squid" # From them, it derives one more: # PACKAGE_STRING , e.g. "SQUID 1.9a" # We define some of our own: # SQUID_RELCODE unique package/version CVS tag without .'s: e.g. "squid1_9a" # SQUID_DATE release date: e.g. "January 2003" # SQUID_COPYRIGHT one-line copyright string # SQUID_LICENSE one-line license string # SQUID_LICENSETAG which license to bundle from Licenses/ subdirectory. # # Because SQUID is designed to be a library and must coexist with # packages that include it as a subdirectory (HMMER, INFERNAL...), # we don't want to use AC_INIT's PACKAGE_ variables as preprocessor # symbols to put version info into executables; we'll get name clashes, # plus we might want to have both squid version info and main package # version info. So, we use the PACKAGE_ stuff to make a # new preprocessor symbol of our own: # SQUID_VERSION e.g. "1.9a" # # The preprocessor symbols (version info) goes into squidconf.h. # Output variables are used in Makefiles. # AC_PREREQ(2.57) AC_INIT(SQUID, 1.9g, eddy@genetics.wustl.edu, squid) AC_MSG_NOTICE([configuring the SQUID library for your system.]) SQUID_RELCODE="squid1_9g" SQUID_DATE="January 2003" SQUID_COPYRIGHT="Copyright (C) 1992-2003 HHMI/Washington University School of Medicine" SQUID_LICENSE="Freely distributed under the GNU General Public License (GPL)" SQUID_LICENSETAG=gnu SQUID_VERSION=$PACKAGE_VERSION # Make output variables. AC_SUBST(SQUID_RELCODE) AC_SUBST(SQUID_DATE) AC_SUBST(SQUID_COPYRIGHT) AC_SUBST(SQUID_LICENSE) AC_SUBST(SQUID_LICENSETAG) AC_SUBST(SQUID_VERSION) # Make preprocessor symbols. AC_DEFINE_UNQUOTED(SQUID_DATE, "$SQUID_DATE") AC_DEFINE_UNQUOTED(SQUID_COPYRIGHT, "$SQUID_COPYRIGHT") AC_DEFINE_UNQUOTED(SQUID_LICENSE, "$SQUID_LICENSE") AC_DEFINE_UNQUOTED(SQUID_VERSION, "$SQUID_VERSION") # Checks for programs. # AC_PROG_CC AC_PROG_RANLIB AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin]) # GNU make check; format of makefile dependency lines for executables. # original from John Darrington # w/ heavy modifications. # # We need this because GNU make and SYSV make use different systems # specifying variables for dependencies: $$@ in sysv, %: %.o in GNU. # Would love to hear a better way of doing this. # # I use two different conventions in my Makefiles. Sometimes # executable "foo" has a file "foo.c" - this is the HMMER convention. # Sometimes executable "foo" has a file "foo_main.c" - this is # the SQUID convention. The configure script sets the # EXEC_DEPENDENCY appropriately: here, HMMER style. # # This creates a function CHECK_GNU_MAKE, which we immediately call. # It sets an output variable EXEC_DEPENDENCY. # This is used in the src/Makefile.in. # AC_DEFUN(CHECK_GNU_MAKE,[ AC_MSG_CHECKING(whether your make is GNU make) foundGNUmake='nope, assuming sysv make.' ; EXEC_DEPENDENCY=[\$\$\@_main.o] ; if ( make --version nothing 2> /dev/null | grep GNU > /dev/null ) ; then foundGNUmake='yes, it is.' ; EXEC_DEPENDENCY='%: %_main.o' ; fi AC_MSG_RESULT($foundGNUmake) AC_SUBST(EXEC_DEPENDENCY) ]) CHECK_GNU_MAKE # ================================================================ # Provide for unsigned integers of known size # Sets SQD_UINT16, 32, and 64. # Will substitute for @SQD_UINT16@, etc. in an output file (config.h) # Substitutes "FIXME" if no appropriate typedef is found. # This info is substituted in squid.h. # SRE, Thu Dec 28 13:58:51 2000 # AC_C_BIGENDIAN() AC_CHECK_FUNCS(ntohs, , AC_CHECK_LIB(socket, ntohs)) AC_CHECK_FUNCS(ntohl, , AC_CHECK_LIB(socket, ntohl)) AC_CHECK_FUNCS(htons, , AC_CHECK_LIB(socket, htons)) AC_CHECK_FUNCS(htonl, , AC_CHECK_LIB(socket, htonl)) AC_CHECK_SIZEOF(unsigned short, 2) AC_CHECK_SIZEOF(unsigned int, 4) AC_CHECK_SIZEOF(unsigned long, 4) AC_CHECK_SIZEOF(unsigned long long, 8) AC_CHECK_FUNCS(strtoul strtoull) if test "$ac_cv_sizeof_unsigned_short" = "2"; then SQD_UINT16="unsigned short " else SQD_UINT16="FIXME" AC_MSG_WARN("No 16-bit int? Manually edit config file to typedef sqd_uint16.") fi if test "$ac_cv_sizeof_unsigned_int" = "4"; then SQD_UINT32="unsigned int " elif test "$ac_cv_sizeof_unsigned_long" = "4"; then SQD_UINT32="unsigned long " else SQD_UINT32="FIXME" AC_MSG_WARN("No 32-bit int? Manually edit config file to typedef sqd_uint32.") fi if test "$ac_cv_sizeof_unsigned_long" = "8"; then SQD_UINT64="unsigned long " elif test "$ac_cv_sizeof_unsigned_long_long" = "8"; then SQD_UINT64="unsigned long long" else SQD_UINT64="FIXME" AC_MSG_WARN("No 64-bit int? Manually edit config file to typedef sqd_uint64.") fi AC_SUBST(SQD_UINT16) AC_SUBST(SQD_UINT32) AC_SUBST(SQD_UINT64) # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # ================================================================ # Test for whether we can cheat and treat fpos_t # (used by fgetpos() and fsetpos()) as an arithmetic datatype. # This is essential if we're to be able to save an fpos_t to a file # in an architecture-neutral format. We need this on FreeBSD # systems, which don't provide a 64-bit ftell64() or ftello(), # so we have to use fgetpos(). # # if true, squidconf.h will contain # #define ARITHMETIC_FPOS_T 1 # else if false, # #undef ARITHMETIC_FPOS_T AC_DEFUN(SQ_ARITHMETIC_FPOS_T, [ AC_MSG_CHECKING(whether fpos_t is an arithmetic datatype) fpos_arithmetic="no." AC_TRY_COMPILE([#include ], [int main(void) { fpos_t f1, f2; if (f1 == f2) f1 = 0;}], [AC_DEFINE(ARITHMETIC_FPOS_T) fpos_arithmetic="yes."]) AC_MSG_RESULT($fpos_arithmetic) ]) SQ_ARITHMETIC_FPOS_T() # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # ================================================================ # Tests for 64-bit file offset functions # Note: only AC_CHECK_FUNCS seems to properly define HAVE_FOO? # AC_CHECK_FUNCS(strtoull) AC_CHECK_FUNCS(ftello fseeko) AC_CHECK_FUNCS(ftello64 fseeko64) AC_CHECK_FUNCS(ftell64 fseek64) AC_CHECK_FUNC(stat64, [AC_MSG_CHECKING(for struct stat64) stat64_struct="no!" AC_TRY_COMPILE([#include #include #include ], [int main(void) { struct stat64 s1;} ], [AC_DEFINE(HAVE_STAT64) stat64_struct="yes."]) AC_MSG_RESULT($stat64_struct)] ) AC_CHECK_SIZEOF(off_t) AC_CHECK_SIZEOF(off64_t) AC_CHECK_SIZEOF(fpos_t) # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ################################################################################# # Now we're into our "optional features" ################################################################################# # --enable-ccmalloc - configure for compiling in ccmalloc memory checks # # The CC output variable is modified. # Requires ccmalloc version >= 0.4.0, because it uses --no-wrapper. # AC_ARG_ENABLE(ccmalloc, [ --enable-ccmalloc turn ccmalloc memory debugging on ], [case $enable_ccmalloc in yes) AC_MSG_NOTICE([enabled ccmalloc memory debugging]) CC="ccmalloc --no-wrapper $CC" ;; no) AC_MSG_NOTICE([ccmalloc memory debug/tracing disabled]) ;; *) echo "Ignoring unknown argument to --enable-ccmalloc: $enable_ccmalloc" ;; esac]) # --enable-debugging=x - set debugging level to (1-3) # # At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc). # Sets the DEBUGLEVEL preprocessor symbol to # AC_ARG_ENABLE(debugging, [ --enable-debugging set CFLAGS for debugging --enable-debugging=x also set diagnostics level to (1-3) (3 = most verbose)], [ case $enable_debugging in yes) AC_MSG_NOTICE([enabled debugging diagnostics level 0 (CFLAGS only, no verbosity)]) CFLAGS="-g -Wall" AC_DEFINE(DEBUGLEVEL, 0) ;; 1) AC_MSG_NOTICE([enabled debugging diagnostics level 1 (low verbosity)]) CFLAGS="-g -Wall" AC_DEFINE(DEBUGLEVEL, 1) ;; 2) AC_MSG_NOTICE([enabled debugging diagnostics level 2 (moderate verbosity)]) CFLAGS="-g -Wall" AC_DEFINE(DEBUGLEVEL, 2) ;; 3) AC_MSG_NOTICE([enabled debugging diagnostics level 3 (high verbosity)]) CFLAGS="-g -Wall" AC_DEFINE(DEBUGLEVEL, 3) ;; no) AC_MSG_NOTICE([debugging diagnostics disabled]) AC_DEFINE(DEBUGLEVEL, 0) ;; *) echo "Ignoring unknown argument to --enable-debugging: $enable_debugging" ;; esac]) # --enable-lfs Large File Summit (LFS) support for >2GB files # See: http://ftp.sas.com/standards/large.file/x_open.20Mar96.html # AC_ARG_ENABLE(lfs, [ --enable-lfs enable LFS, Large File Support], [case $enable_lfs in yes) AC_MSG_NOTICE([configured for optional LFS, large file support]) AC_DEFINE(_LARGEFILE_SOURCE) AC_DEFINE(_LARGEFILE64_SOURCE) AC_DEFINE(_FILE_OFFSET_BITS, 64) ;; no) ;; *) echo "Ignoring unknown argument to --enable-lfs: $enable_lfs" ;; esac]) # --enable-pvm Enable Parallel Virtual Machine (PVM) support # # Sets PVMLIBDIR, PVMINCDIR, PCMPROGS, PVMLIBS output variables # Sets SRE_ENABLE_PVM preprocessor variable. # AC_ARG_ENABLE(pvm, [ --enable-pvm enable PVM, Parallel Virtual Machine], [case $enable_pvm in yes) AC_MSG_NOTICE([enabled optional PVM (Parallel Virtual Machine) support]) PVMLIBDIR="-L${PVM_ROOT}/lib/${PVM_ARCH}" PVMINCDIR="-I${PVM_ROOT}/include" PVMLIBS="-lpvm3" AC_DEFINE(SRE_ENABLE_PVM) ;; no) AC_MSG_NOTICE([PVM (Parallel Virtual machine) support disabled]) ;; *) echo "Ignoring unknown argument to --enable-pvm: $enable_pvm" ;; esac]) AC_SUBST(PVMLIBDIR) AC_SUBST(PVMINCDIR) AC_SUBST(PVMLIBS) # Write out squidconf.h header AC_CONFIG_HEADER(squidconf.h) # Write out Makefiles, and squid.h also has some output variable substitution. AC_CONFIG_FILES(Makefile) AC_CONFIG_FILES(Testsuite/Makefile) AC_CONFIG_FILES(squid.h) AC_OUTPUT squid/install-sh0000640000175000017520000001273610463223377014125 0ustar naolivbiolinux#!/bin/sh # # install - install a program, script, or datafile # This comes from X11R5 (mit/util/scripts/install.sh). # # Copyright 1991 by the Massachusetts Institute of Technology # # Permission to use, copy, modify, distribute, and sell this software and its # documentation for any purpose is hereby granted without fee, provided that # the above copyright notice appear in all copies and that both that # copyright notice and this permission notice appear in supporting # documentation, and that the name of M.I.T. not be used in advertising or # publicity pertaining to distribution of the software without specific, # written prior permission. M.I.T. makes no representations about the # suitability of this software for any purpose. It is provided "as is" # without express or implied warranty. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. It can only install one file at a time, a restriction # shared with many OS's install programs. # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit="${DOITPROG-}" # put in absolute paths if you don't have them in your path; or use env. vars. mvprog="${MVPROG-mv}" cpprog="${CPPROG-cp}" chmodprog="${CHMODPROG-chmod}" chownprog="${CHOWNPROG-chown}" chgrpprog="${CHGRPPROG-chgrp}" stripprog="${STRIPPROG-strip}" rmprog="${RMPROG-rm}" mkdirprog="${MKDIRPROG-mkdir}" transformbasename="" transform_arg="" instcmd="$mvprog" chmodcmd="$chmodprog 0755" chowncmd="" chgrpcmd="" stripcmd="" rmcmd="$rmprog -f" mvcmd="$mvprog" src="" dst="" dir_arg="" while [ x"$1" != x ]; do case $1 in -c) instcmd="$cpprog" shift continue;; -d) dir_arg=true shift continue;; -m) chmodcmd="$chmodprog $2" shift shift continue;; -o) chowncmd="$chownprog $2" shift shift continue;; -g) chgrpcmd="$chgrpprog $2" shift shift continue;; -s) stripcmd="$stripprog" shift continue;; -t=*) transformarg=`echo $1 | sed 's/-t=//'` shift continue;; -b=*) transformbasename=`echo $1 | sed 's/-b=//'` shift continue;; *) if [ x"$src" = x ] then src=$1 else # this colon is to work around a 386BSD /bin/sh bug : dst=$1 fi shift continue;; esac done if [ x"$src" = x ] then echo "install: no input file specified" exit 1 else true fi if [ x"$dir_arg" != x ]; then dst=$src src="" if [ -d $dst ]; then instcmd=: chmodcmd="" else instcmd=mkdir fi else # Waiting for this to be detected by the "$instcmd $src $dsttmp" command # might cause directories to be created, which would be especially bad # if $src (and thus $dsttmp) contains '*'. if [ -f $src -o -d $src ] then true else echo "install: $src does not exist" exit 1 fi if [ x"$dst" = x ] then echo "install: no destination specified" exit 1 else true fi # If destination is a directory, append the input filename; if your system # does not like double slashes in filenames, you may need to add some logic if [ -d $dst ] then dst="$dst"/`basename $src` else true fi fi ## this sed command emulates the dirname command dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'` # Make sure that the destination directory exists. # this part is taken from Noah Friedman's mkinstalldirs script # Skip lots of stat calls in the usual case. if [ ! -d "$dstdir" ]; then defaultIFS=' ' IFS="${IFS-${defaultIFS}}" oIFS="${IFS}" # Some sh's can't handle IFS=/ for some reason. IFS='%' set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'` IFS="${oIFS}" pathcomp='' while [ $# -ne 0 ] ; do pathcomp="${pathcomp}${1}" shift if [ ! -d "${pathcomp}" ] ; then $mkdirprog "${pathcomp}" else true fi pathcomp="${pathcomp}/" done fi if [ x"$dir_arg" != x ] then $doit $instcmd $dst && if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi && if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi && if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi && if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi else # If we're going to rename the final executable, determine the name now. if [ x"$transformarg" = x ] then dstfile=`basename $dst` else dstfile=`basename $dst $transformbasename | sed $transformarg`$transformbasename fi # don't allow the sed command to completely eliminate the filename if [ x"$dstfile" = x ] then dstfile=`basename $dst` else true fi # Make a temp file name in the proper directory. dsttmp=$dstdir/#inst.$$# # Move or copy the file name to the temp name $doit $instcmd $src $dsttmp && trap "rm -f ${dsttmp}" 0 && # and set any options; do chmod last to preserve setuid bits # If any of these fail, we abort the whole thing. If we want to # ignore errors from any of these, just make sure not to ignore # errors from the above "$doit $instcmd $src $dsttmp" command. if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi && if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi && if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi && if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi && # Now rename the file to the real destination. $doit $rmcmd -f $dstdir/$dstfile && $doit $mvcmd $dsttmp $dstdir/$dstfile fi && exit 0 squid/squid.h.in0000640000175000017520000004213710463223377014025 0ustar naolivbiolinux/* @configure_input@ */ /***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SQUIDH_INCLUDED #define SQUIDH_INCLUDED /* squid.h * Header file for my library of sequence functions. * * CVS $Id: squid.h.in,v 1.6 2003/04/14 16:00:16 eddy Exp $ */ #include #include #include #include /* for sysconf() #define's */ #if DEBUGLEVEL > 0 #include /* for SQD_DASSERT1(), etc. */ #endif /***************************************************************** * Integers of guaranteed size. (used for instance in gsi.c, gsi2.c) * These are set by the ./configure script; if they show up as FIXME, * they must be manually edited to appropriate type definitions. You * do need 64-bit integers in the current code; email me if this * prevents you from compiling SQUID and tell me your system (I don't * know of any systems that don't have 64-bit integers these days). *****************************************************************/ typedef @SQD_UINT16@ sqd_uint16; typedef @SQD_UINT32@ sqd_uint32; typedef @SQD_UINT64@ sqd_uint64; #ifdef USE_HOST_BYTESWAP_FUNCTIONS #include /* only for ntohl() and friends. */ #include /* only for ntohl() and friends. */ #define sre_ntoh16(x) ntohs(x); #define sre_ntoh32(x) ntohl(x); #define sre_hton16(x) htons(x); #define sre_hton32(x) htonl(x); #endif /* USE_HOST_BYTESWAP_FUNCTIONS */ /* Library version info is made available as a global to * any interested program. These are defined in iupac.c * with the other globals. */ extern char squid_version[]; /* version number */ extern char squid_date[]; /* date of release */ extern int squid_errno; /* error codes */ /**************************************************** * Error codes returned by squid library functions (squid_errno) ****************************************************/ #define SQERR_OK 0 /* no error */ #define SQERR_UNKNOWN 1 /* generic error, unidentified */ #define SQERR_NODATA 2 /* unexpectedly NULL stream */ #define SQERR_MEM 3 /* malloc or realloc failed */ #define SQERR_NOFILE 4 /* file not found */ #define SQERR_FORMAT 5 /* file format not recognized */ #define SQERR_PARAMETER 6 /* bad parameter passed to func */ #define SQERR_DIVZERO 7 /* error in sre_math.c */ #define SQERR_INCOMPAT 8 /* incompatible parameters */ #define SQERR_EOD 9 /* end-of-data (often normal) */ /**************************************************** * Single sequence information ****************************************************/ #define SQINFO_NAMELEN 64 #define SQINFO_DESCLEN 128 struct seqinfo_s { int flags; /* what extra data are available */ char name[SQINFO_NAMELEN];/* up to 63 characters of name */ char id[SQINFO_NAMELEN]; /* up to 63 char of database identifier */ char acc[SQINFO_NAMELEN]; /* up to 63 char of database accession # */ char desc[SQINFO_DESCLEN];/* up to 127 char of description */ int len; /* length of this seq */ int start; /* (1..len) start position on source seq */ int stop; /* (1..len) end position on source seq */ int olen; /* original length of source seq */ int type; /* kRNA, kDNA, kAmino, or kOther */ char *ss; /* 0..len-1 secondary structure string */ char *sa; /* 0..len-1 % side chain surface access. */ }; typedef struct seqinfo_s SQINFO; #define SQINFO_NAME (1 << 0) #define SQINFO_ID (1 << 1) #define SQINFO_ACC (1 << 2) #define SQINFO_DESC (1 << 3) #define SQINFO_START (1 << 4) #define SQINFO_STOP (1 << 5) #define SQINFO_LEN (1 << 6) #define SQINFO_TYPE (1 << 7) #define SQINFO_OLEN (1 << 8) #define SQINFO_SS (1 << 9) #define SQINFO_SA (1 << 10) /**************************************************** * Sequence alphabet: see also iupac.c ****************************************************/ /* IUPAC symbols defined globally in iupac.c */ struct iupactype { char sym; /* character representation */ char symcomp; /* complement (regular char */ char code; /* my binary rep */ char comp; /* binary encoded complement */ }; extern struct iupactype iupac[]; #define IUPACSYMNUM 17 extern char *stdcode1[]; /* 1-letter amino acid translation code */ extern char *stdcode3[]; /* 3-letter amino acid translation code */ extern float dnafq[]; /* nucleotide occurrence frequencies */ extern float aafq[]; /* amino acid occurrence frequencies */ extern char aa_alphabet[]; /* amino acid alphabet */ extern int aa_index[]; /* convert 0..19 indices to 0..26 */ /* valid symbols in IUPAC code */ #define NUCLEOTIDES "ACGTUNRYMKSWHBVDacgtunrymkswhbvd" #define AMINO_ALPHABET "ACDEFGHIKLMNPQRSTVWY" #define DNA_ALPHABET "ACGT" #define RNA_ALPHABET "ACGU" #define WHITESPACE " \t\n" #define isgap(c) ((c) == ' ' || (c) == '.' || (c) == '_' || (c) == '-' || (c) == '~') /**************************************************** * Sequence i/o: originally from Don Gilbert's readseq ****************************************************/ #include "msa.h" /* for multiple sequence alignment support */ /* buffer size for reading in lines from sequence files*/ #define LINEBUFLEN 4096 /* sequence types parsed by Seqtype() */ /* note that these must match hmmAMINO and hmmNUCLEIC in HMMER */ #define kOtherSeq 0 /* hmmNOTSETYET */ #define kDNA 1 #define kRNA 2 /* hmmNUCLEIC */ #define kAmino 3 /* hmmAMINO */ /* Unaligned sequence file formats recognized * Coexists with definitions of multiple alignment formats in msa.h: * >100 reserved for alignment formats * <100 reserved for unaligned formats * 0 reserved for unknown * * Some "legacy" formats are supported only when explicitly * requested; not autodetected by SeqfileFormat(). * * DON'T REASSIGN THESE CODES. They're written into * GSI index files. You can use new ones, but reassigning * the sense of old ones will break GSI indices. * Alignment format codes were reassigned with the creation * of msa.c, but before Stockholm format, there were no * indexed alignment databases. */ #define SQFILE_UNKNOWN 0 /* unknown format */ #define SQFILE_IG 1 /* Intelligenetics (!) */ #define SQFILE_GENBANK 2 /* GenBank flatfile */ /* 3 was A2M. Now an alignment format */ #define SQFILE_EMBL 4 /* EMBL or Swissprot flatfile */ #define SQFILE_GCG 5 /* GCG single sequence files */ #define SQFILE_STRIDER 6 /* MacStrider (!!) */ #define SQFILE_FASTA 7 /* FASTA format: default */ #define SQFILE_ZUKER 8 /* Zuker MFOLD format (legacy) */ #define SQFILE_IDRAW 9 /* Idraw-style PostScript (legacy) */ /* 10 was SELEX. Now alignment format */ /* 11 was MSF. Now alignment format */ #define SQFILE_PIR 12 /* PIR format */ #define SQFILE_RAW 13 /* raw sequence */ #define SQFILE_SQUID 14 /* my obsolete squid format */ /* 15 was kXPearson, extended FASTA; withdrawn */ #define SQFILE_GCGDATA 16 /* GCG data library file */ /* 17 was Clustal. Now alignment format*/ #define IsUnalignedFormat(fmt) ((fmt) && (fmt) < 100) #include "ssi.h" struct ReadSeqVars { FILE *f; /* open file pointer */ char *fname; /* name of file; used for diagnostics */ int linenumber; /* what line are we on in the file */ char *buf; /* dynamically allocated sre_fgets() buffer */ int buflen; /* allocation length for buf */ int ssimode; /* SSI_OFFSET_I32 or SSI_OFFSET_I64 */ SSIOFFSET ssioffset; /* disk offset to last line read into buf */ SSIOFFSET r_off; /* offset to start of record */ SSIOFFSET d_off; /* offset to start of sequence data */ int rpl; /* residues per data line for this file; -1 if unset, 0 if invalid */ int lastrpl; /* rpl on last line seen */ int maxrpl; /* max rpl on any line of the file */ int bpl; /* bytes per data line; -1 if unset, 0 if invalid */ int lastbpl; /* bpl on last line seen */ int maxbpl; /* max bpl on any line of the file */ char *seq; /* growing sequence during parse */ SQINFO *sqinfo; /* name, id, etc, gathered during parse */ char *sp; int seqlen; /* current sequence length */ int maxseq; /* current allocation length for seq */ int format; /* format of seqfile we're reading. */ int do_gzip; /* TRUE if f is a pipe from gzip -dc */ int do_stdin; /* TRUE if f is stdin */ /* An (important) hack for sequential access of multiple alignment files: * we read the whole alignment in, * and then copy it one sequence at a time into seq and sqinfo. * It is active if msa is non NULL. * msa->lastidx is reused/overloaded: used to keep track of what * seq we'll return next. * afp->format is the real format, while SQFILE->format is kMSA. * Because we keep it in the SQFILE structure, * ReadSeq() and friends are always reentrant for multiple seqfiles. */ MSA *msa; MSAFILE *afp; }; typedef struct ReadSeqVars SQFILE; /**************************************************** * Cluster analysis and phylogenetic tree support ****************************************************/ /* struct phylo_s - a phylogenetic tree * * For N sequences, there will generally be an array of 0..N-2 * phylo_s structures representing the nodes of a tree. * [0] is the root. The indexes of left and * right children are somewhat confusing so be careful. The * indexes can have values of 0..2N-2. If they are 0..N-1, they * represent pointers to individual sequences. If they are * >= N, they represent pointers to a phylo_s structure * at (index - N). */ struct phylo_s { int parent; /* index of parent, N..2N-2, or -1 for root */ int left; /* index of one of the branches, 0..2N-2 */ int right; /* index of other branch, 0..2N-2 */ float diff; /* difference score between seqs */ float lblen; /* left branch length */ float rblen; /* right branch length */ char *is_in; /* 0..N-1 flag array, 1 if seq included */ int incnum; /* number of seqs included at this node */ }; /* Strategies for cluster analysis; cluster by mean distance, * minimum distance, or maximum distance. */ enum clust_strategy { CLUSTER_MEAN, CLUSTER_MAX, CLUSTER_MIN }; /**************************************************** * Generic data structure support ****************************************************/ /* a struct intstack_s implements a pushdown stack for storing * single integers. */ struct intstack_s { int data; struct intstack_s *nxt; }; /**************************************************** * Binary nucleotide alphabet support ****************************************************/ /* Binary encoding of the IUPAC code for nucleotides * * four-bit "word", permitting rapid degenerate matching * A C G T/U * 0 0 1 0 */ #define NTA 8 #define NTC 4 #define NTG 2 #define NTT 1 #define NTU 1 #define NTN 15 /* A|C|G|T */ #define NTR 10 /* A|G */ #define NTY 5 /* C|T */ #define NTM 12 /* A|C */ #define NTK 3 /* G|T */ #define NTS 6 /* C|G */ #define NTW 9 /* A|T */ #define NTH 13 /* A|C|T */ #define NTB 7 /* C|G|T */ #define NTV 14 /* A|C|G */ #define NTD 11 /* A|G|T */ #define NTGAP 16 /* GAP */ #define NTEND 0 /* null string terminator */ /* ntmatch(): bitwise comparison of two nuc's * note that it's sensitive to the order; * probe may be degenerate but target should not be */ #define ntmatch(probe, target) ((probe & target) == target) /**************************************************** * Support for a portable, flexible Getopt() ****************************************************/ /* Structure: opt_s * * Structure for declaring options to a main(). */ struct opt_s { char *name; /* name of option, e.g. "--option1" or "-o" */ int single; /* TRUE if a single letter option */ int argtype; /* for typechecking, e.g. sqdARG_INT */ }; /* acceptable argtype's... */ #define sqdARG_NONE 0 /* no argument */ #define sqdARG_INT 1 /* something that atoi() can grok */ #define sqdARG_FLOAT 2 /* something that atof() can grok */ #define sqdARG_CHAR 3 /* require single character or digit */ #define sqdARG_STRING 4 /* anything goes */ /**************************************************** * Support for convenient Perl-y regexp matching * See hsregexp.c for copyright notice: this code is derived * from Henry Spencer's freely distributed regexp library. ****************************************************/ #define NSUBEXP 10 typedef struct sqd_regexp { char *startp[NSUBEXP]; char *endp[NSUBEXP]; char regstart; /* Internal use only. */ char reganch; /* Internal use only. */ char *regmust; /* Internal use only. */ int regmlen; /* Internal use only. */ char program[1]; /* Unwarranted chumminess with compiler. */ } sqd_regexp; /* Strparse() defines and manages these. * sqd_parse[0] contains the substring that matched the pattern. * sqd_parse[1-9] contain substrings matched with ()'s. */ extern char *sqd_parse[10]; /**************************************************** * Portable detection of multiprocessor # of CPUs. * #include * long foo = SQD_NPROC; * returns the number of available processors. * if foo == -1, we failed. ****************************************************/ /* Our problem here is that POSIX apparently doesn't specify * a standard for how to get sysconf() to report the number of * processors on-line. _SC_NPROCESSORS_ONLN is specified * by SVR4.0MP. Thanks to W. Gish for help here. */ #undef SQD_NPROC #if defined(_SC_NPROCESSORS_ONLN) /* Sun Solaris, Digital UNIX */ #define SQD_NPROC sysconf(_SC_NPROCESSORS_ONLN) #elif defined(_SC_NPROC_ONLN) /* Silicon Graphics IRIX */ #define SQD_NPROC sysconf(_SC_NPROC_ONLN) #elif defined(_SC_NPROCESSORS_CONF) /* _ONLN is favored over _CONF */ #define SQD_NPROC sysconf(_SC_NPROCESSORS_CONF) #else /* some systems don't support getting ncpu via sysconf() */ #define SQD_NPROC -1 #endif /**************************************************** * Three levels of debugging printf's and assert's * level 1: little impact on verbosity or performance * level 2: moderate impact * level 3: high impact * Example: * SQD_DPRINTF3(("Matrix row %d col %d = %f\n", i, j, val)); * Note the double parentheses; these are important. ****************************************************/ #ifndef DEBUGLEVEL #define DEBUGLEVEL 0 #endif #if (DEBUGLEVEL >= 1) #define SQD_DPRINTF1(x) printf x #define SQD_DASSERT1(x) assert x #else #define SQD_DPRINTF1(x) #define SQD_DASSERT1(x) #endif #if (DEBUGLEVEL >= 2) #define SQD_DPRINTF2(x) printf x #define SQD_DASSERT2(x) assert x #else #define SQD_DPRINTF2(x) #define SQD_DASSERT2(x) #endif #if (DEBUGLEVEL >= 3) #define SQD_DPRINTF3(x) printf x #define SQD_DASSERT3(x) assert x #else #define SQD_DPRINTF3(x) #define SQD_DASSERT3(x) #endif /* PANIC is called for failures of Std C/POSIX functions, * instead of my own functions. Panic() calls perror() and exits * abnormally. */ #define PANIC Panic(__FILE__, __LINE__) /* Malloc/realloc calls are wrapped */ #define MallocOrDie(x) sre_malloc(__FILE__, __LINE__, (x)) #define ReallocOrDie(x,y) sre_realloc(__FILE__, __LINE__, (x), (y)) /**************************************************** * Miscellaneous macros and defines ****************************************************/ #define SQDCONST_E 2.71828182845904523536028747135 #define SQDCONST_PI 3.14159265358979323846264338328 /* must declare swapfoo to use SWAP() */ #define SWAP(a,b) {swapfoo = b; b = a; a = swapfoo;} #define ScalarsEqual(a,b) (fabs((a)-(b)) < 1e-7) #ifndef MIN #define MIN(a,b) (((a)<(b))?(a):(b)) #endif #ifndef MAX #define MAX(a,b) (((a)>(b))?(a):(b)) #endif /* For convenience and (one hopes) clarity in boolean tests: */ #ifndef TRUE #define TRUE 1 #endif #ifndef FALSE #define FALSE 0 #endif /* Somewhere, there is a universe in which Unix vendors comply * with the ANSI C standard. Unfortunately, it is not ours: */ #ifndef EXIT_SUCCESS #define EXIT_SUCCESS 0 #endif #ifndef EXIT_FAILURE #define EXIT_FAILURE 1 #endif #include "sqfuncs.h" /* squid function declarations */ #include "sre_random.h" /* random number generator and samplers */ #include "vectorops.h" /* vector operations */ #endif /* SQUIDH_INCLUDED */ squid/squidconf.h.in0000640000175000017520000000770410463223377014674 0ustar naolivbiolinux/* @configure_input@ */ /***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SQUIDCONFH_INCLUDED #define SQUIDCONFH_INCLUDED /* squidconf.h * Captures #define's generated by the ./configure script; * this file must be the first header included in any squid file. */ /***************************************************************** * Version info that's set by the ./configure script. *****************************************************************/ #undef SQUID_VERSION #undef SQUID_DATE #undef SQUID_COPYRIGHT #undef SQUID_LICENSE /***************************************************************** * Optional feature enabling that's done by the ./configure script. *****************************************************************/ /* --enable-debugging=x debugging diagnostics (development versions only) */ #ifndef DEBUGLEVEL #undef DEBUGLEVEL #endif /* --enable-lfs Large File Summit (LFS) support for >2GB files */ #undef _LARGEFILE_SOURCE #undef _LARGEFILE64_SOURCE #undef _FILE_OFFSET_BITS /* --enable-pvm Parallel Virtual Machine (PVM) */ #undef SRE_ENABLE_PVM /***************************************************************** * Sizes of integer types. * various things are set by ./configure; the code * uses WORDS_BIGENDIAN and USE_HOST_BYTESWAP_FUNCTIONS. *****************************************************************/ #undef WORDS_BIGENDIAN #define SIZEOF_UNSIGNED_SHORT 0 #define SIZEOF_UNSIGNED_INT 0 #define SIZEOF_UNSIGNED_LONG 0 #define SIZEOF_UNSIGNED_LONG_LONG 0 #undef HAVE_NTOHS /* if defined, system provides ntohs() */ #undef HAVE_NTOHL /* if defined, system provides ntohl() */ #undef HAVE_HTONS /* if defined, system provides htons() */ #undef HAVE_HTONL /* if defined, system provides htonl() */ #undef HAVE_STRTOUL #undef HAVE_STRTOULL #if defined HAVE_NTOHL && defined HAVE_NTOHS && defined HAVE_HTONS && defined HAVE_HTONL #define USE_HOST_BYTESWAP_FUNCTIONS 1 #endif /* On some machines like Alphas, strtoull doesn't exist, but since * longs are 64 bits anyway and we never call strtoull except for * a sqd_uint64, strotul will work... probably. */ #if SIZEOF_UNSIGNED_LONG == 8 && defined HAVE_STRTOUL && ! defined HAVE_STRTOULL #define strtoull strtoul #define HAVE_STRTOULL /* liar! */ #endif /***************************************************************** * Can we support arithmetic 64-bit file offsets? * four possible models checked for: * 1. ftello(), fseeko() with 64-bit off_t * 2. ftello64(), fseeko64() with 64-bit off64_t * 3. ftell64(), fseek64() with 64-bit integer * 4. fgetpos(), fsetpos() with an fpos_t that happens to be a * 64-bit integer, even though ANSI says we're not supposed to know * anything about fpos_t's internals. * Based on what ./configure tells us about these, we set * HAS_64BIT_FILE_OFFSETS or not. * * In all cases, we also check that we HAVE_STRTOULL; ssi.c has to * make a call. HP/UX 11, for example, does not provide strtoull(), * despite being 64-bit. *****************************************************************/ #undef HAVE_FTELLO #undef HAVE_FSEEKO #undef HAVE_FTELLO64 #undef HAVE_FSEEKO64 #undef HAVE_FTELL64 #undef HAVE_FSEEK64 #undef ARITHMETIC_FPOS_T #undef HAVE_STAT64 #define SIZEOF_FPOS_T -1 #define SIZEOF_OFF_T -1 #define SIZEOF_OFF64_T -1 #if defined HAVE_STRTOULL && defined HAVE_FTELLO && defined HAVE_FSEEKO && SIZEOF_OFF_T == 8 #define HAS_64BIT_FILE_OFFSETS 1 #elif defined HAVE_STRTOULL && defined HAVE_FTELLO64 && defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8 #define HAS_64BIT_FILE_OFFSETS 1 #elif defined HAVE_STRTOULL && defined HAVE_FTELL64 && defined HAVE_FSEEK64 #define HAS_64BIT_FILE_OFFSETS 1 #elif defined HAVE_STRTOULL && defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8 #define HAS_64BIT_FILE_OFFSETS 1 #else #undef HAS_64BIT_FILE_OFFSETS #endif #endif /* SQUIDCONFH_INCLUDED */ squid/a2m.c0000640000175000017520000000531110463223377012736 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* a2m.c * * reading/writing A2M (aligned FASTA) files. * * CVS $Id: a2m.c,v 1.2 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "msa.h" /* Function: ReadA2M() * Date: SRE, Sun Jun 6 17:11:29 1999 [bus from Madison 1999 worm mtg] * * Purpose: Parse an alignment read from an open A2M format * alignment file. A2M is a single alignment format. * Return the alignment, or NULL if we've already * read the alignment. * * Args: afp - open alignment file * * Returns: MSA * - an alignment object. * Caller responsible for an MSAFree() */ MSA * ReadA2M(MSAFILE *afp) { MSA *msa; char *buf; char *name; char *desc; char *seq; int idx; int len1, len2; if (feof(afp->f)) return NULL; name = NULL; msa = MSAAlloc(10, 0); idx = 0; while ((buf = MSAFileGetLine(afp)) != NULL) { if (*buf == '>') { buf++; /* skip the '>' */ if ((name = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) Die("Blank name in A2M file %s (line %d)\n", afp->fname, afp->linenumber); desc = sre_strtok(&buf, "\n", &len2); idx = GKIStoreKey(msa->index, name); if (idx >= msa->nseqalloc) MSAExpand(msa); msa->sqname[idx] = sre_strdup(name, len1); if (desc != NULL) MSASetSeqDescription(msa, idx, desc); msa->nseq++; } else if (name != NULL) { if ((seq = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) continue; msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], seq, len1); } } if (name == NULL) { MSAFree(msa); return NULL; } MSAVerifyParse(msa); return msa; } /* Function: WriteA2M() * Date: SRE, Sun Jun 6 17:40:35 1999 [bus from Madison, 1999 worm mtg] * * Purpose: Write an "aligned FASTA" (aka a2m, to UCSC) formatted * alignment. * * Args: fp - open FILE to write to. * msa - alignment to write * * Returns: void */ void WriteA2M(FILE *fp, MSA *msa) { int idx; /* sequence index */ int pos; /* position in sequence */ char buf[64]; /* buffer for individual lines */ int cpl = 60; /* char per line; must be < 64 unless buf is bigger */ buf[cpl] = '\0'; for (idx = 0; idx < msa->nseq; idx++) { fprintf(fp, ">%s %s\n", msa->sqname[idx], (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) ? msa->sqdesc[idx] : ""); for (pos = 0; pos < msa->alen; pos+=cpl) { strncpy(buf, &(msa->aseq[idx][pos]), cpl); fprintf(fp, "%s\n", buf); } } } squid/afetch_main.c0000640000175000017520000001170710463223377014523 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* afetch_main.c * SRE, Tue Nov 9 18:47:02 1999 [Saint Louis] * * afetch -- a program to extract alignments from the Pfam database * * CVS $Id: afetch_main.c,v 1.6 2003/05/26 16:21:50 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "msa.h" #include "ssi.h" static char banner[] = "afetch - retrieve an alignment from Pfam"; static char usage[] = "\ Usage: afetch [-options] \n\ or: afetch --index \n\ \n\ Get an alignment from a database.\n\ Available options:\n\ -h : help; print version and usage info\n\ "; static char experts[] = "\ --index : construct indices for the database\n\ "; static struct opt_s OPTIONS[] = { { "-h", TRUE, sqdARG_NONE }, { "--index", FALSE, sqdARG_NONE } }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *afile; /* name of alignment file to read */ MSAFILE *afp; /* pointer to open index file */ char *key; /* name/accession of alignment to fetch */ MSA *msa; /* the fetched alignment */ int format; /* format of afile */ int do_index; /* TRUE to index instead of retrieve */ char *optname; char *optarg; int optind; /*********************************************** * Parse the command line ***********************************************/ /* initializations and defaults */ format = MSAFILE_STOCKHOLM; /* period. It's the only multi-MSA file format. */ do_index = FALSE; key = NULL; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "--index") == 0) { do_index = TRUE; } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if ((do_index && argc - optind != 1) || (! do_index && argc - optind != 2)) Die("Incorrect number of command line arguments.\n%s\n", usage); afile = argv[optind++]; if (! do_index) key = argv[optind++]; if ((afp = MSAFileOpen(afile, format, NULL)) == NULL) Die("Alignment file %s could not be opened for reading", afile); /*********************************************** * Section 1. Alignment database indexing ***********************************************/ if (do_index) { int mode; char *ssifile; SSIINDEX *si; int fh; int status; SSIOFFSET offset; int n = 0; /* Not that we're expecting an alignment file so * large that it would require a 64-bit index, but... */ if ((mode = SSIRecommendMode(afile)) == -1) Die("File %s doesn't exist, or is too large for your OS", afile); ssifile = sre_strdup(afile, -1); sre_strcat(&ssifile, -1, ".ssi", -1); if ((si = SSICreateIndex(mode)) == NULL) Die("Couldn't allocate/initialize the new SSI index"); if (SSIAddFileToIndex(si, afile, afp->format, &fh) != 0) Die("SSIAddFileToIndex() failed"); status = SSIGetFilePosition(afp->f, mode, &offset); if (status != 0) Die("SSIGetFilePosition() failed"); while ((msa = MSAFileRead(afp)) != NULL) { if (msa->name == NULL) Die("SSI index requires that every MSA has a name"); status = SSIAddPrimaryKeyToIndex(si, msa->name, fh, &offset, NULL, 0); if (status != 0) Die("SSIAddPrimaryKeyToIndex() failed"); if (msa->acc != NULL) { status = SSIAddSecondaryKeyToIndex(si, msa->acc, msa->name); if (status != 0) Die("SSIAddSecondaryKeyToIndex() failed"); } status = SSIGetFilePosition(afp->f, mode, &offset); if (status != 0) Die("SSIGetFilePosition() failed"); n++; MSAFree(msa); } status = SSIWriteIndex(ssifile, si); if (status != 0) Die("SSIWriteIndex() failed"); printf ("%d alignments indexed in SSI index %s\n", n, ssifile); free(ssifile); MSAFileClose(afp); SSIFreeIndex(si); SqdClean(); exit (0); /* exit indexing program here */ } /*********************************************** * Section 2. Alignment retrieval ***********************************************/ /* Indexed retrieval: */ if (afp->ssi != NULL) { if (! MSAFilePositionByKey(afp, key)) Die("No such alignment %s found in file %s", key, afile); msa = MSAFileRead(afp); } /* Brute force retrieval: */ else { while ((msa = MSAFileRead(afp)) != NULL) { if (strcmp(msa->name, key) == 0) break; if (strcmp(msa->acc, key) == 0) break; MSAFree(msa); } } if (msa == NULL) Die("Failed to retrieve %s from file %s", key, afile); /* Output the alignment we retrieved */ WriteStockholm(stdout, msa); MSAFileClose(afp); MSAFree(msa); exit (0); } squid/aligneval.c0000640000175000017520000003743410463223377014234 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* aligneval.c * * Comparison of multiple alignments. Three functions are * provided, using subtly different scoring schemes: * CompareMultAlignments() - basic scoring scheme * CompareRefMultAlignments() - only certain "canonical" columns * are scored * * The similarity measure is a fractional alignment identity averaged * over all sequence pairs. The score for all pairs is: * (identically aligned symbols) / (total aligned columns in * known alignment) * * A column c is identically aligned for sequences i, j if: * 1) both i,j have a symbol aligned in column c, and the * same pair of symbols is aligned somewhere in the test * alignment * 2) S[i][c] is aligned to a gap in sequence j, and that symbol * is aligned to a gap in the test alignment * 3) converse of 2) * * * The algorithm is as follows: * 1) For each known/test aligned pair of sequences (k1,k2 and t1,t2) * construct a list for each sequence, in which for every * counted symbol we record the raw index of the symbol in * the other sequence that it aligns to, or -1 if it aligns * to a gap or uncounted symbol. * * 2) Compare the list for k1 to the list for t1 and count an identity * for each correct alignment. * * 3) Repeat 2) for comparing k2 to t2. Note that this means correct sym/sym * alignments count for 2; correct sym/gap alignments count for 1. * * 4) The score is (identities from 2 + identities from 3) / * (totals from 2 + totals from 3). * * Written originally for koala's ss2 pairwise alignment package. * * Sean Eddy, Sun Nov 1 12:45:11 1992 * SRE, Thu Jul 29 16:47:18 1993: major revision: all functions replaced by new algorithm * CVS $Id: aligneval.c,v 1.9 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "sre_random.h" static int make_alilist(char *s1, char *s2, int **ret_s1_list, int *ret_listlen); static int make_ref_alilist(int *refcoords, char *k1, char *k2, char *s1, char *s2, int **ret_s1_list, int *ret_listlen); static int compare_lists(int *k1, int *k2, int *t1, int *t2, int len1, int len2, float *ret_sc); /* Function: ComparePairAlignments * * Purpose: Calculate and return a number representing how well two different alignments * of a pair of sequences compare. The number is, roughly speaking, * the fraction of columns which are identically aligned. * * For all columns c in which either known1[c] or known2[c] * is a non-gap, count an identity if those same symbols are * aligned somewhere in calc1/calc2. The score is identities/total * columns examined. (i.e. fully gapped columns don't count) * * more explicitly, identities come from: * both known and test aligned pairs have the same symbol in the first sequence aligned to * a gap in the second sequence; * both known and test aligned pairs have the same symbol in the second sequence * aligned to a gap in the first sequence; * the known alignment has symbols aligned at this column, and the test * alignment aligns the same two symbols. * * Args: known1, known2: trusted alignment of two sequences * calc1, calc2: test alignment of two sequences * * Return: Returns -1.0 on internal failure. */ float ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2) { int *klist1; int *klist2; int *tlist1; int *tlist2; int len1, len2; float score; if (! make_alilist(calc1, calc2, &tlist1, &len1)) return -1.0; if (! make_alilist(calc2, calc1, &tlist2, &len2)) return -1.0; if (! make_alilist(known1, known2, &klist1, &len1)) return -1.0; if (! make_alilist(known2, known1, &klist2, &len2)) return -1.0; if (! compare_lists(klist1, klist2, tlist1, tlist2, len1, len2, &score)) return -1.0; free(klist1); free(klist2); free(tlist1); free(tlist2); return score; } /* Function: CompareRefPairAlignments() * * Same as above, but the only columns that count are the ones * with indices in *refcoord. *refcoord and the known1, known2 * pair must be in sync with each other (come from the same * multiple sequence alignment) * * Args: ref - 0..alen-1 array of 1 or 0 * known1,known2 - trusted alignment * calc1, calc2 - test alignment * * Return: the fractional alignment identity on success, -1.0 on failure. */ float CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2) { int *klist1; int *klist2; int *tlist1; int *tlist2; int len1, len2; float score; if (! make_ref_alilist(ref, known1, known2, calc1, calc2, &tlist1, &len1)) return -1.0; if (! make_ref_alilist(ref, known2, known1, calc2, calc1, &tlist2, &len2)) return -1.0; if (! make_ref_alilist(ref, known1, known2, known1, known2, &klist1, &len1)) return -1.0; if (! make_ref_alilist(ref, known2, known1, known2, known1, &klist2, &len2)) return -1.0; if (! compare_lists(klist1, klist2, tlist1, tlist2, len1, len2, &score)) return -1.0; free(klist1); free(klist2); free(tlist1); free(tlist2); return score; } /* Function: make_alilist() * * Purpose: Construct a list (array) mapping the raw symbols of s1 * onto the indexes of the aligned symbols in s2 (or -1 * for gaps in s2). The list (s1_list) will be of the * length of s1's raw sequence. * * Args: s1 - sequence to construct the list for * s2 - sequence s1 is aligned to * ret_s1_list - RETURN: the constructed list (caller must free) * ret_listlen - RETURN: length of the list * * Returns: 1 on success, 0 on failure */ static int make_alilist(char *s1, char *s2, int **ret_s1_list, int *ret_listlen) { int *s1_list; int col; /* column position in alignment */ int r1, r2; /* raw symbol index at current col in s1, s2 */ /* Malloc for s1_list. It can't be longer than s1 itself; we just malloc * for that (and waste a wee bit of space) */ s1_list = (int *) MallocOrDie (sizeof(int) * strlen(s1)); r1 = r2 = 0; for (col = 0; s1[col] != '\0'; col++) { /* symbol in s1? Record what it's aligned to, and bump * the r1 counter. */ if (! isgap(s1[col])) { s1_list[r1] = isgap(s2[col]) ? -1 : r2; r1++; } /* symbol in s2? bump the r2 counter */ if (! isgap(s2[col])) r2++; } *ret_listlen = r1; *ret_s1_list = s1_list; return 1; } /* Function: make_ref_alilist() * * Purpose: Construct a list (array) mapping the raw symbols of s1 * which are under canonical columns of the ref alignment * onto the indexes of the aligned symbols in s2 (or -1 * for gaps in s2 or noncanonical symbols in s2). * * Args: ref: - array of indices of canonical coords (1 canonical, 0 non) * k1 - s1's known alignment (w/ respect to refcoords) * k2 - s2's known alignment (w/ respect to refcoords) * s1 - sequence to construct the list for * s2 - sequence s1 is aligned to * ret_s1_list - RETURN: the constructed list (caller must free) * ret_listlen - RETURN: length of the list * * Returns: 1 on success, 0 on failure */ /*ARGSUSED*/ static int make_ref_alilist(int *ref, char *k1, char *k2, char *s1, char *s2, int **ret_s1_list, int *ret_listlen) { int *s1_list; int col; /* column position in alignment */ int r1, r2; /* raw symbol index at current col in s1, s2 */ int *canons1; /* flag array, 1 if position i in s1 raw seq is canonical */ int lpos; /* position in list */ /* Allocations. No arrays can exceed the length of their * appropriate parent (s1 or s2) */ s1_list = (int *) MallocOrDie (sizeof(int) * strlen(s1)); canons1 = (int *) MallocOrDie (sizeof(int) * strlen(s1)); /* First we use refcoords and k1,k2 to construct an array of 1's * and 0's, telling us whether s1's raw symbol number i is countable. * It's countable simply if it's under a canonical column. */ r1 = 0; for (col = 0; k1[col] != '\0'; col++) { if (! isgap(k1[col])) { canons1[r1] = ref[col] ? 1 : 0; r1++; } } /* Now we can construct the list. We don't count pairs if the sym in s1 * is non-canonical. * We have to keep separate track of our position in the list (lpos) * from our positions in the raw sequences (r1,r2) */ r1 = r2 = lpos = 0; for (col = 0; s1[col] != '\0'; col++) { if (! isgap(s1[col]) && canons1[r1]) { s1_list[lpos] = isgap(s2[col]) ? -1 : r2; lpos++; } if (! isgap(s1[col])) r1++; if (! isgap(s2[col])) r2++; } free(canons1); *ret_listlen = lpos; *ret_s1_list = s1_list; return 1; } /* Function: compare_lists() * * Purpose: Given four alignment lists (k1,k2, t1,t2), calculate the * alignment score. * * Args: k1 - list of k1's alignment to k2 * k2 - list of k2's alignment to k1 * t1 - list of t1's alignment to t2 * t2 - list of t2's alignment to t2 * len1 - length of k1, t1 lists (same by definition) * len2 - length of k2, t2 lists (same by definition) * ret_sc - RETURN: identity score of alignment * * Return: 1 on success, 0 on failure. */ static int compare_lists(int *k1, int *k2, int *t1, int *t2, int len1, int len2, float *ret_sc) { float id; float tot; int i; id = tot = 0.0; for (i = 0; i < len1; i++) { tot += 1.0; if (t1[i] == k1[i]) id += 1.0; } for ( i = 0; i < len2; i++) { tot += 1.0; if (k2[i] == t2[i]) id += 1.0; } *ret_sc = id / tot; return 1; } /* Function: CompareMultAlignments * * Purpose: Invokes pairwise alignment comparison for every possible pair, * and returns the average score over all N(N-1) of them or -1.0 * on an internal failure. * * Can be slow for large N, since it's quadratic. * * Args: kseqs - trusted multiple alignment * tseqs - test multiple alignment * N - number of sequences * * Return: average identity score, or -1.0 on failure. */ float CompareMultAlignments(char **kseqs, char **tseqs, int N) { int i, j; /* counters for sequences */ float score; float tot_score = 0.0; /* do all pairwise comparisons */ for (i = 0; i < N; i++) for (j = i+1; j < N; j++) { score = ComparePairAlignments(kseqs[i], kseqs[j], tseqs[i], tseqs[j]); if (score < 0.0) return -1.0; tot_score += score; } return ((tot_score * 2.0) / ((float) N * ((float) N - 1.0))); } /* Function: CompareRefMultAlignments() * * Purpose: Same as above, except an array of reference coords for * the canonical positions of the known alignment is also * provided. * * Args: ref : 0..alen-1 array of 1/0 flags, 1 if canon * kseqs : trusted alignment * tseqs : test alignment * N : number of sequences * * Return: average identity score, or -1.0 on failure */ float CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N) { int i, j; /* counters for sequences */ float score; float tot_score = 0.0; /* do all pairwise comparisons */ for (i = 0; i < N; i++) for (j = i+1; j < N; j++) { score = CompareRefPairAlignments(ref, kseqs[i], kseqs[j], tseqs[i], tseqs[j]); if (score < 0.0) return -1.0; tot_score += score; } return ((tot_score * 2.0)/ ((float) N * ((float) N - 1.0))); } /* Function: PairwiseIdentity() * * Purpose: Calculate the pairwise fractional identity between * two aligned sequences s1 and s2. This is simply * (idents / MIN(len1, len2)). * * Note how many ways there are to calculate pairwise identity, * because of the variety of choices for the denominator: * idents/(idents+mismat) has the disadvantage that artifactual * gappy alignments would have high "identities". * idents/(AVG|MAX)(len1,len2) both have the disadvantage that * alignments of fragments to longer sequences would have * artifactually low "identities". * * Case sensitive; also, watch out in nucleic acid alignments; * U/T RNA/DNA alignments will be counted as mismatches! */ float PairwiseIdentity(char *s1, char *s2) { int idents; /* total identical positions */ int len1, len2; /* lengths of seqs */ int x; /* position in aligned seqs */ idents = len1 = len2 = 0; for (x = 0; s1[x] != '\0' && s2[x] != '\0'; x++) { if (!isgap(s1[x])) { len1++; if (s1[x] == s2[x]) idents++; } if (!isgap(s2[x])) len2++; } if (len2 < len1) len1 = len2; return (len1 == 0 ? 0.0 : (float) idents / (float) len1); } /* Function: AlignmentIdentityBySampling() * Date: SRE, Mon Oct 19 14:29:01 1998 [St. Louis] * * Purpose: Estimate and return the average pairwise * fractional identity of an alignment, * using sampling. * * For use when there's so many sequences that * an all vs. all rigorous calculation will * take too long. * * Case sensitive! * * Args: aseq - aligned sequences * L - length of alignment * N - number of seqs in alignment * nsample - number of samples * * Returns: average fractional identity, 0..1. */ float AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample) { int x, i, j; /* counters */ float sum; if (N < 2) return 1.0; sum = 0.; for (x = 0; x < nsample; x++) { i = CHOOSE(N); do { j = CHOOSE(N); } while (j == i); /* make sure j != i */ sum += PairwiseIdentity(aseq[i], aseq[j]); } return sum / (float) nsample; } /* Function: MajorityRuleConsensus() * Date: SRE, Tue Mar 7 15:30:30 2000 [St. Louis] * * Purpose: Given a set of aligned sequences, produce a * majority rule consensus sequence. If >50% nonalphabetic * (usually meaning gaps) in the column, ignore the column. * * Args: aseq - aligned sequences, [0..nseq-1][0..alen-1] * nseq - number of sequences * alen - length of alignment * * Returns: ptr to allocated consensus sequence. * Caller is responsible for free'ing this. */ char * MajorityRuleConsensus(char **aseq, int nseq, int alen) { char *cs; /* RETURN: consensus sequence */ int count[27]; /* counts for a..z and gaps in a column */ int idx,apos; /* counters for seq, column */ int spos; /* position in cs */ int x; /* counter for characters */ int sym; int max, bestx; cs = MallocOrDie(sizeof(char) * (alen+1)); for (spos=0,apos=0; apos < alen; apos++) { for (x = 0; x < 27; x++) count[x] = 0; for (idx = 0; idx < nseq; idx++) { if (isalpha((int) aseq[idx][apos])) { sym = toupper((int) aseq[idx][apos]); count[sym-'A']++; } else { count[26]++; } } if ((float) count[26] / (float) nseq <= 0.5) { max = bestx = -1; for (x = 0; x < 26; x++) if (count[x] > max) { max = count[x]; bestx = x; } cs[spos++] = (char) ('A' + bestx); } } cs[spos] = '\0'; return cs; } squid/alignio.c0000640000175000017520000004541210463223377013707 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* alignio.c * SRE, Mon Jul 12 11:57:37 1993 * CVS $Id: alignio.c,v 1.12 2003/04/14 16:00:16 eddy Exp $ * * Input/output of sequence alignments. */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "sre_random.h" /* Function: AllocAlignment() * * Purpose: Allocate space for an alignment, given the number * of sequences and the alignment length in columns. * * Args: nseq - number of sequences * alen - width of alignment * ret_aseq - RETURN: alignment itself * ainfo - RETURN: other info associated with alignment * * Return: (void) * aseq, ainfo free'd by caller: FreeAlignment(aseq, &ainfo). * note that ainfo itself is alloc'ed in caller, usually * just by a "AINFO ainfo" definition. */ void AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo) { char **aseq; int idx; InitAinfo(ainfo); aseq = (char **) MallocOrDie (sizeof(char *) * nseq); for (idx = 0; idx < nseq; idx++) aseq[idx] = (char *) MallocOrDie (sizeof(char) * (alen+1)); ainfo->alen = alen; ainfo->nseq = nseq; ainfo->wgt = (float *) MallocOrDie (sizeof(float) * nseq); FSet(ainfo->wgt, nseq, 1.0); ainfo->sqinfo = (SQINFO *) MallocOrDie (sizeof(SQINFO) * nseq); for (idx = 0; idx < nseq; idx++) ainfo->sqinfo[idx].flags = 0; *ret_aseq = aseq; } /* Function: InitAinfo() * Date: SRE, Tue Jan 19 10:16:02 1999 [St. Louis] * * Purpose: Initialize the fields in ainfo structure to * default (null) values. Does nothing with * fields that are dependent on nseq or alen. * * Args: ainfo - optional info structure for an alignment * * Returns: (void). ainfo is modified. */ void InitAinfo(AINFO *ainfo) { ainfo->name = NULL; ainfo->desc = NULL; ainfo->cs = NULL; ainfo->rf = NULL; ainfo->acc = NULL; ainfo->au = NULL; ainfo->flags = 0; ainfo->tc1 = ainfo->tc2 = 0.0; ainfo->nc1 = ainfo->nc2 = 0.0; ainfo->ga1 = ainfo->ga2 = 0.0; } /* Function: FreeAlignment() * * Purpose: Free the space allocated to alignment, names, and optional * information. * * Args: aseqs - sequence alignment * ainfo - associated alignment data. */ void FreeAlignment(char **aseqs, AINFO *ainfo) { int i; for (i = 0; i < ainfo->nseq; i++) { if (ainfo->sqinfo[i].flags & SQINFO_SS) free(ainfo->sqinfo[i].ss); if (ainfo->sqinfo[i].flags & SQINFO_SA) free(ainfo->sqinfo[i].sa); } if (ainfo->cs != NULL) free(ainfo->cs); if (ainfo->rf != NULL) free(ainfo->rf); if (ainfo->name != NULL) free(ainfo->name); if (ainfo->desc != NULL) free(ainfo->desc); if (ainfo->acc != NULL) free(ainfo->acc); if (ainfo->au != NULL) free(ainfo->au); free(ainfo->sqinfo); free(ainfo->wgt); Free2DArray((void **) aseqs, ainfo->nseq); } /* Function: SAMizeAlignment() * Date: SRE, Tue Jun 30 09:49:40 1998 [St. Louis] * * Purpose: Make a "best effort" attempt to convert an alignment * to SAM gap format: - in delete col, . in insert col. * Only works if alignment adheres to SAM's upper/lower * case convention, which is true for instance of old * HMMER alignments. * * Args: aseq - alignment to convert * nseq - number of seqs in alignment * alen - length of alignment * * Returns: (void) */ void SAMizeAlignment(char **aseq, int nseq, int alen) { int col; /* counter for aligned columns */ int i; /* counter for seqs */ int sawlower, sawupper, sawgap; char gapchar; for (col = 0; col < alen; col++) { sawlower = sawupper = sawgap = 0; /* pass 1: do we see only upper or lower? */ for (i = 0; i < nseq; i++) { if (isgap(aseq[i][col])) { sawgap = 1; continue; } if (isupper((int) aseq[i][col])) { sawupper = 1; continue; } if (islower((int) aseq[i][col])) sawlower = 1; } /* select gap character for column */ gapchar = '-'; /* default */ if (sawlower && ! sawupper) gapchar = '.'; /* pass 2: set gap char */ for (i = 0; i < nseq; i++) if (isgap(aseq[i][col])) aseq[i][col] = gapchar; } } /* Function: SAMizeAlignmentByGapFrac() * Date: SRE, Tue Jun 30 10:58:38 1998 [St. Louis] * * Purpose: Convert an alignment to SAM's gap and case * conventions, using gap fraction in a column * to choose match versus insert columns. In match columns, * residues are upper case and gaps are '-'. * In insert columns, residues are lower case and * gaps are '.' * * Args: aseq - aligned sequences * nseq - number of sequences * alen - length of alignment * maxgap - if more gaps than this fraction, column is insert. * * Returns: (void) Characters in aseq may be altered. */ void SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap) { int apos; /* counter over columns */ int idx; /* counter over sequences */ int ngap; /* number of gaps seen */ for (apos = 0; apos < alen; apos++) { /* count gaps */ ngap = 0; for (idx = 0; idx < nseq; idx++) if (isgap(aseq[idx][apos])) ngap++; /* convert to SAM conventions */ if ((float) ngap / (float) nseq > maxgap) { /* insert column */ for (idx = 0; idx < nseq; idx++) if (isgap(aseq[idx][apos])) aseq[idx][apos] = '.'; else aseq[idx][apos] = (char) tolower((int) aseq[idx][apos]); } else { /* match column */ for (idx = 0; idx < nseq; idx++) if (isgap(aseq[idx][apos])) aseq[idx][apos] = '-'; else aseq[idx][apos] = (char) toupper((int) aseq[idx][apos]); } } } /* Function: MakeAlignedString() * * Purpose: Given a raw string of some type (secondary structure, say), * align it to a given aseq by putting gaps wherever the * aseq has gaps. * * Args: aseq: template for alignment * alen: length of aseq * ss: raw string to align to aseq * ret_s: RETURN: aligned ss * * Return: 1 on success, 0 on failure (and squid_errno is set.) * ret_ss is malloc'ed here and must be free'd by caller. */ int MakeAlignedString(char *aseq, int alen, char *ss, char **ret_s) { char *new; int apos, rpos; new = (char *) MallocOrDie ((alen+1) * sizeof(char)); for (apos = rpos = 0; apos < alen; apos++) if (! isgap(aseq[apos])) { new[apos] = ss[rpos]; rpos++; } else new[apos] = '.'; new[apos] = '\0'; if (rpos != strlen(ss)) { squid_errno = SQERR_PARAMETER; free(new); return 0; } *ret_s = new; return 1; } /* Function: MakeDealignedString() * * Purpose: Given an aligned string of some type (either sequence or * secondary structure, for instance), dealign it relative * to a given aseq. Return a ptr to the new string. * * Args: aseq : template alignment * alen : length of aseq * ss: : string to make dealigned copy of; same length as aseq * ret_s : RETURN: dealigned copy of ss * * Return: 1 on success, 0 on failure (and squid_errno is set) * ret_s is alloc'ed here and must be freed by caller */ int MakeDealignedString(char *aseq, int alen, char *ss, char **ret_s) { char *new; int apos, rpos; new = (char *) MallocOrDie ((alen+1) * sizeof(char)); for (apos = rpos = 0; apos < alen; apos++) if (! isgap(aseq[apos])) { new[rpos] = ss[apos]; rpos++; } new[rpos] = '\0'; if (alen != strlen(ss)) { squid_errno = SQERR_PARAMETER; free(new); return 0; } *ret_s = new; return 1; } /* Function: DealignedLength() * * Purpose: Count the number of non-gap symbols in seq. * (i.e. find the length of the unaligned sequence) * * Args: aseq - aligned sequence to count symbols in, \0 terminated * * Return: raw length of seq. */ int DealignedLength(char *aseq) { int rlen; for (rlen = 0; *aseq; aseq++) if (! isgap(*aseq)) rlen++; return rlen; } /* Function: WritePairwiseAlignment() * * Purpose: Write a nice formatted pairwise alignment out, * with a BLAST-style middle line showing identities * as themselves (single letter) and conservative * changes as '+'. * * Args: ofp - open fp to write to (stdout, perhaps) * aseq1, aseq2 - alignments to write (not necessarily * flushed right with gaps) * name1, name2 - names of sequences * spos1, spos2 - starting position in each (raw) sequence * pam - PAM matrix; positive values define * conservative changes * indent - how many extra spaces to print on left * * Return: 1 on success, 0 on failure */ int WritePairwiseAlignment(FILE *ofp, char *aseq1, char *name1, int spos1, char *aseq2, char *name2, int spos2, int **pam, int indent) { char sname1[11]; /* shortened name */ char sname2[11]; int still_going; /* True if writing another block */ char buf1[61]; /* buffer for writing seq1; CPL+1*/ char bufmid[61]; /* buffer for writing consensus */ char buf2[61]; char *s1, *s2; /* ptrs into each sequence */ int count1, count2; /* number of symbols we're writing */ int rpos1, rpos2; /* position in raw seqs */ int rawcount1, rawcount2; /* number of nongap symbols written */ int apos; strncpy(sname1, name1, 10); sname1[10] = '\0'; strtok(sname1, WHITESPACE); strncpy(sname2, name2, 10); sname2[10] = '\0'; strtok(sname2, WHITESPACE); s1 = aseq1; s2 = aseq2; rpos1 = spos1; rpos2 = spos2; still_going = TRUE; while (still_going) { still_going = FALSE; /* get next line's worth from both */ strncpy(buf1, s1, 60); buf1[60] = '\0'; strncpy(buf2, s2, 60); buf2[60] = '\0'; count1 = strlen(buf1); count2 = strlen(buf2); /* is there still more to go? */ if ((count1 == 60 && s1[60] != '\0') || (count2 == 60 && s2[60] != '\0')) still_going = TRUE; /* shift seq ptrs by a line */ s1 += count1; s2 += count2; /* assemble the consensus line */ for (apos = 0; apos < count1 && apos < count2; apos++) { if (!isgap(buf1[apos]) && !isgap(buf2[apos])) { if (buf1[apos] == buf2[apos]) bufmid[apos] = buf1[apos]; else if (pam[buf1[apos] - 'A'][buf2[apos] - 'A'] > 0) bufmid[apos] = '+'; else bufmid[apos] = ' '; } else bufmid[apos] = ' '; } bufmid[apos] = '\0'; rawcount1 = 0; for (apos = 0; apos < count1; apos++) if (!isgap(buf1[apos])) rawcount1++; rawcount2 = 0; for (apos = 0; apos < count2; apos++) if (!isgap(buf2[apos])) rawcount2++; (void) fprintf(ofp, "%*s%-10.10s %5d %s %5d\n", indent, "", sname1, rpos1, buf1, rpos1 + rawcount1 -1); (void) fprintf(ofp, "%*s %s\n", indent, "", bufmid); (void) fprintf(ofp, "%*s%-10.10s %5d %s %5d\n", indent, "", sname2, rpos2, buf2, rpos2 + rawcount2 -1); (void) fprintf(ofp, "\n"); rpos1 += rawcount1; rpos2 += rawcount2; } return 1; } /* Function: MingapAlignment() * * Purpose: Remove all-gap columns from a multiple sequence alignment * and its associated data. The alignment is assumed to be * flushed (all aseqs the same length). */ int MingapAlignment(char **aseqs, AINFO *ainfo) { int apos; /* position in original alignment */ int mpos; /* position in new alignment */ int idx; /* We overwrite aseqs, using its allocated memory. */ for (apos = 0, mpos = 0; aseqs[0][apos] != '\0'; apos++) { /* check for all-gap in column */ for (idx = 0; idx < ainfo->nseq; idx++) if (! isgap(aseqs[idx][apos])) break; if (idx == ainfo->nseq) continue; /* shift alignment and ainfo */ if (mpos != apos) { for (idx = 0; idx < ainfo->nseq; idx++) aseqs[idx][mpos] = aseqs[idx][apos]; if (ainfo->cs != NULL) ainfo->cs[mpos] = ainfo->cs[apos]; if (ainfo->rf != NULL) ainfo->rf[mpos] = ainfo->rf[apos]; } mpos++; } /* null terminate everything */ for (idx = 0; idx < ainfo->nseq; idx++) aseqs[idx][mpos] = '\0'; ainfo->alen = mpos; /* set new length */ if (ainfo->cs != NULL) ainfo->cs[mpos] = '\0'; if (ainfo->rf != NULL) ainfo->rf[mpos] = '\0'; return 1; } /* Function: RandomAlignment() * * Purpose: Create a random alignment from raw sequences. * * Ideally, we would like to sample an alignment from the * space of possible alignments according to its probability, * given a prior probability distribution for alignments. * I don't see how to describe such a distribution, let alone * sample it. * * This is a rough approximation that tries to capture some * desired properties. We assume the alignment is generated * by a simple HMM composed of match and insert states. * Given parameters (pop, pex) for the probability of opening * and extending an insertion, we can find the expected number * of match states, M, in the underlying model for each sequence. * We use an average M taken over all the sequences (this is * an approximation. The expectation of M given all the sequence * lengths is a nasty-looking summation.) * * M = len / ( 1 + pop ( 1 + 1/ (1-pex) ) ) * * Then, we assign positions in each raw sequence onto the M match * states and M+1 insert states of this "HMM", by rolling random * numbers and inserting the (rlen-M) inserted positions randomly * into the insert slots, taking into account the relative probability * of open vs. extend. * * The resulting alignment has two desired properties: insertions * tend to follow the HMM-like exponential distribution, and * the "sparseness" of the alignment is controllable through * pop and pex. * * Args: rseqs - raw sequences to "align", 0..nseq-1 * sqinfo - array of 0..nseq-1 info structures for the sequences * nseq - number of sequences * pop - probability to open insertion (0 minlen) M = minlen; /* make arrays that count insertions in M+1 possible insert states */ ins = (int **) MallocOrDie (sizeof(int *) * nseq); master_ins = (int *) MallocOrDie (sizeof(int) * (M+1)); for (idx = 0; idx < nseq; idx++) { ins[idx] = (int *) MallocOrDie (sizeof(int) * (M+1)); for (rpos = 0; rpos <= M; rpos++) ins[idx][rpos] = 0; } /* normalize */ pop = pop / (pop+pex); pex = 1.0 - pop; /* make insertions for individual sequences */ for (idx = 0; idx < nseq; idx++) { apos = -1; for (rpos = 0; rpos < rlen[idx]-M; rpos++) { if (sre_random() < pop || apos == -1) /* open insertion */ apos = CHOOSE(M+1); /* choose 0..M */ ins[idx][apos]++; } } /* calculate master_ins, max inserts */ alen = M; for (apos = 0; apos <= M; apos++) { master_ins[apos] = 0; for (idx = 0; idx < nseq; idx++) if (ins[idx][apos] > master_ins[apos]) master_ins[apos] = ins[idx][apos]; alen += master_ins[apos]; } /* Now, construct alignment */ aseqs = (char **) MallocOrDie (sizeof (char *) * nseq); for (idx = 0; idx < nseq; idx++) aseqs[idx] = (char *) MallocOrDie (sizeof(char) * (alen+1)); for (idx = 0; idx < nseq; idx++) { apos = rpos = 0; for (statepos = 0; statepos <= M; statepos++) { for (count = 0; count < ins[idx][statepos]; count++) aseqs[idx][apos++] = rseqs[idx][rpos++]; for (; count < master_ins[statepos]; count++) aseqs[idx][apos++] = ' '; if (statepos != M) aseqs[idx][apos++] = rseqs[idx][rpos++]; } aseqs[idx][alen] = '\0'; } ainfo->flags = 0; ainfo->alen = alen; ainfo->nseq = nseq; ainfo->sqinfo = (SQINFO *) MallocOrDie (sizeof(SQINFO) * nseq); for (idx = 0; idx < nseq; idx++) SeqinfoCopy(&(ainfo->sqinfo[idx]), &(sqinfo[idx])); free(rlen); free(master_ins); Free2DArray((void **) ins, nseq); *ret_aseqs = aseqs; return 1; } /* Function: AlignmentHomogenousGapsym() * Date: SRE, Sun Mar 19 19:37:12 2000 [wren, St. Louis] * * Purpose: Sometimes we've got to convert alignments to * a lowest common denominator, and we need * a single specific gap character -- for example, * PSI-BLAST blastpgp -B takes a very simplistic * alignment input format which appears to only * allow '-' as a gap symbol. * * Anything matching the isgap() macro is * converted. * * Args: aseq - aligned character strings, [0..nseq-1][0..alen-1] * nseq - number of aligned strings * alen - length of alignment * gapsym - character to use for gaps. * * Returns: void ("never fails") */ void AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym) { int i, apos; for (i = 0; i < nseq; i++) for (apos = 0; apos < alen; apos++) if (isgap(aseq[i][apos])) aseq[i][apos] = gapsym; } squid/alistat_main.c0000640000175000017520000002117310463223377014730 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* alistat_main.c * Fri Jan 27 10:41:41 1995 * CVS $Id: alistat_main.c,v 1.8 2003/04/14 16:00:16 eddy Exp $ * * Look at an alignment file, determine some simple statistics. */ #include "squidconf.h" #include #include #include #include "squid.h" #include "msa.h" static char banner[] = "alistat - show some simple statistics on an alignment file"; static char usage[] = "\ Usage: alistat [-options] \n\ Available options:\n\ -a : report per-sequence info, not just a summary\n\ -f : fast: estimate average %id by sampling (not compatible with -a)\n\ -h : help: display usage and version\n\ -q : quiet: suppress verbose header\n\ "; static char experts[] = "\ Expert options:\n\ --consensus : write majority rule consensus sequence(s) in FASTA\n\ format to file \n\ --identmx : save a report on all NxN pairwise identities to file \n\ --informat : specify alignment file format \n\ allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP\n\ "; struct opt_s OPTIONS[] = { { "-a", TRUE, sqdARG_NONE }, { "-f", TRUE, sqdARG_NONE }, { "-h", TRUE, sqdARG_NONE }, { "-q", TRUE, sqdARG_NONE }, { "--consensus", FALSE, sqdARG_STRING }, { "--identmx", FALSE, sqdARG_STRING }, { "--informat", FALSE, sqdARG_STRING }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *afile; /* name of aligned sequence file */ MSAFILE *afp; /* pointer to open alignment file*/ MSA *msa; /* multiple sequence alignment */ int fmt; /* format of afile */ int rlen; /* raw sequence length */ int nres; /* number of residues */ float **imx; /* identity matrix */ int i,j; int small, large; int bestj, worstj; float sum, best, worst; float worst_worst, worst_best, best_best; float avgid; int nsample; int allreport; int do_fast; int be_quiet; char *consfile; FILE *consfp = NULL; char *identmx_report; /* file to save identity matrix info to */ FILE *identmx_fp = NULL; char *optname; char *optarg; int optind; /* These inits are solely to silence gcc warnings about * uninitialized variables */ worst_worst = worst_best = best_best = 0.0; bestj = worstj = -1; /*********************************************** * Parse command line ***********************************************/ fmt = MSAFILE_UNKNOWN; /* by default, we autodetect file format */ allreport = FALSE; do_fast = FALSE; be_quiet = FALSE; consfile = NULL; identmx_report = NULL; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-a") == 0) { allreport = TRUE; } else if (strcmp(optname, "-f") == 0) { do_fast = TRUE; } else if (strcmp(optname, "-q") == 0) { be_quiet = TRUE; } else if (strcmp(optname, "--consensus") == 0) { consfile = optarg; } else if (strcmp(optname, "--identmx") == 0) { identmx_report = optarg; } else if (strcmp(optname, "--informat") == 0) { fmt = String2SeqfileFormat(optarg); if (fmt == MSAFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); if (! IsAlignmentFormat(fmt)) Die("%s is an unaligned format, can't read as an alignment", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 1) Die("Incorrect number of arguments.\n%s\n", usage); afile = argv[optind]; if (do_fast && allreport) Die("Verbose reports (-a, --identmx) are incompatible with fast sampling (-f)"); if (do_fast && identmx_report != NULL) Die("Verbose reports (-a, --identmx) are incompatible with fast sampling (-f)"); if (! be_quiet) SqdBanner(stdout, banner); /*********************************************** * Loop over every alignment in the file. ***********************************************/ if ((afp = MSAFileOpen(afile, fmt, NULL)) == NULL) Die("Alignment file %s could not be opened for reading", afile); if (consfile != NULL && (consfp = fopen(consfile, "w")) == NULL) Die("Failed to open consensus sequence file %s for writing", consfile); if (identmx_report != NULL && (identmx_fp = fopen(identmx_report, "w")) == NULL) Die("Failed to open identity matrix report file %s for writing", identmx_report); while ((msa = MSAFileRead(afp)) != NULL) { for (i = 0; i < msa->nseq; i++) s2upper(msa->aseq[i]); /* Statistics we always collect: * unaligned sequence lengths; mean and range */ nres = 0; small = large = -1; for (i = 0; i < msa->nseq; i++) { rlen = DealignedLength(msa->aseq[i]); nres += rlen; if (small == -1 || rlen < small) small = rlen; if (large == -1 || rlen > large) large = rlen; } /* Statistics we have to be careful about * collecting, because of time constraints on NxN operations */ if (do_fast) { nsample = 1000; avgid = AlignmentIdentityBySampling(msa->aseq, msa->alen, msa->nseq, nsample); } else { /* In a full report, for each sequence, find the best relative, * and the worst relative. For overall statistics, save the * worst best (most distant single seq) and the best best * (most closely related pair) and the worst worst (most * distantly related pair) and yes, I know it's confusing. */ MakeIdentityMx(msa->aseq, msa->nseq, &imx); if (allreport) { printf(" %-15s %5s %7s %-15s %7s %-15s\n", "NAME", "LEN", "HIGH ID", "(TO)", "LOW ID", "(TO)"); printf(" --------------- ----- ------- --------------- ------- ---------------\n"); } /* Print the identity matrix report: one line per pair of sequences. */ if (identmx_report != NULL) { for (i = 0; i < msa->nseq; i++) for (j = i+1; j < msa->nseq; j++) fprintf(identmx_fp, "%-4d %-4d %-15s %-15s %.3f\n", i, j, msa->sqname[i], msa->sqname[j], imx[i][j]); } sum = 0.0; worst_best = 1.0; best_best = 0.0; worst_worst = 1.0; for (i = 0; i < msa->nseq; i++) { worst = 1.0; best = 0.0; for (j = 0; j < msa->nseq; j++) { /* closest seq to this one = best */ if (i != j && imx[i][j] > best) { best = imx[i][j]; bestj = j; } if (imx[i][j] < worst) { worst = imx[i][j]; worstj = j; } } if (allreport) printf("* %-15s %5d %7.1f %-15s %7.1f %-15s\n", msa->sqname[i], DealignedLength(msa->aseq[i]), best * 100., msa->sqname[bestj], worst * 100., msa->sqname[worstj]); if (best > best_best) best_best = best; if (best < worst_best) worst_best = best; if (worst < worst_worst) worst_worst = worst; for (j = 0; j < i; j++) sum += imx[i][j]; } avgid = sum / (float) (msa->nseq * (msa->nseq-1)/2.0); if (allreport) puts(""); FMX2Free(imx); } /* Print output. * Some fields aren't available if -f (fast) was chosen. */ if (msa->name != NULL) printf("Alignment name: %s\n", msa->name); printf("Format: %s\n", SeqfileFormat2String(afp->format)); printf("Number of sequences: %d\n", msa->nseq); printf("Total # residues: %d\n", nres); printf("Smallest: %d\n", small); printf("Largest: %d\n", large); printf("Average length: %.1f\n", (float) nres / (float) msa->nseq); printf("Alignment length: %d\n", msa->alen); printf("Average identity: %.0f%%\n", 100.*avgid); if (! do_fast) { printf("Most related pair: %.0f%%\n", 100.*best_best); printf("Most unrelated pair: %.0f%%\n", 100.*worst_worst); printf("Most distant seq: %.0f%%\n", 100.*worst_best); } /* Save majority rule consensus sequence if we were asked */ if (consfile != NULL) { char *cs; cs = MajorityRuleConsensus(msa->aseq, msa->nseq, msa->alen); WriteSimpleFASTA(consfp, cs, msa->name != NULL? msa->name : "consensus", msa->desc); free(cs); printf("Consensus: written to %s\n", consfile); } puts("//"); MSAFree(msa); } MSAFileClose(afp); if (consfile != NULL) fclose(consfp); return 0; } squid/clustal.c0000640000175000017520000001122510463223377013727 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* clustal.c * SRE, Sun Jun 6 17:50:45 1999 [bus from Madison, 1999 worm mtg] * * Import/export of ClustalV/W multiple sequence alignment * formatted files. Derivative of msf.c; MSF is a pretty * generic interleaved format. * * CVS $Id: clustal.c,v 1.3 2004/10/08 12:14:21 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "msa.h" #ifdef TESTDRIVE_CLUSTAL /***************************************************************** * msf.c test driver: * cc -DTESTDRIVE_CLUSTAL -g -O2 -Wall -o test clustal.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm * */ int main(int argc, char **argv) { MSAFILE *afp; MSA *msa; char *file; file = argv[1]; if ((afp = MSAFileOpen(file, MSAFILE_CLUSTAL, NULL)) == NULL) Die("Couldn't open %s\n", file); while ((msa = ReadClustal(afp)) != NULL) { WriteClustal(stdout, msa); MSAFree(msa); } MSAFileClose(afp); exit(0); } /******************************************************************/ #endif /* testdrive_clustal */ /* Function: ReadClustal() * Date: SRE, Sun Jun 6 17:53:49 1999 [bus from Madison, 1999 worm mtg] * * Purpose: Parse an alignment read from an open Clustal format * alignment file. Clustal is a single-alignment format. * Return the alignment, or NULL if we have no data. * * Args: afp - open alignment file * * Returns: MSA * - an alignment object * caller responsible for an MSAFree() * NULL if no more alignments * * Diagnostics: * Will Die() here with a (potentially) useful message * if a parsing error occurs. */ MSA * ReadClustal(MSAFILE *afp) { MSA *msa; char *s; int slen; int sqidx; char *name; char *seq; char *s2; if (feof(afp->f)) return NULL; /* Skip until we see the CLUSTAL header */ while ((s = MSAFileGetLine(afp)) != NULL) { if (strncmp(s, "CLUSTAL ", 8) == 0) break; } if (s == NULL) return NULL; msa = MSAAlloc(10, 0); /* Now we're in the sequence section. * As discussed above, if we haven't seen a sequence name, then we * don't include the sequence in the alignment. * Watch out for conservation markup lines that contain *.: chars */ while ((s = MSAFileGetLine(afp)) != NULL) { if ((name = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; if ((seq = sre_strtok(&s, WHITESPACE, &slen)) == NULL) continue; s2 = sre_strtok(&s, "\n", NULL); /* The test for a conservation markup line */ if (strpbrk(name, ".*:") != NULL && strpbrk(seq, ".*:") != NULL) continue; if (s2 != NULL) Die("Parse failed at line %d, file %s: possibly using spaces as gaps", afp->linenumber, afp->fname); /* It's not blank, and it's not a coord line: must be sequence */ sqidx = MSAGetSeqidx(msa, name, msa->lastidx+1); msa->lastidx = sqidx; msa->sqlen[sqidx] = sre_strcat(&(msa->aseq[sqidx]), msa->sqlen[sqidx], seq, slen); } MSAVerifyParse(msa); /* verifies, and also sets alen and wgt. */ return msa; } /* Function: WriteClustal() * Date: SRE, Sun Jun 6 18:12:47 1999 [bus from Madison, worm mtg 1999] * * Purpose: Write an alignment in Clustal format to an open file. * * Args: fp - file that's open for writing. * msa - alignment to write. * * Returns: (void) */ void WriteClustal(FILE *fp, MSA *msa) { int idx; /* counter for sequences */ int len; /* tmp variable for name lengths */ int namelen; /* maximum name length used */ int pos; /* position counter */ char buf[64]; /* buffer for writing seq */ int cpl = 50; /* char per line (< 64) */ /* calculate max namelen used */ namelen = 0; for (idx = 0; idx < msa->nseq; idx++) if ((len = strlen(msa->sqname[idx])) > namelen) namelen = len; fprintf(fp, "CLUSTAL W(1.5) multiple sequence alignment\n"); /***************************************************** * Write the sequences *****************************************************/ for (pos = 0; pos < msa->alen; pos += cpl) { fprintf(fp, "\n"); /* Blank line between sequence blocks */ for (idx = 0; idx < msa->nseq; idx++) { strncpy(buf, msa->aseq[idx] + pos, cpl); buf[cpl] = '\0'; fprintf(fp, "%*s %s\n", namelen, msa->sqname[idx], buf); } } return; } squid/cluster.c0000640000175000017520000004157110463223377013750 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* cluster.c * SRE, Sun Jul 18 09:49:47 1993 * moved to squid Thu Mar 3 08:42:57 1994 * CVS $Id: cluster.c,v 1.5 2003/10/11 16:03:41 eddy Exp $ * * almost identical to bord.c, from fd * also now contains routines for constructing difference matrices * from alignments * * "branch ordering": Input a symmetric or upper-right-diagonal * NxN difference matrix (usually constructed by pairwise alignment * and similarity calculations for N sequences). Use the simple * cluster analysis part of the Fitch/Margoliash tree-building algorithm * (as described by Fitch and Margoliash 1967 as well as Feng * and Doolittle 1987) to calculate the topology of an "evolutionary * tree" consistent with the difference matrix. Returns an array * which represents the tree. * * The input difference matrix is just an NxN matrix of floats. * A good match is a small difference score (the algorithm is going * to search for minima among the difference scores). The original difference * matrix remains unchanged by the calculations. * * The output requires some explanation. A phylogenetic * tree is a binary tree, with N "leaves" and N-1 "nodes". The * topology of the tree may be completely described by N-1 structures * containing two pointers; each pointer points to either a leaf * or another node. Here, this is implemented with integer indices * rather than pointers. An array of N-1 pairs of ints is returned. * If the index is in the range (0..N-1), it is a "leaf" -- the * number of one of the sequences. If the index is in the range * (N..2N-2), it is another "node" -- (index-N) is the index * of the node in the returned array. * * If both indices of a member of the returned array point to * nodes, the tree is "compound": composed of more than one * cluster of related sequences. * * The higher-numbered elements of the returned array were the * first constructed, and hence represent the distal tips * of the tree -- the most similar sequences. The root * is node 0. ****************************************************************** * * Algorithm * * INITIALIZATIONS: * - copy the difference matrix (otherwise the caller's copy would * get destroyed by the operations of this algorithm). If * it's asymmetric, make it symmetric. * - make a (0..N-1) array of ints to keep track of the indices in * the difference matrix as they get swapped around. Initialize * this matrix to 0..N-1. * - make a (0..N-2) array of int[2] to store the results (the tree * topology). Doesn't need to be initialized. * - keep track of a "N'", the current size of the difference * matrix being operated on. * * PROCESSING THE DIFFERENCE MATRIX: * - for N' = N down to N' = 2 (N-1 steps): * - in the half-diagonal N'xN' matrix, find the indices i,j at which * there's the minimum difference score * * Store the results: * - at position N'-2 of the result array, store coords[i] and * coords[j]. * * Move i,j rows, cols to the outside edges of the matrix: * - swap row i and row N'-2 * - swap row j and row N'-1 * - swap column i and column N'-2 * - swap column j and column N'-1 * - swap indices i, N'-2 in the index array * - swap indices j, N'-1 in the index array * * Build a average difference score for differences to i,j: * - for all columns, find avg difference between rows i and j and store in row i: * row[i][col] = (row[i][col] + row[j][col]) / 2.0 * - copy the contents of row i to column i (it's a symmetric * matrix, no need to recalculate) * - store an index N'+N-2 at position N'-2 of the index array: means * that this row/column is now a node rather than a leaf, and * contains minimum values * * Continue: * - go to the next N' * * GARBAGE COLLECTION & RETURN. * ********************************************************************** * * References: * * Feng D-F and R.F. Doolittle. "Progressive sequence alignment as a * prerequisite to correct phylogenetic trees." J. Mol. Evol. * 25:351-360, 1987. * * Fitch W.M. and Margoliash E. "Construction of phylogenetic trees." * Science 155:279-284, 1967. * ********************************************************************** * * SRE, 18 March 1992 (bord.c) * SRE, Sun Jul 18 09:52:14 1993 (cluster.c) * added to squid Thu Mar 3 09:13:56 1994 ********************************************************************** * Mon May 4 09:47:02 1992: keep track of difference scores at each node */ #include "squidconf.h" #include #include #include #include "squid.h" #include "sqfuncs.h" #include "sre_stack.h" /* Function: Cluster() * * Purpose: Cluster analysis on a distance matrix. Constructs a * phylogenetic tree which contains the topology * and info for each node: branch lengths, how many * sequences are included under the node, and which * sequences are included under the node. * * Args: dmx - the NxN distance matrix ( >= 0.0, larger means more diverged) * N - size of mx (number of sequences) * mode - CLUSTER_MEAN, CLUSTER_MAX, or CLUSTER_MIN * ret_tree- RETURN: the tree * * Return: 1 on success, 0 on failure. * The caller is responsible for freeing the tree's memory, * by calling FreePhylo(tree, N). */ int Cluster(float **dmx, int N, enum clust_strategy mode, struct phylo_s **ret_tree) { struct phylo_s *tree; /* (0..N-2) phylogenetic tree */ float **mx; /* copy of difference matrix */ int *coord; /* (0..N-1), indices for matrix coords */ int i, j; /* coords of minimum difference */ int idx; /* counter over seqs */ int Np; /* N', a working copy of N */ int row, col; /* loop variables */ float min; /* best minimum score found */ float *trow; /* tmp pointer for swapping rows */ float tcol; /* tmp storage for swapping cols */ float *diff; /* (0..N-2) difference scores at nodes */ int swapfoo; /* for SWAP() macro */ /************************** * Initializations. **************************/ /* We destroy the matrix we work on, so make a copy of dmx. */ mx = MallocOrDie (sizeof(float *) * N); for (i = 0; i < N; i++) { mx[i] = MallocOrDie (sizeof(float) * N); for (j = 0; j < N; j++) mx[i][j] = dmx[i][j]; } /* coord array alloc, (0..N-1) */ coord = MallocOrDie (N * sizeof(int)); diff = MallocOrDie ((N-1) * sizeof(float)); /* init the coord array to 0..N-1 */ for (col = 0; col < N; col++) coord[col] = col; for (i = 0; i < N-1; i++) diff[i] = 0.0; /* tree array alloc, (0..N-2) */ if ((tree = AllocPhylo(N)) == NULL) Die("AllocPhylo() failed"); /********************************* * Process the difference matrix *********************************/ /* N-prime, for an NxN down to a 2x2 diffmx */ j= 0; /* just to silence gcc uninit warnings */ for (Np = N; Np >= 2; Np--) { /* find a minimum on the N'xN' matrix*/ min = 999999.; for (row = 0; row < Np; row++) for (col = row+1; col < Np; col++) if (mx[row][col] < min) { min = mx[row][col]; i = row; j = col; } /* We're clustering row i with col j. write necessary * data into a node on the tree */ /* topology info */ tree[Np-2].left = coord[i]; tree[Np-2].right = coord[j]; if (coord[i] >= N) tree[coord[i]-N].parent = N + Np - 2; if (coord[j] >= N) tree[coord[j]-N].parent = N + Np - 2; /* keep score info */ diff[Np-2] = tree[Np-2].diff = min; /* way-simple branch length estimation */ tree[Np-2].lblen = tree[Np-2].rblen = min; if (coord[i] >= N) tree[Np-2].lblen -= diff[coord[i]-N]; if (coord[j] >= N) tree[Np-2].rblen -= diff[coord[j]-N]; /* number seqs included at node */ if (coord[i] < N) { tree[Np-2].incnum ++; tree[Np-2].is_in[coord[i]] = 1; } else { tree[Np-2].incnum += tree[coord[i]-N].incnum; for (idx = 0; idx < N; idx++) tree[Np-2].is_in[idx] |= tree[coord[i]-N].is_in[idx]; } if (coord[j] < N) { tree[Np-2].incnum ++; tree[Np-2].is_in[coord[j]] = 1; } else { tree[Np-2].incnum += tree[coord[j]-N].incnum; for (idx = 0; idx < N; idx++) tree[Np-2].is_in[idx] |= tree[coord[j]-N].is_in[idx]; } /* Now build a new matrix, by merging row i with row j and * column i with column j; see Fitch and Margoliash */ /* Row and column swapping. */ /* watch out for swapping i, j away: */ if (i == Np-1 || j == Np-2) SWAP(i,j); if (i != Np-2) { /* swap row i, row N'-2 */ trow = mx[Np-2]; mx[Np-2] = mx[i]; mx[i] = trow; /* swap col i, col N'-2 */ for (row = 0; row < Np; row++) { tcol = mx[row][Np-2]; mx[row][Np-2] = mx[row][i]; mx[row][i] = tcol; } /* swap coord i, coord N'-2 */ SWAP(coord[i], coord[Np-2]); } if (j != Np-1) { /* swap row j, row N'-1 */ trow = mx[Np-1]; mx[Np-1] = mx[j]; mx[j] = trow; /* swap col j, col N'-1 */ for (row = 0; row < Np; row++) { tcol = mx[row][Np-1]; mx[row][Np-1] = mx[row][j]; mx[row][j] = tcol; } /* swap coord j, coord N'-1 */ SWAP(coord[j], coord[Np-1]); } /* average i and j together; they're now at Np-2 and Np-1 though */ i = Np-2; j = Np-1; /* merge by saving avg of cols of row i and row j */ for (col = 0; col < Np; col++) { switch (mode) { case CLUSTER_MEAN: mx[i][col] =(mx[i][col]+ mx[j][col]) / 2.0; break; case CLUSTER_MIN: mx[i][col] = MIN(mx[i][col], mx[j][col]); break; case CLUSTER_MAX: mx[i][col] = MAX(mx[i][col], mx[j][col]); break; default: mx[i][col] =(mx[i][col]+ mx[j][col]) / 2.0; break; } } /* copy those rows to columns */ for (col = 0; col < Np; col++) mx[col][i] = mx[i][col]; /* store the node index in coords */ coord[Np-2] = Np+N-2; } /************************** * Garbage collection and return **************************/ Free2DArray((void **) mx, N); free(coord); free(diff); *ret_tree = tree; return 1; } /* Function: AllocPhylo() * * Purpose: Allocate space for a phylo_s array. N-1 structures * are allocated, one for each node; in each node, a 0..N * is_in flag array is also allocated and initialized to * all zeros. * * Args: N - size; number of sequences being clustered * * Return: pointer to the allocated array * */ struct phylo_s * AllocPhylo(int N) { struct phylo_s *tree; int i; if ((tree = (struct phylo_s *) malloc ((N-1) * sizeof(struct phylo_s))) == NULL) return NULL; for (i = 0; i < N-1; i++) { tree[i].diff = 0.0; tree[i].lblen = tree[i].rblen = 0.0; tree[i].left = tree[i].right = tree[i].parent = -1; tree[i].incnum = 0; if ((tree[i].is_in = (char *) calloc (N, sizeof(char))) == NULL) return NULL; } return tree; } /* Function: FreePhylo() * * Purpose: Free a clustree array that was built to cluster N sequences. * * Args: tree - phylogenetic tree to free * N - size of clustree; number of sequences it clustered * * Return: (void) */ void FreePhylo(struct phylo_s *tree, int N) { int idx; for (idx = 0; idx < N-1; idx++) free(tree[idx].is_in); free(tree); } /* Function: MakeDiffMx() * * Purpose: Given a set of aligned sequences, construct * an NxN fractional difference matrix. (i.e. 1.0 is * completely different, 0.0 is exactly identical). * * Args: aseqs - flushed, aligned sequences * num - number of aseqs * ret_dmx - RETURN: difference matrix * * Return: 1 on success, 0 on failure. * Caller must free diff matrix with FMX2Free(dmx) */ void MakeDiffMx(char **aseqs, int num, float ***ret_dmx) { float **dmx; /* RETURN: distance matrix */ int i,j; /* counters over sequences */ /* Allocate 2D float matrix */ dmx = FMX2Alloc(num, num); /* Calculate distances; symmetric matrix * record difference, not identity (1 - identity) */ for (i = 0; i < num; i++) for (j = i; j < num; j++) dmx[i][j] = dmx[j][i] = 1.0 - PairwiseIdentity(aseqs[i], aseqs[j]); *ret_dmx = dmx; return; } /* Function: MakeIdentityMx() * * Purpose: Given a set of aligned sequences, construct * an NxN fractional identity matrix. (i.e. 1.0 is * completely identical, 0.0 is completely different). * Virtually identical to MakeDiffMx(). It's * less confusing to have two distinct functions, I find. * * Args: aseqs - flushed, aligned sequences * num - number of aseqs * ret_imx - RETURN: identity matrix (caller must free) * * Return: 1 on success, 0 on failure. * Caller must free imx using FMX2Free(imx) */ void MakeIdentityMx(char **aseqs, int num, float ***ret_imx) { float **imx; /* RETURN: identity matrix */ int i,j; /* counters over sequences */ /* Allocate 2D float matrix */ imx = FMX2Alloc(num, num); /* Calculate distances, symmetric matrix */ for (i = 0; i < num; i++) for (j = i; j < num; j++) imx[i][j] = imx[j][i] = PairwiseIdentity(aseqs[i], aseqs[j]); *ret_imx = imx; return; } /* Function: PrintNewHampshireTree() * * Purpose: Print out a tree in the "New Hampshire" standard * format. See PHYLIP's draw.doc for a definition of * the New Hampshire format. * * Like a CFG, we generate the format string left to * right by a preorder tree traversal. * * Args: fp - file to print to * ainfo- alignment info, including sequence names * tree - tree to print * N - number of leaves * */ void PrintNewHampshireTree(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N) { Nstack_t *stack; int code; float *blen; int docomma; blen = (float *) MallocOrDie (sizeof(float) * (2*N-1)); stack = CreateNstack(); PushNstack(stack, N); /* push root on stack */ docomma = FALSE; /* node index code: * 0..N-1 = leaves; indexes of sequences. * N..2N-2 = interior nodes; node-N = index of node in tree structure. * code N is the root. * 2N..3N-2 = special flags for closing interior nodes; node-2N = index in tree */ while (PopNstack(stack, &code)) { if (code < N) /* we're a leaf. */ { /* 1) print name:branchlength */ if (docomma) fputs(",", fp); fprintf(fp, "%s:%.5f", ainfo->sqinfo[code].name, blen[code]); docomma = TRUE; } else if (code < 2*N) /* we're an interior node */ { /* 1) print a '(' */ if (docomma) fputs(",\n", fp); fputs("(", fp); /* 2) push on stack: ), rchild, lchild */ PushNstack(stack, code+N); PushNstack(stack, tree[code-N].right); PushNstack(stack, tree[code-N].left); /* 3) record branch lengths */ blen[tree[code-N].right] = tree[code-N].rblen; blen[tree[code-N].left] = tree[code-N].lblen; docomma = FALSE; } else /* we're closing an interior node */ { /* print a ):branchlength */ if (code == 2*N) fprintf(fp, ");\n"); else fprintf(fp, "):%.5f", blen[code-N]); docomma = TRUE; } } FreeNstack(stack); free(blen); return; } /* Function: PrintPhylo() * * Purpose: Debugging output of a phylogenetic tree structure. */ void PrintPhylo(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N) { int idx; for (idx = 0; idx < N-1; idx++) { fprintf(fp, "Interior node %d (code %d)\n", idx, idx+N); fprintf(fp, "\tParent: %d (code %d)\n", tree[idx].parent-N, tree[idx].parent); fprintf(fp, "\tLeft: %d (%s) %f\n", tree[idx].left < N ? tree[idx].left-N : tree[idx].left, tree[idx].left < N ? ainfo->sqinfo[tree[idx].left].name : "interior", tree[idx].lblen); fprintf(fp, "\tRight: %d (%s) %f\n", tree[idx].right < N ? tree[idx].right-N : tree[idx].right, tree[idx].right < N ? ainfo->sqinfo[tree[idx].right].name : "interior", tree[idx].rblen); fprintf(fp, "\tHeight: %f\n", tree[idx].diff); fprintf(fp, "\tIncludes:%d seqs\n", tree[idx].incnum); } } squid/compalign_main.c0000640000175000017520000001674410463223377015250 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* main for compalign * * Compalign -- a program to compare two sequence alignments * SRE, Tue Nov 3 07:38:03 1992 * RCS $Id: compalign_main.c,v 1.6 2003/04/14 16:00:16 eddy Exp $ * * incorporated into SQUID, Thu Jan 26 16:52:41 1995 * * Usage: compalign * * Calculate the fractional "identity" between the trusted alignment * and the test alignment. The two files must contain exactly the same * sequences, in exactly the same order. * * The identity of the multiple sequence alignments is defined as * the averaged identity over all N(N-1)/2 pairwise alignments. * * The fractional identity of two sets of pairwise alignments * is in turn defined as follows (for aligned known sequences k1 and k2, * and aligned test sequences t1 and t2): * * matched columns / total columns, * * where total columns = the total number of columns in * which there is a valid (nongap) symbol in k1 or k2; * * matched columns = the number of columns in which one of the * following is true: * * k1 and k2 both have valid symbols at a given column; t1 and t2 * have the same symbols aligned in a column of the t1/t2 * alignment; * * k1 has a symbol aligned to a gap in k2; that symbol in t1 * is also aligned to a gap; * * k2 has a symbol aligned to a gap in k1; that symbol in t2 * is also aligned to a gap. * * Because scores for all possible pairs are calculated, the * algorithm is of order (N^2)L for N sequences of length L; * large sequence sets will take a while. * * Sean Eddy, Tue Nov 3 07:46:59 1992 * */ #include "squidconf.h" #include #include #include "squid.h" #include "msa.h" static char banner[] = "compalign - compare two multiple alignments"; static char usage[] = "\ Usage: compalign [-options] \n\ Available options:\n\ -c : only compare under marked #=CS consensus structure\n\ -h : print short help and usage info\n\ "; static char experts[] = "\ --informat : specify that both alignments are in format (MSF, for instance)\n\ --quiet : suppress verbose header (used in regression testing)\n\ "; struct opt_s OPTIONS[] = { { "-c", TRUE, sqdARG_NONE }, { "-h", TRUE, sqdARG_NONE }, { "--informat", FALSE, sqdARG_STRING }, { "--quiet", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *kfile; /* name of file of trusted (known) alignment */ char *tfile; /* name of file of test alignment */ MSAFILE *kfp; /* open ptr into trusted (known) alignfile */ MSAFILE *tfp; /* open ptr into test alignment file */ int format; /* expected format of alignment files */ MSA *kmsa; /* a trusted (known) alignment */ MSA *tmsa; /* a test alignment */ char **kraw; /* dealigned trusted seqs */ char **traw; /* dealigned test sequences */ int idx; /* counter for sequences */ int apos; /* position in alignment */ float score; /* RESULT: score for the comparison */ int cs_only; /* TRUE to compare under #=CS annotation only */ int *ref = NULL; /* init only to silence gcc warning */ int be_quiet; /* TRUE to suppress verbose header */ char *optname; char *optarg; int optind; /*********************************************** * Parse command line ***********************************************/ format = MSAFILE_UNKNOWN; cs_only = FALSE; be_quiet = FALSE; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-c") == 0) cs_only = TRUE; else if (strcmp(optname, "--quiet") == 0) be_quiet = TRUE; else if (strcmp(optname, "--informat") == 0) { format = String2SeqfileFormat(optarg); if (format == MSAFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); if (! IsAlignmentFormat(format)) Die("%s is an unaligned format, can't read as an alignment", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 2) Die("Incorrect number of command line arguments.\n%s\n", usage); kfile = argv[optind++]; tfile = argv[optind]; if (! be_quiet) SqdBanner(stdout, banner); /*********************************************** * Read in the alignments * Capable of handling full Stockholm: >1 alignment/file ***********************************************/ if ((kfp = MSAFileOpen(kfile, format, NULL)) == NULL) Die("Trusted alignment file %s could not be opened for reading", kfile); if ((tfp = MSAFileOpen(tfile, format, NULL)) == NULL) Die("Test alignment file %s could not be opened for reading", tfile); while ((kmsa = MSAFileRead(kfp)) != NULL) { if ((tmsa = MSAFileRead(tfp)) == NULL) Die("Failed to get a test alignment to match with the trusted alignment"); /* test that they're the same! */ if (kmsa->nseq != tmsa->nseq) Die("files %s and %s do not contain same number of seqs!\n", kfile, tfile); for (idx = 0; idx < kmsa->nseq; idx++) { s2upper(kmsa->aseq[idx]); s2upper(tmsa->aseq[idx]); } /* another sanity check */ for (idx = 0; idx < kmsa->nseq; idx++) if (strcmp(kmsa->sqname[idx], tmsa->sqname[idx]) != 0) Die("seqs in %s and %s don't seem to be in the same order\n (%s != %s)", kfile, tfile, kmsa->sqname[idx], tmsa->sqname[idx]); /* and *another* sanity check */ DealignAseqs(kmsa->aseq, kmsa->nseq, &kraw); DealignAseqs(tmsa->aseq, tmsa->nseq, &traw); for (idx = 0; idx < kmsa->nseq; idx++) if (strcmp(kraw[idx], traw[idx]) != 0) Die("raw seqs in %s and %s are not the same (died at %s, number %d)\n", kfile, tfile, kmsa->sqname[idx], idx); Free2DArray((void **) kraw, kmsa->nseq); Free2DArray((void **) traw, tmsa->nseq); if (cs_only) { if (kmsa->ss_cons == NULL) Die("Trusted alignment %s has no consensus structure annotation\n -- can't use -c!\n", kfile); ref = (int *) MallocOrDie (sizeof(int) * kmsa->alen); for (apos = 0; apos < kmsa->alen; apos++) ref[apos] = (isgap(kmsa->ss_cons[apos])) ? FALSE : TRUE; } /*********************************************** * Compare the alignments, print results ***********************************************/ if (cs_only) score = CompareRefMultAlignments(ref, kmsa->aseq, tmsa->aseq, kmsa->nseq); else score = CompareMultAlignments(kmsa->aseq, tmsa->aseq, kmsa->nseq); printf("Trusted alignment: %s\n", kmsa->name != NULL ? kmsa->name : kfile); printf("Test alignment: %s\n", tmsa->name != NULL ? tmsa->name : tfile); printf("Total sequences: %d\n", kmsa->nseq); printf("Alignment identity: %.4f\n", score); puts("//"); if (cs_only) free(ref); MSAFree(kmsa); MSAFree(tmsa); } MSAFileClose(kfp); MSAFileClose(tfp); return 0; } squid/compstruct_main.c0000640000175000017520000003207410463223377015474 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* compstruct_main.c * SRE, Tue Aug 30 10:35:31 1994 * * Compare RNA secondary structures. * ***************************************************************** * Note on obtaining sd/variance on individual measurements: * The output is structured so it can be easily postprocessed to obtain * more detailed summary statistics. Output for an individual structure * looks like: * * DA0261: == 100.00 100.00 * 21/21 trusted pairs correctly predicted (100.00% sensitivity) * 21/21 predicted pairs are true (100.00% PPV/specificity) * * If any error occurs parsing a structure, it won't be included * in the totals, and its output would look like: * * seq2: [REJECTED: no test or trusted structure] * * The string "==", therefore, is a unique tag for individual * sequence results. The first number is the sensitivity; the second * is the PPV (specificity) for this structure. * * So, to get variance/sd info, pipe through grep and the avg script: * * Sensitivity statistics: * compstruct trna1415.sto trna1415.sto | grep "==" | avg -f2 * PPV statistics * compstruct trna1415.sto trna1415.sto | grep "==" | avg -f3 * * SRE, Wed Feb 4 08:42:58 2004 * ***************************************************************** * CVS $Id: compstruct_main.c,v 1.11 2004/03/30 21:40:01 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "msa.h" #include "sre_stack.h" static char banner[] = "compstruct - calculate accuracy of RNA secondary structure predictions"; char usage[] = "\ Usage: compstruct [-options] \n\ Both files must contain secondary structure markup (e.g. Stockholm, SQUID,\n\ SELEX formats), and sequences must occur in the same order in the two files.\n\ The markup must be in WUSS notation.\n\ \n\ Available options are:\n\ -h : print short help and usage info\n\ -m : use Mathews' more relaxed criterion for correctness; allow +/-1 slip\n\ -p : count pseudoknotted base pairs (default: ignore them)\n\ "; static char experts[] = "\ --informat : specify that both alignments are in format (SELEX, for instance)\n\ --quiet : suppress verbose header (used in regression testing)\n\ "; struct opt_s OPTIONS[] = { { "-h", TRUE, sqdARG_NONE }, { "-m", TRUE, sqdARG_NONE }, { "-p", TRUE, sqdARG_NONE }, { "--informat", FALSE, sqdARG_STRING }, { "--quiet", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *kfile, *tfile; /* known, test structure file */ int format; /* expected format of kfile, tfile */ SQFILE *kfp, *tfp; /* open kfile, tfile */ char *kseq, *tseq; /* known, test sequence */ SQINFO kinfo, tinfo; /* known, test info */ int *kct, *tct; /* known, test CT rep of structure */ int pos; int nseq; /* total number of sequences in the files */ int nseq_rejected; /* total number of sequences rejected */ int kpairs; /* count of base pairs in a known (trusted) structure */ int tpairs; /* count of base pairs in a test (predicted) structure */ int kcorrect; /* # bp in a known structure that are correctly predicted */ int tcorrect; /* # bp in a test structure that are true */ int tot_kpairs; /* total base pairs in all known structures */ int tot_tpairs; /* total base pairs in all predicted structures */ int tot_kcorrect; /* total correctly predicted pairs in all known structures*/ int tot_tcorrect; /* total true pairs in all test structures */ int tot_positions; /* total # of bases */ int be_quiet; /* TRUE to silence verbose banner */ int do_mathews; /* TRUE to use Mathews' relaxed +/-1 criterion for "correct" */ int count_pseudoknots; /* TRUE to count pseudoknotted base pairs */ char *optname; char *optarg; int optind; /*********************************************** * Parse command line ***********************************************/ format = MSAFILE_UNKNOWN; be_quiet = FALSE; do_mathews = FALSE; count_pseudoknots = FALSE; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-m") == 0) do_mathews = TRUE; else if (strcmp(optname, "-p") == 0) count_pseudoknots = TRUE; else if (strcmp(optname, "--quiet") == 0) be_quiet = TRUE; else if (strcmp(optname, "--informat") == 0) { format = String2SeqfileFormat(optarg); if (format == MSAFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); if (! IsAlignmentFormat(format)) Die("%s is an unaligned format, can't read as an alignment", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 2) Die("Incorrect number of command line arguments.\n%s\n", usage); kfile = argv[optind++]; tfile = argv[optind]; if (! be_quiet) SqdBanner(stdout, banner); /*********************************************** * Open the files ***********************************************/ if ((kfp = SeqfileOpen(kfile, format, NULL)) == NULL) Die("Failed to open trusted structure file %s for reading", kfile); if ((tfp = SeqfileOpen(tfile, format, NULL)) == NULL) Die("Failed to open test structure file %s for reading", tfile); /*********************************************** * Do structure comparisons, one seq at a time ***********************************************/ tot_kpairs = tot_kcorrect = 0; tot_tpairs = tot_tcorrect = 0; nseq = nseq_rejected = 0; tot_positions = 0; while (ReadSeq(kfp, kfp->format, &kseq, &kinfo) && ReadSeq(tfp, tfp->format, &tseq, &tinfo)) { nseq++; printf("%s: ", kinfo.name); /* no \n is deliberate. rest of line is either error msg, or %/% result */ /* We might reject a structure comparison for a variety of * QC reasons. We print "REJECTED" as a greppable tag, with an explanation; * we bump the rejected counter. * * beware: those last two tests are not just tests; they're also running * WUSS2ct() to create the kct,tct structures that we need. So don't muck * around with those tests without preserving the function calls. */ if (strcmp(tinfo.name, kinfo.name) != 0) { printf("[REJECTED: Trusted sequence %s, test sequence %s -- names not identical]\n\n", kinfo.name, tinfo.name); nseq_rejected++; } else if (strcmp(kseq, tseq) != 0) { printf("[REJECTED: Trusted sequence %s, test sequence %s -- sequences not identical]\n\n", kinfo.name, tinfo.name); nseq_rejected++; } else if (! (tinfo.flags & SQINFO_SS) && ! (kinfo.flags & SQINFO_SS)) { printf("[REJECTED: no test or trusted structure]\n\n"); nseq_rejected++; } else if (! (tinfo.flags & SQINFO_SS)) { printf("[REJECTED: no test structure]\n\n"); nseq_rejected++; } else if (! (kinfo.flags & SQINFO_SS)) { printf("[REJECTED: no trusted structure]\n\n"); nseq_rejected++; } else if (! WUSS2ct(kinfo.ss, kinfo.len, count_pseudoknots, &kct)) { printf("[REJECTED: bad trusted structure]\n"); nseq_rejected++; } else if (! WUSS2ct(tinfo.ss, kinfo.len, count_pseudoknots, &tct)) { printf("[bad test structure]\n"); free(kct); /* because the WUSS2ct() call above us must've succeeded */ nseq_rejected++; } else { /* OK, we're all set up, and we're about to count up our correctly predicted * pairs. A brief digression/commentary first. We have to * define what you mean by a "correctly predicted" base * pair. * * Our default criterion is simple and strict: the known base pair * must be exactly present in the prediction; kct[pos] == tct[pos] * where kct[pos] > 0. * * Dave Mathews [MathewsTurner99] uses a more relaxed * criterion that allows a little helix slippage in the prediction. * For a known pair (i,j), he considers the prediction to be correct if * the prediction contains a base pair (i,j), (i+1,j), (i-1,j), (i,j+1), * or (i,j-1). * * A problem that arises here is that the mapping of known * to predicted base pairs is not one-to-one under Mathews' * rule: a single predicted pair can cause two known pairs * to be considered to be "correctly predicted". You'd sort * of like to run some sort of maximum matching algorithm to * assign a one-to-one correspondence between known and * predicted pairs. It does not appear that Mathews does this, * though. * * And for us, the problem becomes a little worse. Mathews only * tabulates "correct" base pairs (our "sensitivity"), and * does not run a calculation of how many predicted pairs * are true (our "specificity", or positive predictive * value). * * So: when we implement the Mathews rule, we do it the most * simple and obvious way. We apply his correctness rule in * both directions. A known pair i,j is considered to be correctly predicted * if the prediction contains any one of the pairs (i,j), (i+1,j), (i-1,j), (i,j+1), * or (i,j-1), for the purposes of sensitivity. Conversely, * a predicted pair i,j is considered to be correct if the * known structure contains any one of the pairs (i,j), (i+1,j), (i-1,j), (i,j+1), * or (i,j-1), for the purposes of PPV. That is, we do not * worry at all about establishing an optimal one-to-one mapping between * known and predicted pairs. We think that this is likely * to reflect Mathews' own implementation, but have not verified this. */ tpairs = tcorrect = 0; /* predicted "test" structure */ kpairs = kcorrect = 0; /* trusted "known" structure */ for (pos = 1; pos <= kinfo.len; pos++) { /* sensitivity; looking from the known (trusted) structure's base pairs. */ if (kct[pos] > pos) /* there is a known base pair between (pos, kct[pos]) */ { kpairs++; /* don't doublecount */ if (do_mathews) { if (tct[pos] == kct[pos] || /* i,j */ (pos > 1 && tct[pos-1] == kct[pos]) || /* i-1, j */ (pos < kinfo.len && tct[pos+1] == kct[pos]) || /* i+1, j */ (tct[pos] > 0 && tct[pos] == kct[pos]-1) || /* i, j-1 */ (tct[pos] > 0 && tct[pos] == kct[pos]+1)) /* i, j+1 */ kcorrect++; } else { if (tct[pos] == kct[pos]) kcorrect++; } } /* specificity; looking from the test (predicted) structure's base pairs. */ if (tct[pos] > pos) /* we have a predicted base pair (pos, tct[pos]) */ { tpairs++; if (do_mathews) { if (kct[pos] == tct[pos] || /* i,j */ (pos > 1 && kct[pos-1] == tct[pos]) || /* i-1, j */ (pos < tinfo.len && kct[pos+1] == tct[pos]) || /* i+1, j */ (kct[pos] > 0 && kct[pos] == tct[pos]-1) || /* i, j-1 */ (kct[pos] > 0 && kct[pos] == tct[pos]+1)) /* i, j+1 */ tcorrect++; } else { if (kct[pos] == tct[pos]) tcorrect++; } } } /* side note: under the default rule, tcorrect==kcorrect, because there's * a one-to-one mapping of known to predicted pairs; but this is not * necessarily the case for the relaxed Mathews rule. */ tot_tpairs += tpairs; tot_tcorrect += tcorrect; tot_kpairs += kpairs; tot_kcorrect += kcorrect; tot_positions += kinfo.len; /* print out per sequence info */ printf(" == %.2f %.2f\n", 100. * (float) kcorrect/ (float) kpairs, 100. * (float) tcorrect/ (float) tpairs); printf(" %d/%d trusted pairs correctly predicted (%.2f%% sensitivity)\n", kcorrect, kpairs, 100. * (float) kcorrect/ (float) kpairs); printf(" %d/%d predicted pairs are true (%.2f%% PPV/specificity)\n", tcorrect, tpairs, 100. * (float) tcorrect/ (float) tpairs); puts(""); free(kct); free(tct); } FreeSequence(kseq, &kinfo); FreeSequence(tseq, &tinfo); } /* And the final summary: */ puts(""); if (nseq_rejected > 0) { printf("%d total sequences; %d counted towards comparison; %d rejected\n", nseq, nseq-nseq_rejected, nseq_rejected); printf(" (grep for \"REJECTED\" in the above output to identify the problems)\n\n"); } printf("Overall structure prediction accuracy (%d sequences, %d positions)\n", nseq - nseq_rejected, tot_positions); printf(" %d/%d trusted pairs predicted (%.2f%% sensitivity)\n", tot_kcorrect, tot_kpairs, 100. * (float) tot_kcorrect/ (float) tot_kpairs); printf(" %d/%d predicted pairs correct (%.2f%% PPV, specificity)\n", tot_tcorrect, tot_tpairs, 100. * (float) tot_tcorrect/ (float) tot_tpairs); puts(""); SeqfileClose(tfp); SeqfileClose(kfp); return 0; } squid/dayhoff.c0000640000175000017520000001222610463223377013702 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* dayhoff.c * * Routines for dealing with PAM matrices. * * Includes: * ParsePAMFile() -- read a PAM matrix from disk. * * * SRE - Fri Apr 2 11:23:45 1993 * CVS $Id: dayhoff.c,v 1.7 2003/05/26 16:21:50 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include #include "squid.h" /* Function: ParsePAMFile() * * Purpose: Given a pointer to an open file containing a PAM matrix, * parse the file and allocate and fill a 2D array of * floats containing the matrix. The PAM file is * assumed to be in the format that NCBI distributes * with BLAST. BLOSUM matrices also work fine, as * produced by Henikoff's program "MATBLAS". * * Parses both old format and new format BLAST matrices. * Old format just had rows of integers. * New format includes a leading character on each row. * * The PAM matrix is a 27x27 matrix, 0=A..25=Z,26=*. * Note that it's not a 20x20 matrix as you might expect; * this is for speed of indexing as well as the ability * to deal with ambiguous characters. * * Args: fp - open PAM file * ret_pam - RETURN: pam matrix, integers * ret_scale - RETURN: scale factor for converting * to real Sij. For instance, PAM120 is * given in units of ln(2)/2. This may * be passed as NULL if the caller * doesn't care. * * Returns: 1 on success; 0 on failure and sets squid_errno to * indicate the cause. ret_pam is allocated here and * must be freed by the caller (use FreePAM). */ int ParsePAMFile(FILE *fp, int ***ret_pam, float *ret_scale) { int **pam; char buffer[512]; /* input buffer from fp */ int order[27]; /* order of fields, obtained from header */ int nsymbols; /* total number of symbols in matrix */ char *sptr; int idx; int row, col; float scale; int gotscale = FALSE; scale = 0.0; /* just to silence gcc uninit warnings */ if (fp == NULL) { squid_errno = SQERR_NODATA; return 0; } /* Look at the first non-blank, non-comment line in the file. * It gives single-letter codes in the order the PAM matrix * is arrayed in the file. */ do { if (fgets(buffer, 512, fp) == NULL) { squid_errno = SQERR_NODATA; return 0; } /* Get the scale factor from the header. * For BLOSUM files, we assume the line looks like: * BLOSUM Clustered Scoring Matrix in 1/2 Bit Units * and we assume that the fraction is always 1/x; * * For PAM files, we assume the line looks like: * PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574 * and we assume that the number following the final '=' is our scale */ if (strstr(buffer, "BLOSUM Clustered Scoring Matrix") != NULL && (sptr = strchr(buffer, '/')) != NULL) { sptr++; if (! isdigit((int) (*sptr))) { squid_errno = SQERR_FORMAT; return 0; } scale = (float) ( (log(2.0)) / (atof(sptr))); gotscale = TRUE; } else if (strstr(buffer, "substitution matrix,") != NULL) { while ((sptr = strrchr(buffer, '=')) != NULL) { sptr += 2; if (IsReal(sptr)) { scale = atof(sptr); gotscale = TRUE; break; } } } } while ((sptr = strtok(buffer, " \t\n")) == NULL || *sptr == '#'); idx = 0; do { order[idx] = (int) *sptr - (int) 'A'; if (order[idx] < 0 || order[idx] > 25) order[idx] = 26; idx++; } while ((sptr = strtok(NULL, " \t\n")) != NULL); nsymbols = idx; /* Allocate a pam matrix. For speed of indexing, we use * a 27x27 matrix so we can do lookups using the ASCII codes * of amino acid single-letter representations, plus one * extra field to deal with the "*" (terminators). */ if ((pam = (int **) calloc (27, sizeof(int *))) == NULL) Die("calloc failed"); for (idx = 0; idx < 27; idx++) if ((pam[idx] = (int *) calloc (27, sizeof(int))) == NULL) Die("calloc failed"); /* Parse the rest of the file. */ for (row = 0; row < nsymbols; row++) { if (fgets(buffer, 512, fp) == NULL) { squid_errno = SQERR_NODATA; return 0; } if ((sptr = strtok(buffer, " \t\n")) == NULL) { squid_errno = SQERR_NODATA; return 0; } for (col = 0; col < nsymbols; col++) { if (sptr == NULL) { squid_errno = SQERR_NODATA; return 0; } /* Watch out for new BLAST format, with leading characters */ if (*sptr == '*' || isalpha((int) *sptr)) col--; /* hack hack */ else pam [order[row]] [order[col]] = atoi(sptr); sptr = strtok(NULL, " \t\n"); } } /* Return */ if (ret_scale != NULL) { if (gotscale) *ret_scale = scale; else { Warn("Failed to parse PAM matrix scale factor. Defaulting to ln(2)/2!"); *ret_scale = log(2.0) / 2.0; } } *ret_pam = pam; return 1; } squid/dirichlet.c0000644000175000017520000003065110463223377014237 0ustar naolivbiolinux/* dirichlet.c * SRE, Sat Oct 25 09:50:56 2003 [Stanford] * * Evaluation of and sampling from Dirichlet densities, mixture * Dirichlet densities, Beta densities, and Gamma densities. * * CVS $Id: dirichlet.c,v 1.1 2003/10/27 21:08:13 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "vectorops.h" #include "sre_random.h" #include "dirichlet.h" /* Function: Gammln() * * Purpose: Returns natural log of gamma(x). * x is > 0.0. * * Adapted from a public domain implementation in the * NCBI core math library. Thanks to John Spouge and * the NCBI. (According to the NCBI, that's Dr. John * "Gammas Galore" Spouge to you, pal.) */ double Gammln(double x) { int i; double xx, tx; double tmp, value; static double cof[11] = { 4.694580336184385e+04, -1.560605207784446e+05, 2.065049568014106e+05, -1.388934775095388e+05, 5.031796415085709e+04, -9.601592329182778e+03, 8.785855930895250e+02, -3.155153906098611e+01, 2.908143421162229e-01, -2.319827630494973e-04, 1.251639670050933e-10 }; if (x <= 0.0) { fprintf(stderr, "invalid x <= 0 in gammln (x = %f)\n", x); exit(1); } xx = x - 1.0; tx = tmp = xx + 11.0; value = 1.0; for (i = 10; i >= 0; i--) /* sum least significant terms first */ { value += cof[i] / tmp; tmp -= 1.0; } value = log(value); tx += 0.5; value += 0.918938533 + (xx+0.5)*log(tx) - tx; return value; } /* Function: IncompleteGamma() * * Purpose: Returns 1 - P(a,x) where: * P(a,x) = \frac{1}{\Gamma(a)} \int_{0}^{x} t^{a-1} e^{-t} dt * = \frac{\gamma(a,x)}{\Gamma(a)} * = 1 - \frac{\Gamma(a,x)}{\Gamma(a)} * * Used in a chi-squared test: for a X^2 statistic x * with v degrees of freedom, call: * p = IncompleteGamma(v/2., x/2.) * to get the probability p that a chi-squared value * greater than x could be obtained by chance even for * a correct model. (i.e. p should be large, say * 0.95 or more). * * Method: Based on ideas from Numerical Recipes in C, Press et al., * Cambridge University Press, 1988. * * Args: a - for instance, degrees of freedom / 2 [a > 0] * x - for instance, chi-squared statistic / 2 [x >= 0] * * Return: 1 - P(a,x). */ double IncompleteGamma(double a, double x) { int iter; /* iteration counter */ if (a <= 0.) Die("IncompleteGamma(): a must be > 0"); if (x < 0.) Die("IncompleteGamma(): x must be >= 0"); /* For x > a + 1 the following gives rapid convergence; * calculate 1 - P(a,x) = \frac{\Gamma(a,x)}{\Gamma(a)}: * use a continued fraction development for \Gamma(a,x). */ if (x > a+1) { double oldp; /* previous value of p */ double nu0, nu1; /* numerators for continued fraction calc */ double de0, de1; /* denominators for continued fraction calc */ nu0 = 0.; /* A_0 = 0 */ de0 = 1.; /* B_0 = 1 */ nu1 = 1.; /* A_1 = 1 */ de1 = x; /* B_1 = x */ oldp = nu1; for (iter = 1; iter < 100; iter++) { /* Continued fraction development: * set A_j = b_j A_j-1 + a_j A_j-2 * B_j = b_j B_j-1 + a_j B_j-2 * We start with A_2, B_2. */ /* j = even: a_j = iter-a, b_j = 1 */ /* A,B_j-2 are in nu0, de0; A,B_j-1 are in nu1,de1 */ nu0 = nu1 + ((double)iter - a) * nu0; de0 = de1 + ((double)iter - a) * de0; /* j = odd: a_j = iter, b_j = x */ /* A,B_j-2 are in nu1, de1; A,B_j-1 in nu0,de0 */ nu1 = x * nu0 + (double) iter * nu1; de1 = x * de0 + (double) iter * de1; /* rescale */ if (de1 != 0.) { nu0 /= de1; de0 /= de1; nu1 /= de1; de1 = 1.; } /* check for convergence */ if (fabs((nu1-oldp)/nu1) < 1.e-7) return nu1 * exp(a * log(x) - x - Gammln(a)); oldp = nu1; } Die("IncompleteGamma(): failed to converge using continued fraction approx"); } else /* x <= a+1 */ { double p; /* current sum */ double val; /* current value used in sum */ /* For x <= a+1 we use a convergent series instead: * P(a,x) = \frac{\gamma(a,x)}{\Gamma(a)}, * where * \gamma(a,x) = e^{-x}x^a \sum_{n=0}{\infty} \frac{\Gamma{a}}{\Gamma{a+1+n}} x^n * which looks appalling but the sum is in fact rearrangeable to * a simple series without the \Gamma functions: * = \frac{1}{a} + \frac{x}{a(a+1)} + \frac{x^2}{a(a+1)(a+2)} ... * and it's obvious that this should converge nicely for x <= a+1. */ p = val = 1. / a; for (iter = 1; iter < 10000; iter++) { val *= x / (a+(double)iter); p += val; if (fabs(val/p) < 1.e-7) return 1. - p * exp(a * log(x) - x - Gammln(a)); } Die("IncompleteGamma(): failed to converge using series approx"); } /*NOTREACHED*/ return 0.; } /* Function: SampleGamma() * Date: SRE, Wed Apr 17 13:10:03 2002 [St. Louis] * * Purpose: Return a random deviate distributed as Gamma(a, 1.). * * Follows Knuth, vol. 2 Seminumerical Algorithms, pp.133-134. * Also relies on examination of the implementation in * the GNU Scientific Library (libgsl). The implementation * relies on three separate gamma function algorithms: * gamma_ahrens(), gamma_integer(), and gamma_fraction(). * * Args: alpha - order of the gamma function * * Returns: a gamma-distributed deviate */ static double gamma_ahrens(double a) /* for a >= 3 */ { double V; /* uniform deviates */ double X,Y; double test; do { do { /* generate candidate X */ Y = tan(SQDCONST_PI*sre_random()); X = Y * sqrt(2.*a -1.) + a - 1.; } while (X <= 0.); /* accept/reject X */ V = sre_random(); test = (1+Y*Y) * exp( (a-1.)* log(X/(a-1.)) - Y*sqrt(2.*a-1.)); } while (V > test); return X; } static double gamma_integer(unsigned int a) /* for small integer a, a < 12 */ { int i; double U,X; U = 1.; for (i = 0; i < a; i++) U *= sre_random_positive(); X = -log(U); return X; } static double gamma_fraction(double a) /* for fractional a, 0 < a < 1 */ { /* Knuth 3.4.1, exercise 16, pp. 586-587 */ double p, U, V, X, q; p = SQDCONST_E / (a + SQDCONST_E); do { U = sre_random(); V = sre_random_positive(); if (U < p) { X = pow(V, 1./a); q = exp(-X); } else { X = 1. - log(V); q = pow(X, a-1.); } U = sre_random(); } while (U >= q); return X; } double SampleGamma(double a) { double aint; aint = floor(a); if (a <= 0.) { fprintf(stderr, "no, you can't give a=0 to sample_gamma()."); exit(1); } else if (a == aint && a < 12.) return gamma_integer((unsigned int) a); else if (a > 3.) return gamma_ahrens(a); else if (a < 1.) return gamma_fraction(a); else return (gamma_ahrens(aint) + gamma_fraction(a-aint)); } /* Function: Dchlet_logp_counts() * Returns log P(cvector | Dirichlet), given * a count vector c, and a mixture Dirichlet d, * both of dimension K. */ double Dchlet_logp_counts(double *c, double *alpha, int K) { double lnp; double sum1, sum2, sum3; int x; sum1 = sum2 = sum3 = lnp = 0.0; for (x = 0; x < K; x++) { sum1 += c[x] + alpha[x]; sum2 += alpha[x]; sum3 += c[x]; lnp += Gammln(alpha[x] + c[x]); lnp -= Gammln(c[x] + 1.); lnp -= Gammln(alpha[x]); } lnp -= Gammln(sum1); lnp += Gammln(sum2); lnp += Gammln(sum3 + 1.); return lnp; } /* Dchlet_logp_probs(): * Given Dirichlet distribution parameters alpha for a single * D'chlet component, and a probability vector p, both of * dimension K; return log P(p | alpha). * * This is Sjolander (1996) lemma 2, in the appendix. */ double Dchlet_logp_probs(double *p, double *alpha, int K) { double sum; /* for Gammln(|alpha|) in Z */ double logp; /* RETURN: log P(p|alpha) */ int x; sum = logp = 0.0; for (x = 0; x < K; x++) if (p[x] > 0.0) /* any param that is == 0.0 doesn't exist */ { logp += (alpha[x]-1.0) * log(p[x]); logp -= Gammln(alpha[x]); sum += alpha[x]; } logp += Gammln(sum); return logp; } /* SampleDirichlet(): * Given a single Dirichlet distribution (one component of * a mixture), sample a probability distribution of dimension K. * The returned probability vector must be pre-allocated by the caller. */ void SampleDirichlet(double *alpha, int K, double *p) { int x; for (x = 0; x < K; x++) p[x] = SampleGamma(alpha[x]); DNorm(p, K); } /***************************************************************** * Beta density (special case of Dirichlets) *****************************************************************/ /* Function: SampleBeta() * Incept: SRE, Sat Oct 25 12:20:31 2003 [Stanford] * * Purpose: Returns a sample from a Beta(theta1, theta2) * density. * */ double SampleBeta(double theta1, double theta2) { double p, q; p = SampleGamma(theta1); q = SampleGamma(theta2); p = p / (p+q); return p; } /* AllocDirichlet(): * returns an allocated structure for a mixture Dirichlet with * N components, for a given alphabet (of size K). For example, for the * Sjolander 9-component amino acid prior, * d = AllocDirichlet(9, "ACDEFGHIKLMNPQRSTVWY"); */ MIXDCHLET * AllocDirichlet(int N, char *alphabet) { MIXDCHLET *d; int i; d = malloc(sizeof(MIXDCHLET)); d->N = N; d->K = strlen(alphabet); d->alphabet = malloc(sizeof(char) * d->K); strcpy(d->alphabet, alphabet); d->q = malloc(sizeof(double) * N); d->alpha = malloc(sizeof(double *) * N); d->alpha[0] = malloc(sizeof(double) * (N*d->K)); for (i = 1; i < N; i++) d->alpha[i] = d->alpha[0] + i*d->K; return d; } /* FreeDirichlet: * free's a structure that was allocated by AllocDirichlet(). */ void FreeDirichlet(MIXDCHLET *d) { free(d->alpha[0]); free(d->alpha); free(d->q); free(d); } /* ReadDirichletFile(): Read in mixture Dirichlet from a file. * Really rudimentary. * File format: * First line contains N, K, alphabet. * Second line: N mixture coefficients (probabilities, floats) * N subsequent lines: K Dirichlet parameters per component, positive reals * All fields are whitespace limited. */ MIXDCHLET * ReadDirichletFile(char *file) { FILE *fp; /* an open file pointer being read */ char buf[LINEBUFLEN]; /* one line at a time is read into buf */ char *s; /* tmp ptr to a field in buf */ MIXDCHLET *d; /* the Dirichlet structure we'll return */ int N; /* # of components */ int i,x; /* counters over components, residues */ if ((fp = fopen(file, "r")) == NULL) { fprintf(stderr, "couldn't open %s for reading\n", file); exit(1); } /* First line: M, K, alphabet. */ if (fgets(buf, LINEBUFLEN, fp) == NULL) goto FAILURE; if ((s = strtok(buf, " \t\n")) == NULL) goto FAILURE; N = atoi(s); if ((s = strtok(NULL, " \t\n")) == NULL) goto FAILURE; d = AllocDirichlet(N, s); /* Second line: distribution over mixture components, q[0..N-1] */ if (fgets(buf, LINEBUFLEN, fp) == NULL) goto FAILURE; s = strtok(buf, " \t\n"); for (i = 0; i < N; i++) { if (s == NULL) goto FAILURE; d->q[i] = atof(s); s = strtok(NULL, " \t\n"); } DNorm(d->q, N); /* good practice: renormalize after reading prob's from file*/ /* All remaining lines: N components of the mixture D'chlet, * each containing K parameters, one line per component. */ for (i = 0; i < N; i++) { if (fgets(buf, LINEBUFLEN, fp) == NULL) goto FAILURE; s = strtok(buf, " \t\n"); for (x = 0; x < d->K; x++) { if (s == NULL) goto FAILURE; d->alpha[i][x] = atof(s); s = strtok(NULL, " \t\n"); } } fclose(fp); return d; FAILURE: fprintf(stderr, "bad format in file %s\n", file); exit(1); } /***************************************************************** * @LICENSE@ *****************************************************************/ squid/eps.c0000640000175000017520000000635510463223377013057 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* eps.c * SRE, Thu Jun 21 18:02:31 2001 [St. Louis] * * Some crude support for Encapsulated PostScript (EPS) output, * DSC compliant. * * CVS $Id: eps.c,v 1.5 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "msa.h" /* Function: EPSWriteSmallMSA() * Date: SRE, Thu Jun 21 18:15:21 2001 [St. Louis] * * Purpose: Write an alignment in singleblock, Stockholm/SELEX like * format to an open file. Very crude. * Currently fails if the alignment is >50 columns long, because * it doesn't think it will fit on a single page. * * Args: fp - open file for writing * msa - alignment to write * * Returns: (void) */ void EPSWriteSmallMSA(FILE *fp, MSA *msa) { int namewidth; /* namewidth in PostScript units */ int fontwidth; /* width of a character in this font */ int hspace; /* horizontal space between aligned chars */ int vspace; /* vertical space between sequences */ char *font; /* font name, e.g. "Courier" */ int fontsize; /* font size in pts */ int i,j; /* counter over sequences, columns */ int len; /* tmp var holding length of something */ int width, height; /* width and height of bounding box */ int xpos, ypos; /* x,y position */ /* Set some font characteristics; done here, so it'll * be easy to change. Magic numbers for Courier 12 determined * by trial and error. */ fontwidth = 8; hspace = 9; vspace = 15; font = sre_strdup("Courier", -1); fontsize = 12; /* Find the width of the longest sequence name in characters. */ namewidth = 0; for (i = 0; i < msa->nseq; i++) if ((len = (int) strlen(msa->sqname[i])) > namewidth) namewidth = len; namewidth += 1; /* add a space to separate name & aligned seq */ namewidth *= fontwidth; /* Determine bounding box */ if (msa->alen > 50) Die("No EPS fmt if alignment is >50 columns"); width = namewidth + hspace*msa->alen; if (width > 612) Die("Alignment too wide to write in EPS"); height = vspace*msa->nseq; if (height > 792) Die("Too many seqs to write in EPS"); /* Magic EPS header, bare-bones DSC-compliant. */ fprintf(fp, "%%!PS-Adobe-3.0 EPSF-3.0\n"); fprintf(fp, "%%%%BoundingBox: %d %d %d %d\n", 0, 0, width, height); fprintf(fp, "%%%%Pages: 1\n"); fprintf(fp, "%%%%EndComments\n"); /* More postscript magic before we start the alignment */ fprintf(fp, "/%s findfont\n", font); fprintf(fp, "%d scalefont\n", fontsize); fprintf(fp, "setfont\n"); fprintf(fp, "newpath\n"); /* Write the alignment in PostScript in a single block */ for (i = 0; i < msa->nseq; i++) { ypos = (msa->nseq-i-1)*vspace; /* name first */ fprintf(fp, "%d %d moveto\n", 0, ypos); fprintf(fp, "(%s) show\n", msa->sqname[i]); /* now seq */ xpos = namewidth; for (j = 0; j < msa->alen; j++) { fprintf(fp, "%d %d moveto\n", xpos, ypos); fprintf(fp, "(%c) show\n", msa->aseq[i][j]); xpos+= hspace; } } free(font); } squid/file.c0000640000175000017520000001770310463223377013206 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* file.c * SRE, Wed Jun 19 11:19:22 1996 * * File operation utilities, dealing with pathnames, directories, * and environment variables. * * The goal is to have these be platform-independent but they * currently are UNIX-specific: i.e. this file is currently POSIX compliant * but it is NOT ANSI C compliant. (The sole offender is getenv().) * * CVS $Id: file.c,v 1.9 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "sqfuncs.h" /* * VMS: #define DIRSLASH ']' * MacOS: #define DIRSLASH ':' * DOS: #define DIRSLASH '\\' * * The code assumes that '.' is used for file name extensions, * such as "foo.bar". */ #define DIRSLASH '/' /* UNIX directory paths have /foo/bar */ /* Function: FileDirname() * * Purpose: Returns the path from a filename: * "/foo/bar/baz" -> "/foo/bar" * "foo/bar" -> "foo" * "foo" -> "." * "/" -> "/" * i.e. the string will be non-NULL; it will * contain the string up to but not including the * last '/' character; returns "." if * there are no '/' characters, and returns "/" * if the last slash is the first character. * Modeled on Tcl's "file dirname" command. * * Args: file - name of file "/foo/bar/baz". * * Return: ptr to malloc'ed string "/foo/bar". */ char * FileDirname(char *file) { char *dirname; char *lastslash; int len; lastslash = strrchr(file, DIRSLASH); len = (lastslash == NULL) ? 0 : (int) (lastslash - file); dirname = (char *) MallocOrDie (sizeof(char) * (len+2)); if (len > 0) strncpy(dirname, file, len); else if (*file != DIRSLASH) { *dirname = '.'; len = 1; } else { *dirname = DIRSLASH; len = 1; } dirname[len] = '\0'; return dirname; } /* Function: FileTail() * * Purpose: Return everything after the DIRSLASH: * "/foo/bar/baz.1" -> "baz.1" * "foo/bar" -> "bar" * "foo" -> "foo" * "/" -> "" * If noextension is TRUE, removes a trailing ".foo" extension * too. * * Args: file - name of file "/foo/bar/baz.1" * noextension - TRUE to also remove extensions * * Return: ptr to malloc'ed string "baz.1" */ char * FileTail(char *file, int noextension) { char *tail; char *lastslash; char *lastdot; /* remove directory prefix */ lastslash = strrchr(file, DIRSLASH); tail = (char *) MallocOrDie (sizeof(char) * (strlen(file)+1)); if (lastslash == NULL) strcpy(tail, file); else strcpy(tail, lastslash+1); /* remove trailing suffix */ if (noextension) { if ((lastdot = strrchr(tail, '.')) != NULL) *lastdot = '\0'; } return tail; } /* Function: FileSameDirectory() * Date: SRE, Wed Mar 6 20:03:23 2002 [St. Louis] * * Purpose: Given a path to one file, and the * name of another file in the same directory, * concat the path from file1 onto file2, and * return the result. Caller must free the ptr * that's returned. * * Written for SSI - SSI indices contain filenames * without paths, and we will need to convert that * to a full path. * * Args: file1 - a path to a file, e.g. "/foo/bar/baz.1" * file2 - a simple filename, e.g. "quux.2" * * Returns: path to file2: e.g. "/foo/bar/quux.2" * Returns NULL if file2 already has a path, and the result * would be a different place. */ char * FileSameDirectory(char *file1, char *file2) { char *path; char *tail; char *result; int seems_ok = 1; path = FileDirname(file1); tail = FileTail(file2, FALSE); if (strcmp(file2, tail) != 0) seems_ok = 0; /* ut-oh, file2 *had* a path */ result = FileConcat(path, tail); if (! seems_ok && strcmp(result, file2) != 0) { free(result); result = NULL; } free(path); free(tail); return result; } /* Function: FileConcat() * * Purpose: Concatenate a directory path and a file name, * returning a pointer to a malloc'ed string with the * full filename. This isn't just a string concat, * because we're careful about the dir slash. */ char * FileConcat(char *dir, char *file) { char *full; full = (char *) MallocOrDie (sizeof(char) * (strlen(dir)+strlen(file)+2)); if (*file == DIRSLASH) strcpy(full, file); /* file = "/foo", ignore directory. */ else sprintf(full, "%s%c%s", dir, DIRSLASH, file); return full; } /* Function: FileAddSuffix() * Date: SRE, Wed Aug 1 11:19:33 2001 [Pasadena] * * Purpose: Add a suffix to a filename, return a malloc'ed * string containing the new filename.sfx name. * Example: * FileAddSuffix("genbank", "ssi") * returns "genbank.ssi". */ char * FileAddSuffix(char *filename, char *sfx) { char *new; new = MallocOrDie(strlen(filename) + strlen(sfx) + 2); sprintf(new, "%s.%s", filename, sfx); return new; } /* Function: EnvFileOpen() * Date: Sun Feb 12 10:55:29 1995 * * Purpose: Open a file, given a file name and an environment * variable that contains a directory path. Files * are opened read-only. Does not look at current directory * unless "." is explicitly in the path specified by env. * * For instance: * fp = EnvFileOpen("BLOSUM45", "BLASTMAT", NULL); * or: * fp = EnvFileOpen("swiss", "BLASTDB", NULL); * * Environment variables may contain a colon-delimited * list of more than one path; e.g. * setenv BLASTDB /nfs/databases/foo:/nfs/databases/bar * * Sometimes a group of files may be found in * one directory; for instance, an index file with a * database. The caller can EnvFileOpen() the main * file, and ask to get the name of the * directory back in ret_dir, so it can construct * the other auxiliary file names and fopen() them. (If it called * EnvFileOpen(), it might get confused by * file name clashes and open files in different * directories. * * Args: fname - name of file to open * env - name of environment variable containing path * ret_dir - if non-NULL, RETURN: name of dir that was used. * * Return: FILE * to open file, or NULL on failure -- same as fopen() * Caller must free ret_dir if it passed a non-NULL address. */ FILE * EnvFileOpen(char *fname, char *env, char **ret_dir) { FILE *fp; char *path; char *s; /* ptr to indiv element in env list */ char full[1024]; /* constructed file name */ if (env == NULL) return NULL; if ((path = Strdup(getenv(env))) == NULL) return NULL; fp = NULL; s = strtok(path, ":"); while (s != NULL) { if (((int) strlen(fname) + (int) strlen(s) + 2) > 1024) { free(path); return NULL; } sprintf(full, "%s%c%s", s, DIRSLASH, fname); if ((fp = fopen(full, "r")) != NULL) break; s = strtok(NULL, ":"); } /* Return the path we used, if caller wants it */ if (ret_dir != NULL) *ret_dir = Strdup(s); free(path); return fp; } /* Function: FileExists() * * Purpose: Return TRUE if filename exists. * Testing fopen() is the only possible platform-independent test * I'm aware of. */ int FileExists(char *filename) { FILE *fp; if ((fp = fopen(filename, "r"))) { fclose(fp); return TRUE; } return FALSE; } squid/getopt.c0000640000175000017520000001656610463223377013577 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* CVS $Id: getopt.c,v 1.8 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" /* Function: Getopt() * * Purpose: Portable command line option parsing with abbreviated * option switches. Replaces UNIX getopt(). Using UNIX getopt() * hinders portability to non-UNIX platforms, and getopt() * is also limited to single letter options. * * Getopt() implements a superset of UNIX getopt(). * All of getopt()'s single-character switch behavior * is emulated, and "--" by itself terminates the options. * Additionally, Getopt() provides extended switches * like "--youroptionhere", and Getopt() type checks * arguments. * * Extended options must start with "--", as in "--option1". * Normal options must start with "-", as in "-o". * Normal options may be concatenated, as in "-a -b" == "-ab". * * See bottom of this .c file after #fdef GETOPT_TESTDRIVER * for an example of calling Getopt(). * * Args: argc - from main(). number of elems in argv. * argv - from main(). argv[0] is the name of the command. * opt - array of opt_s structures, defining option switches * nopts - number of switches in opt * usage - a (possibly long) string to print if usage error. * ret_optind - RETURN: the index in argv[] of the next * valid command-line token. * ret_optname- RETURN: ptr to the name of option switch * seen, or NULL if no option was seen. * ret_optarg - RETURN: ptr to the optional argument, if any; * NULL if option takes no argument. * * Return: 1 if a valid option was parsed. * 0 if no option was found, and command-line parsing is complete. * Die()'s here if an error is detected. */ int Getopt(int argc, char **argv, struct opt_s *opt, int nopts, char *usage, int *ret_optind, char **ret_optname, char **ret_optarg) { int i; int arglen; int nmatch; static int optind = 1; /* init to 1 on first call */ static char *optptr = NULL; /* ptr to next valid switch */ int opti = 0; /* init only to silence gcc uninit warnings */ /* Check to see if we've run out of options. * A '-' by itself is an argument (e.g. "read from stdin") * not an option. */ if (optind >= argc || argv[optind][0] != '-' || strcmp(argv[optind], "-") == 0) { *ret_optind = optind; *ret_optarg = NULL; *ret_optname = NULL; return 0; } /* Check to see if we're being told that this is the end * of the options with the special "--" flag. */ if (strcmp(argv[optind], "--") == 0) { optind++; *ret_optind = optind; *ret_optname = NULL; *ret_optarg = NULL; return 0; } /* We have a real option. Find which one it is. * We handle single letter switches "-o" separately * from full switches "--option", based on the "-" vs. "--" * prefix -- single letter switches can be concatenated * as long as they don't have arguments. */ /* full option */ if (optptr == NULL && strncmp(argv[optind], "--", 2) == 0) { /* Use optptr to parse argument in options of form "--foo=666" */ if ((optptr = strchr(argv[optind], '=')) != NULL) { *optptr = '\0'; optptr++; } arglen = strlen(argv[optind]); nmatch = 0; for (i = 0; i < nopts; i++) if (opt[i].single == FALSE && strncmp(opt[i].name, argv[optind], arglen) == 0) { nmatch++; opti = i; if (arglen == strlen(opt[i].name)) break; /* exact match, stop now */ } if (nmatch > 1 && arglen != strlen(opt[i].name)) Die("Option \"%s\" is ambiguous; please be more specific.\n%s", argv[optind], usage); if (nmatch == 0) Die("No such option \"%s\".\n%s", argv[optind], usage); *ret_optname = opt[opti].name; /* Set the argument, if there is one */ if (opt[opti].argtype != sqdARG_NONE) { if (optptr != NULL) { /* --foo=666 style */ *ret_optarg = optptr; optptr = NULL; optind++; } else if (optind+1 >= argc) Die("Option %s requires an argument\n%s", opt[opti].name, usage); else /* "--foo 666" style */ { *ret_optarg = argv[optind+1]; optind+=2; } } else /* sqdARG_NONE */ { if (optptr != NULL) Die("Option %s does not take an argument\n%s", opt[opti].name, usage); *ret_optarg = NULL; optind++; } } else /* else, a single letter option "-o" */ { /* find the option */ if (optptr == NULL) optptr = argv[optind]+1; for (opti = -1, i = 0; i < nopts; i++) if (opt[i].single == TRUE && *optptr == opt[i].name[1]) { opti = i; break; } if (opti == -1) Die("No such option \"%c\".\n%s", *optptr, usage); *ret_optname = opt[opti].name; /* set the argument, if there is one */ if (opt[opti].argtype != sqdARG_NONE) { if (*(optptr+1) != '\0') /* attached argument */ { *ret_optarg = optptr+1; optind++; } else if (optind+1 < argc) /* unattached argument */ { *ret_optarg = argv[optind+1]; optind+=2; } else Die("Option %s requires an argument\n%s", opt[opti].name, usage); optptr = NULL; /* can't concatenate after an argument */ } else /* sqdARG_NONE */ { *ret_optarg = NULL; if (*(optptr+1) != '\0') /* concatenation */ optptr++; else { optind++; /* move to next field */ optptr = NULL; } } } /* Type check the argument, if there is one */ if (opt[opti].argtype != sqdARG_NONE) { if (opt[opti].argtype == sqdARG_INT && ! IsInt(*ret_optarg)) Die("Option %s requires an integer argument\n%s", opt[opti].name, usage); else if (opt[opti].argtype == sqdARG_FLOAT && ! IsReal(*ret_optarg)) Die("Option %s requires a numerical argument\n%s", opt[opti].name, usage); else if (opt[opti].argtype == sqdARG_CHAR && strlen(*ret_optarg) != 1) Die("Option %s requires a single-character argument\n%s", opt[opti].name, usage); /* sqdARG_STRING is always ok, no type check necessary */ } *ret_optind = optind; return 1; } #ifdef GETOPT_TESTDRIVER /* cc -DGETOPT_TESTDRIVER -L ~/lib/squid.linux/ getopt.c -lsquid */ struct opt_s OPTIONS[] = { { "--test1", FALSE, sqdARG_INT }, { "--test2", FALSE, sqdARG_FLOAT }, { "--test3", FALSE, sqdARG_STRING }, { "--test4", FALSE, sqdARG_CHAR }, { "-a", TRUE, sqdARG_NONE }, { "-b", TRUE, sqdARG_INT }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { int optind; char *optarg; char *optname; while (Getopt(argc, argv, OPTIONS, NOPTIONS, "Usage/help here", &optind, &optname, &optarg)) { printf("Option: index: %d name: %s argument: %s\n", optind, optname, optarg); } while (optind < argc) { printf("Argument: index: %d name: %s\n", optind, argv[optind]); optind++; } } #endif /*GETOPT_TESTDRIVER*/ squid/gki.c0000640000175000017520000002554410463223377013043 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* gki.c * SRE, Sat May 1 14:49:08 1999 * * "generic key index" module: emulation of Perl hashes. * Maps keys (ASCII char strings) to array index. Dynamically * resizes the hash table. * * Limitations: * - hash table can only grow; no provision for deleting keys * or downsizing the hash table. * - Maximum hash table size set at 100003. Performance * will degrade for key sets much larger than this. * - Assumes that integers are 32 bits (or greater). * * Defines a typedef'd structure: * gki - a key index hash table. * Provides functions: * GKIInit() - start a hash table. * GKIStoreKey() - store a new key, get a unique index. * GKIKeyIndex() - retrieve an existing key's index. * GKIFree() - free a hash table. * GKIStatus() - Debugging: prints internal status of a hash struct * * * Note that there are no dependencies on squid; the gki.c/gki.h * pair are base ANSI C and can be reused anywhere. ***************************************************************** * * API for storing/reading stuff: * moral equivalent of Perl's $foo{$key} = whatever, $bar{$key} = whatever: * #include "gki.h" * * gki *hash; * int idx; * char *key; * * hash = GKIInit(); * (Storing:) * (foreach key) { * idx = GKIStoreKey(hash, key); * (reallocate foo, bar as needed) * foo[idx] = whatever; * bar[idx] = whatever; * } * (Reading:) * (foreach key) { * idx = GKIKeyIndex(hash, key); * if (idx == -1) {no_such_key; } * (do something with) foo[idx]; * (do something with) bar[idx]; * } * GKIFree(); * ***************************************************************** * * Timings on wrasse for 45402 keys in /usr/dict/words using * Tests/test_gki: * 250 msec store (6 usec/store) * 140 msec retrieve (3 usec/retrieve) * and using the 13408 names of Pfam's GP120.full alignment: * 70 msec store (5 usec/store) * 50 msec retrieve (4 usec/retrieve) * * CVS $Id: gki.c,v 1.4 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "gki.h" /* * Best hash table sizes are prime numbers (see Knuth vol 3, Sorting * and Searching). * gki_primes[] defines the ascending order of hash table sizes * that we use in upsizing the hash table dynamically. * useful site for testing primes: * http://www.idbsu.edu/people/jbrennan/algebra/numbers/sieve.html * Because of the way gki_hashvalue works, the largest number * must be < INT_MAX / 128 / 128 : 131072 on a 32 bit machine. */ static int gki_primes[] = { 101, 1009, 10007, 100003 }; #define GKI_NPRIMES 4 #define GKI_ALPHABETSIZE 128 static GKI *gki_alloc(int primelevel); static int gki_hashvalue(GKI *hash, char *key); static int gki_upsize(GKI *old); /* Function: GKIInit() * Date: SRE, Sat May 1 11:12:24 1999 [May Day geek-out] * * Purpose: Initialize a hash table for key indexing. * Simply a wrapper around a level 0 gki_alloc(). * * Args: (void) * * Returns: An allocated hash table structure. * Caller frees with GKIFree(). */ GKI * GKIInit(void) { GKI *hash; hash = gki_alloc(0); return hash; } /* Function: GKIFree() * Date: SRE, Sat May 1 11:13:26 1999 [May Day geek-out] * * Purpose: Free a key index hash table. * * Args: hash - the gki structure * * Returns: (void). * hash table is destroyed. */ void GKIFree(GKI *hash) { struct gki_elem *ptr; int i; if (hash == NULL) return; /* tolerate a NULL */ for (i = 0; i < hash->nhash; i++) while (hash->table[i] != NULL) { ptr = hash->table[i]->nxt; /* NULL keys can occur after we've gki_upsize'd */ if (hash->table[i]->key != NULL) free(hash->table[i]->key); free(hash->table[i]); hash->table[i] = ptr; } free(hash->table); free(hash); } /* Function: GKIStoreKey() * Date: SRE, Sat May 1 11:16:48 1999 [May Day geek-out] * * Purpose: Store a key in the key index hash table. * Associate it with a unique "key index", counting * from 0. (It's this index that lets us map * the hashed keys to indexed C arrays, (clumsily) * emulating Perl's hashes.) * * Does *not* check to see if the key's already * in the table, so it's possible to store multiple * copies of a key with different indices; probably * not what you want, so if you're not sure the * key is unique, check the table first with * GKIKeyIndex(). * * Args: hash - GKI structure to store the key in * key - string to store * * Returns: the new key's index. Since it's always the * last one in the current array, this index is * just hash->nkeys-1. * On a malloc failure, returns -1. * hash table is modified. */ int GKIStoreKey(GKI *hash, char *key) { int val; struct gki_elem *ptr; val = gki_hashvalue(hash, key); ptr = hash->table[val]; hash->table[val] = MallocOrDie(sizeof(struct gki_elem)); hash->table[val]->key = MallocOrDie(sizeof(char) * (strlen(key)+1)); strcpy(hash->table[val]->key, key); hash->table[val]->idx = hash->nkeys; hash->table[val]->nxt = ptr; hash->nkeys++; /* time to upsize? */ if (hash->nkeys > 3*hash->nhash && hash->primelevel < GKI_NPRIMES-1) gki_upsize(hash); return hash->nkeys-1; } /* Function: GKIKeyIndex() * Date: SRE, Sat May 1 11:20:42 1999 [May Day geek-out] * * Purpose: Look up a key in the hash table. Return * its index (0..nkeys-1), else -1 if the key * isn't in the hash (yet). * * Args: hash - the GKI hash table to search in * key - the key to look up * * Returns: -1 if key is not found; * index of key if it is found (range 0..nkeys-1). * hash table is unchanged. */ int GKIKeyIndex(GKI *hash, char *key) { struct gki_elem *ptr; int val; val = gki_hashvalue(hash, key); for (ptr = hash->table[val]; ptr != NULL; ptr = ptr->nxt) if (strcmp(key, ptr->key) == 0) return ptr->idx; return -1; } /* Function: GKIStatus() * Date: SRE, Sat May 1 11:11:13 1999 [St. Louis] * * Purpose: (DEBUGGING) How are we doing? Calculate some * simple statistics for the hash table. * * Args: hash - the GKI hash table to look at * * Returns: (void) * Prints diagnostics on stdout. * hash table is unchanged. */ void GKIStatus(GKI *hash) { struct gki_elem *ptr; int i; int nkeys; int nempty = 0; int maxkeys = -1; int minkeys = INT_MAX; for (i = 0; i < hash->nhash; i++) { nkeys = 0; for (ptr = hash->table[i]; ptr != NULL; ptr = ptr->nxt) nkeys++; if (nkeys == 0) nempty++; if (nkeys > maxkeys) maxkeys = nkeys; if (nkeys < minkeys) minkeys = nkeys; } printf("Total keys: %d\n", hash->nkeys); printf("Hash table size: %d\n", hash->nhash); printf("Average occupancy: %.1f\n", (float) hash->nkeys / (float) hash->nhash); printf("Unoccupied slots: %d\n", nempty); printf("Most in one slot: %d\n", maxkeys); printf("Least in one slot: %d\n", minkeys); } /* Function: gki_alloc() * Date: SRE, Sat May 1 11:55:47 1999 [May Day geek-out] * * Purpose: Allocate a hash table structure with the * size given by primelevel. * * Args: primelevel - level 0..GKI_NPRIMES-1, specifying * the size of the table; see gki_primes[] * array. * * Returns: An allocated hash table structure. * Caller frees with GKIFree(). */ static GKI * gki_alloc(int primelevel) { GKI *hash; int i; if (primelevel < 0 || primelevel >= GKI_NPRIMES) Die("bad primelevel in gki_alloc()"); hash = MallocOrDie(sizeof(GKI)); hash->primelevel = primelevel; hash->nhash = gki_primes[hash->primelevel]; hash->table = MallocOrDie(sizeof(struct gki_elem) * hash->nhash); for (i = 0; i < hash->nhash; i++) hash->table[i] = NULL; hash->nkeys = 0; return hash; } /* Function: gki_hashvalue() * Date: SRE, Sat May 1 11:14:10 1999 [May Day geek-out] * * Purpose: Calculate the hash value for a key. Usually * we expect a one-word key, but the function will * hash any ASCII string effectively. The hash function * is a simple one (see p. 233 of Sedgewick, * Algorithms in C). * Slightly optimized: does two characters at a time * before doing the modulo; this gives us a significant * speedup. * * Args: hash - the gki structure (we need to know the hash table size) * key - a string to calculate the hash value for * * Returns: a hash value, in the range 0..hash->nhash-1. * hash table is unmodified. */ static int gki_hashvalue(GKI *hash, char *key) { int val = 0; for (; *key != '\0'; key++) { val = GKI_ALPHABETSIZE*val + *key; if (*(++key) == '\0') { val = val % hash->nhash; break; } val = (GKI_ALPHABETSIZE*val + *key) % hash->nhash; } return val; } /* Function: gki_upsize() * Date: SRE, Sat May 1 11:46:07 1999 [May Day geek-out] * * Purpose: Grow the hash table to the next available size. * * Args: old - the GKI hash table to reallocate. * * Returns: 1 on success (the hash table is changed); * 0 on failure; the table is already at its maximum size, * and the hash table is returned unchanged. */ static int gki_upsize(GKI *old) { GKI *new; int i; struct gki_elem *optr; struct gki_elem *nptr; int val; if (old->primelevel >= GKI_NPRIMES-1) return 0; new = gki_alloc(old->primelevel+1); /* Read the old, store in the new, while *not changing* * any key indices. Because of the way the lists are * treated as LIFO stacks, all the lists are reversed * in the new structure. */ for (i = 0; i < old->nhash; i++) { optr = old->table[i]; while (optr != NULL) { val = gki_hashvalue(new, optr->key); nptr = new->table[val]; new->table[val] = optr; optr = optr->nxt; new->table[val]->nxt = nptr; } } free(old->table); /* Now swap within the interior of the structures, so the old * structure is updated to the new structure. * (nkeys is identical, so we don't need to swap that element.) */ old->primelevel = new->primelevel; old->nhash = new->nhash; old->table = new->table; free(new); return 1; } squid/hsregex.c0000640000175000017520000010304010463223377013722 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /***************************************************************** * This code is an altered version of Henry Spencer's * regex library. Alterations are limited to minor streamlining, * and some name changes to protect the SQUID namespace. * Henry's copyright notice appears below. * You can obtain the original from * ftp://ftp.zoo.toronto.edu/pub/bookregex.tar.Z * Thanks, Henry! * * The magic word for compiling a testdriver: NBA_TEAM_IN_STL * gcc -o test -g -DNBA_TEAM_IN_STL -L. hsregex.c -lsquid -lm * * Usage: * test * * SRE, Fri Aug 28 11:10:17 1998 * CVS $Id: hsregex.c,v 1.9 2003/10/04 18:26:49 eddy Exp $ *****************************************************************/ #include "squidconf.h" #include #include #include #include #include "squid.h" /* global sqd_parse[] are managed by Strparse(). * WARNING: TODO: this code is not threadsafe, and needs to be revised. */ char *sqd_parse[10]; /* Function: Strparse() * * Purpose: Match a regexp to a string. Returns 1 if pattern matches, * else 0. * * Much like Perl, Strparse() makes copies of the matching * substrings available via globals, sqd_parse[]. * sqd_parse[0] contains a copy of the complete matched * text. sqd_parse[1-9] contain copies of up to nine * different substrings matched within parentheses. * The memory for these strings is internally managed and * volatile; the next call to Strparse() may destroy them. * If the caller needs the matched substrings to persist * beyond a new Strparse() call, it must make its own * copies. * * A minor drawback of the memory management is that * there will be a small amount of unfree'd memory being * managed by Strparse() when a program exits; this may * confuse memory debugging (Purify, dbmalloc). The * general cleanup function SqdClean() is provided; * you can call this before exiting. * * Uses an extended POSIX regular expression interface. * A copylefted GNU implementation is included in the squid * implementation (gnuregex.c) for use on non-POSIX compliant * systems. POSIX 1003.2-compliant systems (all UNIX, * some WinNT, I believe) can omit the GNU code if necessary. * * I built this for ease of use, not speed nor efficiency. * * Example: Strparse("foo-...-baz", "foo-bar-baz") returns 0 * Strparse("foo-(...)-baz", "foo-bar-baz") * returns 0; sqd_parse[0] is "foo-bar-baz"; * sqd_parse[1] is "bar". * * A real example: * s = ">gnl|ti|3 G10P69425RH2.T0 {SUB 81..737} /len=657" * pat = "SUB ([0-9]+)" * Strparse(pat, s, 1) * returns 1; sqd_parse[1] is "81". * * Args: rexp - regular expression, extended POSIX form * s - string to match against * ntok - number of () substrings we will save (maximum NSUBEXP-1) * * Return: 1 on match, 0 if no match */ int Strparse(char *rexp, char *s, int ntok) { sqd_regexp *pat; int code; int len; int i; /* sanity check */ if (ntok >= NSUBEXP ) Die("Strparse(): ntok must be <= %d", NSUBEXP-1); /* Free previous global substring buffers */ for (i = 0; i <= ntok; i++) if (sqd_parse[i] != NULL) { free(sqd_parse[i]); sqd_parse[i] = NULL; } /* Compile and match the pattern, using our modified * copy of Henry Spencer's regexp library */ if ((pat = sqd_regcomp(rexp)) == NULL) Die("regexp compilation failed."); code = sqd_regexec(pat, s); /* Fill the global substring buffers */ if (code == 1) for (i = 0; i <= ntok; i++) if (pat->startp[i] != NULL && pat->endp[i] != NULL) { len = pat->endp[i] - pat->startp[i]; sqd_parse[i] = (char *) MallocOrDie(sizeof(char) * (len+1)); strncpy(sqd_parse[i], pat->startp[i], len); sqd_parse[i][len] = '\0'; } free(pat); return code; } /* Function: SqdClean() * Date: SRE, Wed Oct 29 12:52:08 1997 [TWA 721] * * Purpose: Clean up any squid library allocations before exiting * a program, so we don't leave unfree'd memory around * and confuse a malloc debugger like Purify or dbmalloc. */ void SqdClean(void) { int i; /* Free global substring buffers that Strparse() uses */ for (i = 0; i <= 9; i++) if (sqd_parse[i] != NULL) { free(sqd_parse[i]); sqd_parse[i] = NULL; } } /* all code below is: * Copyright (c) 1986, 1993, 1995 by University of Toronto. * Written by Henry Spencer. Not derived from licensed software. * * Permission is granted to anyone to use this software for any * purpose on any computer system, and to redistribute it in any way, * subject to the following restrictions: * * 1. The author is not responsible for the consequences of use of * this software, no matter how awful, even if they arise * from defects in it. * * 2. The origin of this software must not be misrepresented, either * by explicit claim or by omission. * * 3. Altered versions must be plainly marked as such, and must not * be misrepresented (by explicit claim or omission) as being * the original software. * * 4. This notice must not be removed or altered. */ /* * sqd_regcomp and sqd_regexec -- sqd_regsub and sqd_regerror are elsewhere */ /* * The first byte of the regexp internal "program" is actually this magic * number; the start node begins in the second byte. */ #define SQD_REGMAGIC 0234 /* * The "internal use only" fields in regexp.h are present to pass info from * compile to execute that permits the execute phase to run lots faster on * simple cases. They are: * * regstart char that must begin a match; '\0' if none obvious * reganch is the match anchored (at beginning-of-line only)? * regmust string (pointer into program) that match must include, or NULL * regmlen length of regmust string * * Regstart and reganch permit very fast decisions on suitable starting points * for a match, cutting down the work a lot. Regmust permits fast rejection * of lines that cannot possibly match. The regmust tests are costly enough * that sqd_regcomp() supplies a regmust only if the r.e. contains something * potentially expensive (at present, the only such thing detected is * or + * at the start of the r.e., which can involve a lot of backup). Regmlen is * supplied because the test in sqd_regexec() needs it and sqd_regcomp() is computing * it anyway. */ /* * Structure for regexp "program". This is essentially a linear encoding * of a nondeterministic finite-state machine (aka syntax charts or * "railroad normal form" in parsing technology). Each node is an opcode * plus a "next" pointer, possibly plus an operand. "Next" pointers of * all nodes except BRANCH implement concatenation; a "next" pointer with * a BRANCH on both ends of it is connecting two alternatives. (Here we * have one of the subtle syntax dependencies: an individual BRANCH (as * opposed to a collection of them) is never concatenated with anything * because of operator precedence.) The operand of some types of node is * a literal string; for others, it is a node leading into a sub-FSM. In * particular, the operand of a BRANCH node is the first node of the branch. * (NB this is *not* a tree structure: the tail of the branch connects * to the thing following the set of BRANCHes.) The opcodes are: */ /* definition number opnd? meaning */ #define END 0 /* no End of program. */ #define BOL 1 /* no Match beginning of line. */ #define EOL 2 /* no Match end of line. */ #define ANY 3 /* no Match any character. */ #define ANYOF 4 /* str Match any of these. */ #define ANYBUT 5 /* str Match any but one of these. */ #define BRANCH 6 /* node Match this, or the next..\&. */ #define BACK 7 /* no "next" ptr points backward. */ #define EXACTLY 8 /* str Match this string. */ #define NOTHING 9 /* no Match empty string. */ #define STAR 10 /* node Match this 0 or more times. */ #define PLUS 11 /* node Match this 1 or more times. */ #define OPEN 20 /* no Sub-RE starts here. */ /* OPEN+1 is number 1, etc. */ #define CLOSE 30 /* no Analogous to OPEN. */ /* * Opcode notes: * * BRANCH The set of branches constituting a single choice are hooked * together with their "next" pointers, since precedence prevents * anything being concatenated to any individual branch. The * "next" pointer of the last BRANCH in a choice points to the * thing following the whole choice. This is also where the * final "next" pointer of each individual branch points; each * branch starts with the operand node of a BRANCH node. * * BACK Normal "next" pointers all implicitly point forward; BACK * exists to make loop structures possible. * * STAR,PLUS '?', and complex '*' and '+', are implemented as circular * BRANCH structures using BACK. Simple cases (one character * per match) are implemented with STAR and PLUS for speed * and to minimize recursive plunges. * * OPEN,CLOSE ...are numbered at compile time. */ /* * A node is one char of opcode followed by two chars of "next" pointer. * "Next" pointers are stored as two 8-bit pieces, high order first. The * value is a positive offset from the opcode of the node containing it. * An operand, if any, simply follows the node. (Note that much of the * code generation knows about this implicit relationship.) * * Using two bytes for the "next" pointer is vast overkill for most things, * but allows patterns to get big without disasters. */ #define OP(p) (*(p)) #define NEXT(p) (((*((p)+1)&0177)<<8) + (*((p)+2)&0377)) #define OPERAND(p) ((p) + 3) /* * Utility definitions. */ #define FAIL(m) { sqd_regerror(m); return(NULL); } #define ISREPN(c) ((c) == '*' || (c) == '+' || (c) == '?') #define META "^$.[()|?+*\\" /* * Flags to be passed up and down. */ #define HASWIDTH 01 /* Known never to match null string. */ #define SIMPLE 02 /* Simple enough to be STAR/PLUS operand. */ #define SPSTART 04 /* Starts with * or +. */ #define WORST 0 /* Worst case. */ /* * Work-variable struct for sqd_regcomp(). */ struct comp { char *regparse; /* Input-scan pointer. */ int regnpar; /* () count. */ char *regcode; /* Code-emit pointer; ®dummy = don't. */ char regdummy[3]; /* NOTHING, 0 next ptr */ long regsize; /* Code size. */ }; #define EMITTING(cp) ((cp)->regcode != (cp)->regdummy) /* * Forward declarations for sqd_regcomp()'s friends. */ static char *reg(struct comp *cp, int paren, int *flagp); static char *regbranch(struct comp *cp, int *flagp); static char *regpiece(struct comp *cp, int *flagp); static char *regatom(struct comp *cp, int *flagp); static char *regnode(struct comp *cp, int op); static char *regnext(char *node); static void regc(struct comp *cp, int c); static void reginsert(struct comp *cp, int op, char *opnd); static void regtail(struct comp *cp, char *p, char *val); static void regoptail(struct comp *cp, char *p, char *val); /* - sqd_regcomp - compile a regular expression into internal code * * We can't allocate space until we know how big the compiled form will be, * but we can't compile it (and thus know how big it is) until we've got a * place to put the code. So we cheat: we compile it twice, once with code * generation turned off and size counting turned on, and once "for real". * This also means that we don't allocate space until we are sure that the * thing really will compile successfully, and we never have to move the * code and thus invalidate pointers into it. (Note that it has to be in * one piece because free() must be able to free it all.) * * Beware that the optimization-preparation code in here knows about some * of the structure of the compiled regexp. */ sqd_regexp * sqd_regcomp(exp) const char *exp; { register sqd_regexp *r; register char *scan; int flags; struct comp co; if (exp == NULL) FAIL("NULL argument to sqd_regcomp"); /* First pass: determine size, legality. */ co.regparse = (char *)exp; co.regnpar = 1; co.regsize = 0L; co.regdummy[0] = NOTHING; co.regdummy[1] = co.regdummy[2] = 0; co.regcode = co.regdummy; regc(&co, SQD_REGMAGIC); if (reg(&co, 0, &flags) == NULL) return(NULL); /* Small enough for pointer-storage convention? */ if (co.regsize >= 0x7fffL) /* Probably could be 0xffffL. */ FAIL("regexp too big"); /* Allocate space. */ r = (sqd_regexp *)malloc(sizeof(sqd_regexp) + (size_t)co.regsize); if (r == NULL) FAIL("out of space"); /* Second pass: emit code. */ co.regparse = (char *)exp; co.regnpar = 1; co.regcode = r->program; regc(&co, SQD_REGMAGIC); if (reg(&co, 0, &flags) == NULL) return(NULL); /* Dig out information for optimizations. */ r->regstart = '\0'; /* Worst-case defaults. */ r->reganch = 0; r->regmust = NULL; r->regmlen = 0; scan = r->program+1; /* First BRANCH. */ if (OP(regnext(scan)) == END) { /* Only one top-level choice. */ scan = OPERAND(scan); /* Starting-point info. */ if (OP(scan) == EXACTLY) r->regstart = *OPERAND(scan); else if (OP(scan) == BOL) r->reganch = 1; /* * If there's something expensive in the r.e., find the * longest literal string that must appear and make it the * regmust. Resolve ties in favor of later strings, since * the regstart check works with the beginning of the r.e. * and avoiding duplication strengthens checking. Not a * strong reason, but sufficient in the absence of others. */ if (flags&SPSTART) { register char *longest = NULL; register size_t len = 0; for (; scan != NULL; scan = regnext(scan)) if (OP(scan) == EXACTLY && strlen(OPERAND(scan)) >= len) { longest = OPERAND(scan); len = strlen(OPERAND(scan)); } r->regmust = longest; r->regmlen = (int)len; } } return(r); } /* - reg - regular expression, i.e. main body or parenthesized thing * * Caller must absorb opening parenthesis. * * Combining parenthesis handling with the base level of regular expression * is a trifle forced, but the need to tie the tails of the branches to what * follows makes it hard to avoid. */ static char * reg(cp, paren, flagp) register struct comp *cp; int paren; /* Parenthesized? */ int *flagp; { register char *ret = NULL; /* SRE: NULL init added to silence gcc */ register char *br; register char *ender; register int parno = 0; /* SRE: init added to silence gcc */ int flags; *flagp = HASWIDTH; /* Tentatively. */ if (paren) { /* Make an OPEN node. */ if (cp->regnpar >= NSUBEXP) FAIL("too many ()"); parno = cp->regnpar; cp->regnpar++; ret = regnode(cp, OPEN+parno); } /* Pick up the branches, linking them together. */ br = regbranch(cp, &flags); if (br == NULL) return(NULL); if (paren) regtail(cp, ret, br); /* OPEN -> first. */ else ret = br; *flagp &= ~(~flags&HASWIDTH); /* Clear bit if bit 0. */ *flagp |= flags&SPSTART; while (*cp->regparse == '|') { cp->regparse++; br = regbranch(cp, &flags); if (br == NULL) return(NULL); regtail(cp, ret, br); /* BRANCH -> BRANCH. */ *flagp &= ~(~flags&HASWIDTH); *flagp |= flags&SPSTART; } /* Make a closing node, and hook it on the end. */ ender = regnode(cp, (paren) ? CLOSE+parno : END); regtail(cp, ret, ender); /* Hook the tails of the branches to the closing node. */ for (br = ret; br != NULL; br = regnext(br)) regoptail(cp, br, ender); /* Check for proper termination. */ if (paren && *cp->regparse++ != ')') { FAIL("unterminated ()"); } else if (!paren && *cp->regparse != '\0') { if (*cp->regparse == ')') { FAIL("unmatched ()"); } else FAIL("internal error: junk on end"); /* NOTREACHED */ } return(ret); } /* - regbranch - one alternative of an | operator * * Implements the concatenation operator. */ static char * regbranch(cp, flagp) register struct comp *cp; int *flagp; { register char *ret; register char *chain; register char *latest; int flags; register int c; *flagp = WORST; /* Tentatively. */ ret = regnode(cp, BRANCH); chain = NULL; while ((c = *cp->regparse) != '\0' && c != '|' && c != ')') { latest = regpiece(cp, &flags); if (latest == NULL) return(NULL); *flagp |= flags&HASWIDTH; if (chain == NULL) /* First piece. */ *flagp |= flags&SPSTART; else regtail(cp, chain, latest); chain = latest; } if (chain == NULL) /* Loop ran zero times. */ (void) regnode(cp, NOTHING); return(ret); } /* - regpiece - something followed by possible [*+?] * * Note that the branching code sequences used for ? and the general cases * of * and + are somewhat optimized: they use the same NOTHING node as * both the endmarker for their branch list and the body of the last branch. * It might seem that this node could be dispensed with entirely, but the * endmarker role is not redundant. */ static char * regpiece(cp, flagp) register struct comp *cp; int *flagp; { register char *ret; register char op; register char *next; int flags; ret = regatom(cp, &flags); if (ret == NULL) return(NULL); op = *cp->regparse; if (!ISREPN(op)) { *flagp = flags; return(ret); } if (!(flags&HASWIDTH) && op != '?') FAIL("*+ operand could be empty"); switch (op) { case '*': *flagp = WORST|SPSTART; break; case '+': *flagp = WORST|SPSTART|HASWIDTH; break; case '?': *flagp = WORST; break; } if (op == '*' && (flags&SIMPLE)) reginsert(cp, STAR, ret); else if (op == '*') { /* Emit x* as (x&|), where & means "self". */ reginsert(cp, BRANCH, ret); /* Either x */ regoptail(cp, ret, regnode(cp, BACK)); /* and loop */ regoptail(cp, ret, ret); /* back */ regtail(cp, ret, regnode(cp, BRANCH)); /* or */ regtail(cp, ret, regnode(cp, NOTHING)); /* null. */ } else if (op == '+' && (flags&SIMPLE)) reginsert(cp, PLUS, ret); else if (op == '+') { /* Emit x+ as x(&|), where & means "self". */ next = regnode(cp, BRANCH); /* Either */ regtail(cp, ret, next); regtail(cp, regnode(cp, BACK), ret); /* loop back */ regtail(cp, next, regnode(cp, BRANCH)); /* or */ regtail(cp, ret, regnode(cp, NOTHING)); /* null. */ } else if (op == '?') { /* Emit x? as (x|) */ reginsert(cp, BRANCH, ret); /* Either x */ regtail(cp, ret, regnode(cp, BRANCH)); /* or */ next = regnode(cp, NOTHING); /* null. */ regtail(cp, ret, next); regoptail(cp, ret, next); } cp->regparse++; if (ISREPN(*cp->regparse)) FAIL("nested *?+"); return(ret); } /* - regatom - the lowest level * * Optimization: gobbles an entire sequence of ordinary characters so that * it can turn them into a single node, which is smaller to store and * faster to run. Backslashed characters are exceptions, each becoming a * separate node; the code is simpler that way and it's not worth fixing. */ static char * regatom(cp, flagp) register struct comp *cp; int *flagp; { register char *ret; int flags; *flagp = WORST; /* Tentatively. */ switch (*cp->regparse++) { case '^': ret = regnode(cp, BOL); break; case '$': ret = regnode(cp, EOL); break; case '.': ret = regnode(cp, ANY); *flagp |= HASWIDTH|SIMPLE; break; case '[': { register int range; register int rangeend; register int c; if (*cp->regparse == '^') { /* Complement of range. */ ret = regnode(cp, ANYBUT); cp->regparse++; } else ret = regnode(cp, ANYOF); if ((c = *cp->regparse) == ']' || c == '-') { regc(cp, c); cp->regparse++; } while ((c = *cp->regparse++) != '\0' && c != ']') { if (c != '-') regc(cp, c); else if ((c = *cp->regparse) == ']' || c == '\0') regc(cp, '-'); else { range = (unsigned char)*(cp->regparse-2); rangeend = (unsigned char)c; if (range > rangeend) FAIL("invalid [] range"); for (range++; range <= rangeend; range++) regc(cp, range); cp->regparse++; } } regc(cp, '\0'); if (c != ']') FAIL("unmatched []"); *flagp |= HASWIDTH|SIMPLE; break; } case '(': ret = reg(cp, 1, &flags); if (ret == NULL) return(NULL); *flagp |= flags&(HASWIDTH|SPSTART); break; case '\0': case '|': case ')': /* supposed to be caught earlier */ FAIL("internal error: \\0|) unexpected"); /*NOTREACHED*/ break; case '?': case '+': case '*': FAIL("?+* follows nothing"); /*NOTREACHED*/ break; case '\\': if (*cp->regparse == '\0') FAIL("trailing \\"); ret = regnode(cp, EXACTLY); regc(cp, *cp->regparse++); regc(cp, '\0'); *flagp |= HASWIDTH|SIMPLE; break; default: { register size_t len; register char ender; cp->regparse--; len = strcspn(cp->regparse, META); if (len == 0) FAIL("internal error: strcspn 0"); ender = *(cp->regparse+len); if (len > 1 && ISREPN(ender)) len--; /* Back off clear of ?+* operand. */ *flagp |= HASWIDTH; if (len == 1) *flagp |= SIMPLE; ret = regnode(cp, EXACTLY); for (; len > 0; len--) regc(cp, *cp->regparse++); regc(cp, '\0'); break; } } return(ret); } /* - regnode - emit a node */ static char * /* Location. */ regnode(cp, op) register struct comp *cp; char op; { register char *const ret = cp->regcode; register char *ptr; if (!EMITTING(cp)) { cp->regsize += 3; return(ret); } ptr = ret; *ptr++ = op; *ptr++ = '\0'; /* Null next pointer. */ *ptr++ = '\0'; cp->regcode = ptr; return(ret); } /* - regc - emit (if appropriate) a byte of code */ static void regc(cp, b) register struct comp *cp; char b; { if (EMITTING(cp)) *cp->regcode++ = b; else cp->regsize++; } /* - reginsert - insert an operator in front of already-emitted operand * * Means relocating the operand. */ static void reginsert(cp, op, opnd) register struct comp *cp; char op; char *opnd; { register char *place; if (!EMITTING(cp)) { cp->regsize += 3; return; } (void) memmove(opnd+3, opnd, (size_t)(cp->regcode - opnd)); cp->regcode += 3; place = opnd; /* Op node, where operand used to be. */ *place++ = op; *place++ = '\0'; *place++ = '\0'; } /* - regtail - set the next-pointer at the end of a node chain */ static void regtail(cp, p, val) register struct comp *cp; char *p; char *val; { register char *scan; register char *temp; register int offset; if (!EMITTING(cp)) return; /* Find last node. */ for (scan = p; (temp = regnext(scan)) != NULL; scan = temp) continue; offset = (OP(scan) == BACK) ? scan - val : val - scan; *(scan+1) = (offset>>8)&0177; *(scan+2) = offset&0377; } /* - regoptail - regtail on operand of first argument; nop if operandless */ static void regoptail(cp, p, val) register struct comp *cp; char *p; char *val; { /* "Operandless" and "op != BRANCH" are synonymous in practice. */ if (!EMITTING(cp) || OP(p) != BRANCH) return; regtail(cp, OPERAND(p), val); } /* * sqd_regexec and friends */ /* * Work-variable struct for sqd_regexec(). */ struct exec { char *reginput; /* String-input pointer. */ char *regbol; /* Beginning of input, for ^ check. */ char **regstartp; /* Pointer to startp array. */ char **regendp; /* Ditto for endp. */ }; /* * Forwards. */ static int regtry(struct exec *ep, sqd_regexp *rp, char *string); static int regmatch(struct exec *ep, char *prog); static size_t regrepeat(struct exec *ep, char *node); #ifdef DEBUG int regnarrate = 0; void regdump(); static char *regprop(); #endif /* - sqd_regexec - match a regexp against a string */ int sqd_regexec(prog, str) register sqd_regexp *prog; const char *str; { register char *string = (char *)str; /* avert const poisoning */ register char *s; struct exec ex; /* Be paranoid. */ if (prog == NULL || string == NULL) { sqd_regerror("NULL argument to sqd_regexec"); return(0); } /* Check validity of program. */ if ((unsigned char)*prog->program != SQD_REGMAGIC) { sqd_regerror("corrupted regexp"); return(0); } /* If there is a "must appear" string, look for it. */ if (prog->regmust != NULL && strstr(string, prog->regmust) == NULL) return(0); /* Mark beginning of line for ^ . */ ex.regbol = string; ex.regstartp = prog->startp; ex.regendp = prog->endp; /* Simplest case: anchored match need be tried only once. */ if (prog->reganch) return(regtry(&ex, prog, string)); /* Messy cases: unanchored match. */ if (prog->regstart != '\0') { /* We know what char it must start with. */ for (s = string; s != NULL; s = strchr(s+1, prog->regstart)) if (regtry(&ex, prog, s)) return(1); return(0); } else { /* We don't -- general case. */ for (s = string; !regtry(&ex, prog, s); s++) if (*s == '\0') return(0); return(1); } /* NOTREACHED */ } /* - regtry - try match at specific point */ static int /* 0 failure, 1 success */ regtry(ep, prog, string) register struct exec *ep; sqd_regexp *prog; char *string; { register int i; register char **stp; register char **enp; ep->reginput = string; stp = prog->startp; enp = prog->endp; for (i = NSUBEXP; i > 0; i--) { *stp++ = NULL; *enp++ = NULL; } if (regmatch(ep, prog->program + 1)) { prog->startp[0] = string; prog->endp[0] = ep->reginput; return(1); } else return(0); } /* - regmatch - main matching routine * * Conceptually the strategy is simple: check to see whether the current * node matches, call self recursively to see whether the rest matches, * and then act accordingly. In practice we make some effort to avoid * recursion, in particular by going through "ordinary" nodes (that don't * need to know whether the rest of the match failed) by a loop instead of * by recursion. */ static int /* 0 failure, 1 success */ regmatch(ep, prog) register struct exec *ep; char *prog; { register char *scan; /* Current node. */ char *next; /* Next node. */ #ifdef DEBUG if (prog != NULL && regnarrate) fprintf(stderr, "%s(\n", regprop(prog)); #endif for (scan = prog; scan != NULL; scan = next) { #ifdef DEBUG if (regnarrate) fprintf(stderr, "%s...\n", regprop(scan)); #endif next = regnext(scan); switch (OP(scan)) { case BOL: if (ep->reginput != ep->regbol) return(0); break; case EOL: if (*ep->reginput != '\0') return(0); break; case ANY: if (*ep->reginput == '\0') return(0); ep->reginput++; break; case EXACTLY: { register size_t len; register char *const opnd = OPERAND(scan); /* Inline the first character, for speed. */ if (*opnd != *ep->reginput) return(0); len = strlen(opnd); if (len > 1 && strncmp(opnd, ep->reginput, len) != 0) return(0); ep->reginput += len; break; } case ANYOF: if (*ep->reginput == '\0' || strchr(OPERAND(scan), *ep->reginput) == NULL) return(0); ep->reginput++; break; case ANYBUT: if (*ep->reginput == '\0' || strchr(OPERAND(scan), *ep->reginput) != NULL) return(0); ep->reginput++; break; case NOTHING: break; case BACK: break; case OPEN+1: case OPEN+2: case OPEN+3: case OPEN+4: case OPEN+5: case OPEN+6: case OPEN+7: case OPEN+8: case OPEN+9: { register const int no = OP(scan) - OPEN; register char *const input = ep->reginput; if (regmatch(ep, next)) { /* * Don't set startp if some later * invocation of the same parentheses * already has. */ if (ep->regstartp[no] == NULL) ep->regstartp[no] = input; return(1); } else return(0); /*NOTREACHED*/ break; } case CLOSE+1: case CLOSE+2: case CLOSE+3: case CLOSE+4: case CLOSE+5: case CLOSE+6: case CLOSE+7: case CLOSE+8: case CLOSE+9: { register const int no = OP(scan) - CLOSE; register char *const input = ep->reginput; if (regmatch(ep, next)) { /* * Don't set endp if some later * invocation of the same parentheses * already has. */ if (ep->regendp[no] == NULL) ep->regendp[no] = input; return(1); } else return(0); /*NOTREACHED*/ break; } case BRANCH: { register char *const save = ep->reginput; if (OP(next) != BRANCH) /* No choice. */ next = OPERAND(scan); /* Avoid recursion. */ else { while (OP(scan) == BRANCH) { if (regmatch(ep, OPERAND(scan))) return(1); ep->reginput = save; scan = regnext(scan); } return(0); /*NOTREACHED*/ } break; } case STAR: case PLUS: { register const char nextch = (OP(next) == EXACTLY) ? *OPERAND(next) : '\0'; register size_t no; register char *const save = ep->reginput; register const size_t min = (OP(scan) == STAR) ? 0 : 1; for (no = regrepeat(ep, OPERAND(scan)) + 1; no > min; no--) { ep->reginput = save + no - 1; /* If it could work, try it. */ if (nextch == '\0' || *ep->reginput == nextch) if (regmatch(ep, next)) return(1); } return(0); /*NOTREACHED*/ break; } case END: return(1); /* Success! */ break; default: sqd_regerror("regexp corruption"); return(0); /*NOTREACHED*/ break; } } /* * We get here only if there's trouble -- normally "case END" is * the terminating point. */ sqd_regerror("corrupted pointers"); return(0); } /* - regrepeat - report how many times something simple would match */ static size_t regrepeat(ep, node) register struct exec *ep; char *node; { register size_t count; register char *scan; register char ch; switch (OP(node)) { case ANY: return(strlen(ep->reginput)); break; case EXACTLY: ch = *OPERAND(node); count = 0; for (scan = ep->reginput; *scan == ch; scan++) count++; return(count); /*NOTREACHED*/ break; case ANYOF: return(strspn(ep->reginput, OPERAND(node))); break; case ANYBUT: return(strcspn(ep->reginput, OPERAND(node))); break; default: /* Oh dear. Called inappropriately. */ sqd_regerror("internal error: bad call of regrepeat"); return(0); /* Best compromise. */ /*NOTREACHED*/ break; } /* NOTREACHED */ } /* - regnext - dig the "next" pointer out of a node */ static char * regnext(p) register char *p; { register const int offset = NEXT(p); if (offset == 0) return(NULL); return((OP(p) == BACK) ? p-offset : p+offset); } #ifdef DEBUG static char *regprop(); /* - regdump - dump a regexp onto stdout in vaguely comprehensible form */ void regdump(r) sqd_regexp *r; { register char *s; register char op = EXACTLY; /* Arbitrary non-END op. */ register char *next; s = r->program + 1; while (op != END) { /* While that wasn't END last time... */ op = OP(s); printf("%2d%s", s-r->program, regprop(s)); /* Where, what. */ next = regnext(s); if (next == NULL) /* Next ptr. */ printf("(0)"); else printf("(%d)", (s-r->program)+(next-s)); s += 3; if (op == ANYOF || op == ANYBUT || op == EXACTLY) { /* Literal string, where present. */ while (*s != '\0') { putchar(*s); s++; } s++; } putchar('\n'); } /* Header fields of interest. */ if (r->regstart != '\0') printf("start `%c' ", r->regstart); if (r->reganch) printf("anchored "); if (r->regmust != NULL) printf("must have \"%s\"", r->regmust); printf("\n"); } /* - regprop - printable representation of opcode */ static char * regprop(op) char *op; { register char *p; static char buf[50]; (void) strcpy(buf, ":"); switch (OP(op)) { case BOL: p = "BOL"; break; case EOL: p = "EOL"; break; case ANY: p = "ANY"; break; case ANYOF: p = "ANYOF"; break; case ANYBUT: p = "ANYBUT"; break; case BRANCH: p = "BRANCH"; break; case EXACTLY: p = "EXACTLY"; break; case NOTHING: p = "NOTHING"; break; case BACK: p = "BACK"; break; case END: p = "END"; break; case OPEN+1: case OPEN+2: case OPEN+3: case OPEN+4: case OPEN+5: case OPEN+6: case OPEN+7: case OPEN+8: case OPEN+9: sprintf(buf+strlen(buf), "OPEN%d", OP(op)-OPEN); p = NULL; break; case CLOSE+1: case CLOSE+2: case CLOSE+3: case CLOSE+4: case CLOSE+5: case CLOSE+6: case CLOSE+7: case CLOSE+8: case CLOSE+9: sprintf(buf+strlen(buf), "CLOSE%d", OP(op)-CLOSE); p = NULL; break; case STAR: p = "STAR"; break; case PLUS: p = "PLUS"; break; default: sqd_regerror("corrupted opcode"); break; } if (p != NULL) (void) strcat(buf, p); return(buf); } #endif /* - sqd_regsub - perform substitutions after a regexp match */ void sqd_regsub(rp, source, dest) const sqd_regexp *rp; const char *source; char *dest; { register sqd_regexp * const prog = (sqd_regexp *)rp; register char *src = (char *)source; register char *dst = dest; register char c; register int no; register size_t len; if (prog == NULL || source == NULL || dest == NULL) { sqd_regerror("NULL parameter to sqd_regsub"); return; } if ((unsigned char)*(prog->program) != SQD_REGMAGIC) { sqd_regerror("damaged regexp"); return; } while ((c = *src++) != '\0') { if (c == '&') no = 0; else if (c == '\\' && isdigit((int) (*src))) no = *src++ - '0'; else no = -1; if (no < 0) { /* Ordinary character. */ if (c == '\\' && (*src == '\\' || *src == '&')) c = *src++; *dst++ = c; } else if (prog->startp[no] != NULL && prog->endp[no] != NULL && prog->endp[no] > prog->startp[no]) { len = prog->endp[no] - prog->startp[no]; (void) strncpy(dst, prog->startp[no], len); dst += len; if (*(dst-1) == '\0') { /* strncpy hit NUL. */ sqd_regerror("damaged match string"); return; } } } *dst++ = '\0'; } void sqd_regerror(s) char *s; { fprintf(stderr, "regexp(3): %s\n", s); exit(EXIT_FAILURE); /* NOTREACHED */ } #ifdef NBA_TEAM_IN_STL int main(int argc, char **argv) { char *pat; int ntok; char *s; int status; pat = argv[1]; ntok = atoi(argv[2]); s = argv[3]; status = Strparse(pat, s, ntok); if (status == 0) { printf("no match\n"); } else { int i; printf("MATCH.\n"); for (i = 1; i <= ntok; i++) printf("matched token %1d: %s\n", i, sqd_parse[i]); } } #endif /*NBA_TEAM_IN_STL*/ squid/iupac.c0000640000175000017520000001132610463223377013363 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* iupac.c * * Globally defines the IUPAC symbols for nucleic acid sequence * Slowly evolving into a repository of globals. Tue Apr 20 1993 * * CVS $Id: iupac.c,v 1.4 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include "squid.h" /* Default expected nucleotide occurrence frequencies, A/C/G/T. * Used (for instance) as the default distribution for * i.i.d. random nucleotide sequences. */ float dnafq[4] = { 0.25, 0.25, 0.25, 0.25 }; /* Dayhoff f(i) amino acid occurrence frequencies. * From SwissProt 34: 21,210,388 residues * In alphabetic order by single-letter code. * Used (for instance) as the default distribution for * i.i.d. random protein sequences. */ float aafq[20] = { 0.075520, /* A */ 0.016973, /* C */ 0.053029, /* D */ 0.063204, /* E */ 0.040762, /* F */ 0.068448, /* G */ 0.022406, /* H */ 0.057284, /* I */ 0.059398, /* K */ 0.093399, /* L */ 0.023569, /* M */ 0.045293, /* N */ 0.049262, /* P */ 0.040231, /* Q */ 0.051573, /* R */ 0.072214, /* S */ 0.057454, /* T */ 0.065252, /* V */ 0.012513, /* W */ 0.031985 /* Y */ }; char aa_alphabet[] = AMINO_ALPHABET; /* aa_index converts to pam's 27x27 scheme */ int aa_index[20] = { 0, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 24 }; /* IUPAC code translations */ /* note: sequence chars are UPPER CASE */ struct iupactype iupac[] = { { 'A', 'T', NTA, NTT, }, { 'C', 'G', NTC, NTG, }, { 'G', 'C', NTG, NTC, }, { 'T', 'A', NTT, NTA, }, { 'U', 'A', NTU, NTA, }, { 'N', 'N', NTN, NTN, }, { ' ', ' ', NTGAP, NTGAP, }, { 'R', 'Y', NTR, NTY, }, { 'Y', 'R', NTY, NTR, }, { 'M', 'K', NTM, NTK, }, { 'K', 'M', NTK, NTM, }, { 'S', 'S', NTS, NTS, }, { 'W', 'W', NTW, NTW, }, { 'H', 'D', NTH, NTD, }, { 'B', 'V', NTB, NTV, }, { 'V', 'B', NTV, NTB, }, { 'D', 'H', NTD, NTH, }, }; char *stdcode1[65] = { "K", /* AAA */ "N", /* AAC */ "K", /* AAG */ "N", /* AAU */ "T", /* ACA */ "T", /* ACC */ "T", /* ACG */ "T", /* ACU */ "R", /* AGA */ "S", /* AGC */ "R", /* AGG */ "S", /* AGU */ "I", /* AUA */ "I", /* AUC */ "M", /* AUG */ "I", /* AUU */ "Q", /* CAA */ "H", /* CAC */ "Q", /* CAG */ "H", /* CAU */ "P", /* CCA */ "P", /* CCC */ "P", /* CCG */ "P", /* CCU */ "R", /* CGA */ "R", /* CGC */ "R", /* CGG */ "R", /* CGU */ "L", /* CUA */ "L", /* CUC */ "L", /* CUG */ "L", /* CUU */ "E", /* GAA */ "D", /* GAC */ "E", /* GAG */ "D", /* GAU */ "A", /* GCA */ "A", /* GCC */ "A", /* GCG */ "A", /* GCU */ "G", /* GGA */ "G", /* GGC */ "G", /* GGG */ "G", /* GGU */ "V", /* GUA */ "V", /* GUC */ "V", /* GUG */ "V", /* GUU */ "*", /* UAA */ "Y", /* UAC */ "*", /* UAG */ "Y", /* UAU */ "S", /* UCA */ "S", /* UCC */ "S", /* UCG */ "S", /* UCU */ "*", /* UGA */ "C", /* UGC */ "W", /* UGG */ "C", /* UGU */ "L", /* UUA */ "F", /* UUC */ "L", /* UUG */ "F", /* UUU */ "X", /* unknown */ }; char *stdcode3[65] = { "Lys", /* AAA */ "Asn", /* AAC */ "Lys", /* AAG */ "Asn", /* AAU */ "Thr", /* ACA */ "Thr", /* ACC */ "Thr", /* ACG */ "Thr", /* ACU */ "Arg", /* AGA */ "Ser", /* AGC */ "Arg", /* AGG */ "Ser", /* AGU */ "Ile", /* AUA */ "Ile", /* AUC */ "Met", /* AUG */ "Ile", /* AUU */ "Gln", /* CAA */ "His", /* CAC */ "Gln", /* CAG */ "His", /* CAU */ "Pro", /* CCA */ "Pro", /* CCC */ "Pro", /* CCG */ "Pro", /* CCU */ "Arg", /* CGA */ "Arg", /* CGC */ "Arg", /* CGG */ "Arg", /* CGU */ "Leu", /* CUA */ "Leu", /* CUC */ "Leu", /* CUG */ "Leu", /* CUU */ "Glu", /* GAA */ "Asp", /* GAC */ "Glu", /* GAG */ "Asp", /* GAU */ "Ala", /* GCA */ "Ala", /* GCC */ "Ala", /* GCG */ "Ala", /* GCU */ "Gly", /* GGA */ "Gly", /* GGC */ "Gly", /* GGG */ "Gly", /* GGU */ "Val", /* GUA */ "Val", /* GUC */ "Val", /* GUG */ "Val", /* GUU */ "***", /* UAA */ "Tyr", /* UAC */ "***", /* UAG */ "Tyr", /* UAU */ "Ser", /* UCA */ "Ser", /* UCC */ "Ser", /* UCG */ "Ser", /* UCU */ "***", /* UGA */ "Cys", /* UGC */ "Trp", /* UGG */ "Cys", /* UGU */ "Leu", /* UUA */ "Phe", /* UUC */ "Leu", /* UUG */ "Trp", /* UUU */ "XXX", /* unknown */ }; squid/msa.c0000640000175000017520000012600110463223377013037 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* msa.c * SRE, Mon May 17 10:48:47 1999 * * SQUID's interface for multiple sequence alignment * manipulation: access to the MSA object. * * CVS $Id: msa.c,v 1.21 2004/02/20 14:39:55 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "msa.h" /* multiple sequence alignment object support */ #include "gki.h" /* string indexing hashtable code */ #include "ssi.h" /* SSI sequence file indexing code */ /* Function: MSAAlloc() * Date: SRE, Tue May 18 10:45:47 1999 [St. Louis] * * Purpose: Allocate an MSA structure, return a pointer * to it. * * Designed to be used in three ways: * 1) We know exactly the dimensions of the alignment: * both nseq and alen. * msa = MSAAlloc(nseq, alen); * * 2) We know the number of sequences but not alen. * (We add sequences later.) * msa = MSAAlloc(nseq, 0); * * 3) We even don't know the number of sequences, so * we'll have to dynamically expand allocations. * We provide a blocksize for the allocation expansion, * and expand when needed. * msa = MSAAlloc(10, 0); * if (msa->nseq == msa->nseqalloc) MSAExpand(msa); * * Args: nseq - number of sequences, or nseq allocation blocksize * alen - length of alignment in columns, or 0 * * Returns: pointer to new MSA object, w/ all values initialized. * Note that msa->nseq is initialized to 0, though space * is allocated. * * Diagnostics: "always works". Die()'s on memory allocation failure. * */ MSA * MSAAlloc(int nseq, int alen) { MSA *msa; int i; msa = MallocOrDie(sizeof(MSA)); msa->aseq = MallocOrDie(sizeof(char *) * nseq); msa->sqname = MallocOrDie(sizeof(char *) * nseq); msa->sqlen = MallocOrDie(sizeof(int) * nseq); msa->wgt = MallocOrDie(sizeof(float) * nseq); for (i = 0; i < nseq; i++) { msa->sqname[i] = NULL; msa->sqlen[i] = 0; msa->wgt[i] = -1.0; if (alen != 0) msa->aseq[i] = MallocOrDie(sizeof(char) * (alen+1)); else msa->aseq[i] = NULL; } msa->alen = alen; msa->nseq = 0; msa->nseqalloc = nseq; msa->nseqlump = nseq; msa->flags = 0; msa->type = kOtherSeq; msa->name = NULL; msa->desc = NULL; msa->acc = NULL; msa->au = NULL; msa->ss_cons = NULL; msa->sa_cons = NULL; msa->rf = NULL; msa->sqacc = NULL; msa->sqdesc = NULL; msa->ss = NULL; msa->sslen = NULL; msa->sa = NULL; msa->salen = NULL; msa->index = GKIInit(); msa->lastidx = 0; for (i = 0; i < MSA_MAXCUTOFFS; i++) { msa->cutoff[i] = 0.; msa->cutoff_is_set[i] = FALSE; } /* Initialize unparsed optional markup */ msa->comment = NULL; msa->ncomment = 0; msa->alloc_ncomment = 0; msa->gf_tag = NULL; msa->gf = NULL; msa->ngf = 0; msa->gs_tag = NULL; msa->gs = NULL; msa->gs_idx = NULL; msa->ngs = 0; msa->gc_tag = NULL; msa->gc = NULL; msa->gc_idx = NULL; msa->ngc = 0; msa->gr_tag = NULL; msa->gr = NULL; msa->gr_idx = NULL; msa->ngr = 0; /* Done. Return the alloced, initialized structure */ return msa; } /* Function: MSAExpand() * Date: SRE, Tue May 18 11:06:53 1999 [St. Louis] * * Purpose: Increase the sequence allocation in an MSA * by msa->nseqlump. (Typically used when we're reading * in an alignment sequentially from a file, * so we don't know nseq until we're done.) * * Args: msa - the MSA object * * Returns: (void) * */ void MSAExpand(MSA *msa) { int i,j; msa->nseqalloc += msa->nseqlump; msa->aseq = ReallocOrDie(msa->aseq, sizeof(char *) * msa->nseqalloc); msa->sqname = ReallocOrDie(msa->sqname, sizeof(char *) * msa->nseqalloc); msa->sqlen = ReallocOrDie(msa->sqlen, sizeof(char *) * msa->nseqalloc); msa->wgt = ReallocOrDie(msa->wgt, sizeof(float) * msa->nseqalloc); if (msa->ss != NULL) { msa->ss = ReallocOrDie(msa->ss, sizeof(char *) * msa->nseqalloc); msa->sslen = ReallocOrDie(msa->sslen, sizeof(int) * msa->nseqalloc); } if (msa->sa != NULL) { msa->sa = ReallocOrDie(msa->sa, sizeof(char *) * msa->nseqalloc); msa->salen = ReallocOrDie(msa->salen, sizeof(int) * msa->nseqalloc); } if (msa->sqacc != NULL) msa->sqacc = ReallocOrDie(msa->sqacc, sizeof(char *) * msa->nseqalloc); if (msa->sqdesc != NULL) msa->sqdesc =ReallocOrDie(msa->sqdesc,sizeof(char *) * msa->nseqalloc); for (i = msa->nseqalloc-msa->nseqlump; i < msa->nseqalloc; i++) { msa->sqname[i] = NULL; msa->wgt[i] = -1.0; if (msa->sqacc != NULL) msa->sqacc[i] = NULL; if (msa->sqdesc != NULL) msa->sqdesc[i] = NULL; if (msa->alen != 0) msa->aseq[i] = ReallocOrDie(msa->aseq[i], sizeof(char) * (msa->alen+1)); else msa->aseq[i] = NULL; msa->sqlen[i] = 0; if (msa->ss != NULL) { if (msa->alen != 0) msa->ss[i] = ReallocOrDie(msa->ss[i], sizeof(char) * (msa->alen+1)); else msa->ss[i] = NULL; msa->sslen[i] = 0; } if (msa->sa != NULL) { if (msa->alen != 0) msa->sa[i] = ReallocOrDie(msa->ss[i], sizeof(char) * (msa->alen+1)); else msa->sa[i] = NULL; msa->salen[i] = 0; } } /* Reallocate and re-init for unparsed #=GS tags, if we have some. * gs is [0..ngs-1][0..nseq-1][], so we're reallocing the middle * set of pointers. */ if (msa->gs != NULL) for (i = 0; i < msa->ngs; i++) { if (msa->gs[i] != NULL) { msa->gs[i] = ReallocOrDie(msa->gs[i], sizeof(char *) * msa->nseqalloc); for (j = msa->nseqalloc-msa->nseqlump; j < msa->nseqalloc; j++) msa->gs[i][j] = NULL; } } /* Reallocate and re-init for unparsed #=GR tags, if we have some. * gr is [0..ngs-1][0..nseq-1][], so we're reallocing the middle * set of pointers. */ if (msa->gr != NULL) for (i = 0; i < msa->ngr; i++) { if (msa->gr[i] != NULL) { msa->gr[i] = ReallocOrDie(msa->gr[i], sizeof(char *) * msa->nseqalloc); for (j = msa->nseqalloc-msa->nseqlump; j < msa->nseqalloc; j++) msa->gr[i][j] = NULL; } } return; } /* Function: MSAFree() * Date: SRE, Tue May 18 11:20:16 1999 [St. Louis] * * Purpose: Free a multiple sequence alignment structure. * * Args: msa - the alignment * * Returns: (void) */ void MSAFree(MSA *msa) { Free2DArray((void **) msa->aseq, msa->nseq); Free2DArray((void **) msa->sqname, msa->nseq); Free2DArray((void **) msa->sqacc, msa->nseq); Free2DArray((void **) msa->sqdesc, msa->nseq); Free2DArray((void **) msa->ss, msa->nseq); Free2DArray((void **) msa->sa, msa->nseq); if (msa->sqlen != NULL) free(msa->sqlen); if (msa->wgt != NULL) free(msa->wgt); if (msa->name != NULL) free(msa->name); if (msa->desc != NULL) free(msa->desc); if (msa->acc != NULL) free(msa->acc); if (msa->au != NULL) free(msa->au); if (msa->ss_cons != NULL) free(msa->ss_cons); if (msa->sa_cons != NULL) free(msa->sa_cons); if (msa->rf != NULL) free(msa->rf); if (msa->sslen != NULL) free(msa->sslen); if (msa->salen != NULL) free(msa->salen); Free2DArray((void **) msa->comment, msa->ncomment); Free2DArray((void **) msa->gf_tag, msa->ngf); Free2DArray((void **) msa->gf, msa->ngf); Free2DArray((void **) msa->gs_tag, msa->ngs); Free3DArray((void ***)msa->gs, msa->ngs, msa->nseq); Free2DArray((void **) msa->gc_tag, msa->ngc); Free2DArray((void **) msa->gc, msa->ngc); Free2DArray((void **) msa->gr_tag, msa->ngr); Free3DArray((void ***)msa->gr, msa->ngr, msa->nseq); GKIFree(msa->index); GKIFree(msa->gs_idx); GKIFree(msa->gc_idx); GKIFree(msa->gr_idx); free(msa); } /* Function: MSASetSeqAccession() * Date: SRE, Mon Jun 21 04:13:33 1999 [Sanger Centre] * * Purpose: Set a sequence accession in an MSA structure. * Handles some necessary allocation/initialization. * * Args: msa - multiple alignment to add accession to * seqidx - index of sequence to attach accession to * acc - accession * * Returns: void */ void MSASetSeqAccession(MSA *msa, int seqidx, char *acc) { int x; if (msa->sqacc == NULL) { msa->sqacc = MallocOrDie(sizeof(char *) * msa->nseqalloc); for (x = 0; x < msa->nseqalloc; x++) msa->sqacc[x] = NULL; } msa->sqacc[seqidx] = sre_strdup(acc, -1); } /* Function: MSASetSeqDescription() * Date: SRE, Mon Jun 21 04:21:09 1999 [Sanger Centre] * * Purpose: Set a sequence description in an MSA structure. * Handles some necessary allocation/initialization. * * Args: msa - multiple alignment to add accession to * seqidx - index of sequence to attach accession to * desc - description * * Returns: void */ void MSASetSeqDescription(MSA *msa, int seqidx, char *desc) { int x; if (msa->sqdesc == NULL) { msa->sqdesc = MallocOrDie(sizeof(char *) * msa->nseqalloc); for (x = 0; x < msa->nseqalloc; x++) msa->sqdesc[x] = NULL; } msa->sqdesc[seqidx] = sre_strdup(desc, -1); } /* Function: MSAAddComment() * Date: SRE, Tue Jun 1 17:37:21 1999 [St. Louis] * * Purpose: Add an (unparsed) comment line to the MSA structure, * allocating as necessary. * * Args: msa - a multiple alignment * s - comment line to add * * Returns: (void) */ void MSAAddComment(MSA *msa, char *s) { /* If this is our first recorded comment, we need to malloc(); * and if we've filled available space, we need to realloc(). * Note the arbitrary lumpsize of 10 lines per allocation... */ if (msa->comment == NULL) { msa->comment = MallocOrDie (sizeof(char *) * 10); msa->alloc_ncomment = 10; } if (msa->ncomment == msa->alloc_ncomment) { msa->alloc_ncomment += 10; msa->comment = ReallocOrDie(msa->comment, sizeof(char *) * msa->alloc_ncomment); } msa->comment[msa->ncomment] = sre_strdup(s, -1); msa->ncomment++; return; } /* Function: MSAAddGF() * Date: SRE, Wed Jun 2 06:53:54 1999 [bus to Madison] * * Purpose: Add an unparsed #=GF markup line to the MSA * structure, allocating as necessary. * * Args: msa - a multiple alignment * tag - markup tag (e.g. "AU") * value - free text markup (e.g. "Alex Bateman") * * Returns: (void) */ void MSAAddGF(MSA *msa, char *tag, char *value) { /* If this is our first recorded unparsed #=GF line, we need to malloc(); * if we've filled availabl space If we already have a hash index, and the GF * Note the arbitrary lumpsize of 10 lines per allocation... */ if (msa->gf_tag == NULL) { msa->gf_tag = MallocOrDie (sizeof(char *) * 10); msa->gf = MallocOrDie (sizeof(char *) * 10); msa->alloc_ngf = 10; } if (msa->ngf == msa->alloc_ngf) { msa->alloc_ngf += 10; msa->gf_tag = ReallocOrDie(msa->gf_tag, sizeof(char *) * msa->alloc_ngf); msa->gf = ReallocOrDie(msa->gf, sizeof(char *) * msa->alloc_ngf); } msa->gf_tag[msa->ngf] = sre_strdup(tag, -1); msa->gf[msa->ngf] = sre_strdup(value, -1); msa->ngf++; return; } /* Function: MSAAddGS() * Date: SRE, Wed Jun 2 06:57:03 1999 [St. Louis] * * Purpose: Add an unparsed #=GS markup line to the MSA * structure, allocating as necessary. * * It's possible that we could get more than one * of the same type of GS tag per sequence; for * example, "DR PDB;" structure links in Pfam. * Hack: handle these by appending to the string, * in a \n separated fashion. * * Args: msa - multiple alignment structure * tag - markup tag (e.g. "AC") * sqidx - index of sequence to assoc markup with (0..nseq-1) * value - markup (e.g. "P00666") * * Returns: 0 on success */ void MSAAddGS(MSA *msa, char *tag, int sqidx, char *value) { int tagidx; int i; /* Is this an unparsed tag name that we recognize? * If not, handle adding it to index, and reallocating * as needed. */ if (msa->gs_tag == NULL) /* first tag? init w/ malloc */ { msa->gs_idx = GKIInit(); tagidx = GKIStoreKey(msa->gs_idx, tag); SQD_DASSERT1((tagidx == 0)); msa->gs_tag = MallocOrDie(sizeof(char *)); msa->gs = MallocOrDie(sizeof(char **)); msa->gs[0] = MallocOrDie(sizeof(char *) * msa->nseqalloc); for (i = 0; i < msa->nseqalloc; i++) msa->gs[0][i] = NULL; } else { /* new tag? */ tagidx = GKIKeyIndex(msa->gs_idx, tag); if (tagidx < 0) { /* it's a new tag name; realloc */ tagidx = GKIStoreKey(msa->gs_idx, tag); /* since we alloc in blocks of 1, we always realloc upon seeing a new tag. */ SQD_DASSERT1((tagidx == msa->ngs)); msa->gs_tag = ReallocOrDie(msa->gs_tag, (msa->ngs+1) * sizeof(char *)); msa->gs = ReallocOrDie(msa->gs, (msa->ngs+1) * sizeof(char **)); msa->gs[msa->ngs] = MallocOrDie(sizeof(char *) * msa->nseqalloc); for (i = 0; i < msa->nseqalloc; i++) msa->gs[msa->ngs][i] = NULL; } } if (tagidx == msa->ngs) { msa->gs_tag[tagidx] = sre_strdup(tag, -1); msa->ngs++; } if (msa->gs[tagidx][sqidx] == NULL) /* first annotation of this seq with this tag? */ msa->gs[tagidx][sqidx] = sre_strdup(value, -1); else { /* >1 annotation of this seq with this tag; append */ int len; if ((len = sre_strcat(&(msa->gs[tagidx][sqidx]), -1, "\n", 1)) < 0) Die("failed to sre_strcat()"); if (sre_strcat(&(msa->gs[tagidx][sqidx]), len, value, -1) < 0) Die("failed to sre_strcat()"); } return; } /* Function: MSAAppendGC() * Date: SRE, Thu Jun 3 06:25:14 1999 [Madison] * * Purpose: Add an unparsed #=GC markup line to the MSA * structure, allocating as necessary. * * When called multiple times for the same tag, * appends value strings together -- used when * parsing multiblock alignment files, for * example. * * Args: msa - multiple alignment structure * tag - markup tag (e.g. "CS") * value - markup, one char per aligned column * * Returns: (void) */ void MSAAppendGC(MSA *msa, char *tag, char *value) { int tagidx; /* Is this an unparsed tag name that we recognize? * If not, handle adding it to index, and reallocating * as needed. */ if (msa->gc_tag == NULL) /* first tag? init w/ malloc */ { msa->gc_tag = MallocOrDie(sizeof(char *)); msa->gc = MallocOrDie(sizeof(char *)); msa->gc_idx = GKIInit(); tagidx = GKIStoreKey(msa->gc_idx, tag); SQD_DASSERT1((tagidx == 0)); msa->gc[0] = NULL; } else { /* new tag? */ tagidx = GKIKeyIndex(msa->gc_idx, tag); if (tagidx < 0) { /* it's a new tag name; realloc */ tagidx = GKIStoreKey(msa->gc_idx, tag); /* since we alloc in blocks of 1, we always realloc upon seeing a new tag. */ SQD_DASSERT1((tagidx == msa->ngc)); msa->gc_tag = ReallocOrDie(msa->gc_tag, (msa->ngc+1) * sizeof(char **)); msa->gc = ReallocOrDie(msa->gc, (msa->ngc+1) * sizeof(char **)); msa->gc[tagidx] = NULL; } } if (tagidx == msa->ngc) { msa->gc_tag[tagidx] = sre_strdup(tag, -1); msa->ngc++; } sre_strcat(&(msa->gc[tagidx]), -1, value, -1); return; } /* Function: MSAGetGC() * Date: SRE, Fri Aug 13 13:25:57 1999 [St. Louis] * * Purpose: Given a tagname for a miscellaneous #=GC column * annotation, return a pointer to the annotation * string. * * Args: msa - alignment and its annotation * tag - name of the annotation * * Returns: ptr to the annotation string. Caller does *not* * free; is managed by msa object still. */ char * MSAGetGC(MSA *msa, char *tag) { int tagidx; if (msa->gc_idx == NULL) return NULL; if ((tagidx = GKIKeyIndex(msa->gc_idx, tag)) < 0) return NULL; return msa->gc[tagidx]; } /* Function: MSAAppendGR() * Date: SRE, Thu Jun 3 06:34:38 1999 [Madison] * * Purpose: Add an unparsed #=GR markup line to the * MSA structure, allocating as necessary. * * When called multiple times for the same tag, * appends value strings together -- used when * parsing multiblock alignment files, for * example. * * Args: msa - multiple alignment structure * tag - markup tag (e.g. "SS") * sqidx - index of seq to assoc markup with (0..nseq-1) * value - markup, one char per aligned column * * Returns: (void) */ void MSAAppendGR(MSA *msa, char *tag, int sqidx, char *value) { int tagidx; int i; /* Is this an unparsed tag name that we recognize? * If not, handle adding it to index, and reallocating * as needed. */ if (msa->gr_tag == NULL) /* first tag? init w/ malloc */ { msa->gr_tag = MallocOrDie(sizeof(char *)); msa->gr = MallocOrDie(sizeof(char **)); msa->gr[0] = MallocOrDie(sizeof(char *) * msa->nseqalloc); for (i = 0; i < msa->nseqalloc; i++) msa->gr[0][i] = NULL; msa->gr_idx = GKIInit(); tagidx = GKIStoreKey(msa->gr_idx, tag); SQD_DASSERT1((tagidx == 0)); } else { /* new tag? */ tagidx = GKIKeyIndex(msa->gr_idx, tag); if (tagidx < 0) { /* it's a new tag name; realloc */ tagidx = GKIStoreKey(msa->gr_idx, tag); /* since we alloc in blocks of 1, we always realloc upon seeing a new tag. */ SQD_DASSERT1((tagidx == msa->ngr)); msa->gr_tag = ReallocOrDie(msa->gr_tag, (msa->ngr+1) * sizeof(char *)); msa->gr = ReallocOrDie(msa->gr, (msa->ngr+1) * sizeof(char **)); msa->gr[msa->ngr] = MallocOrDie(sizeof(char *) * msa->nseqalloc); for (i = 0; i < msa->nseqalloc; i++) msa->gr[msa->ngr][i] = NULL; } } if (tagidx == msa->ngr) { msa->gr_tag[tagidx] = sre_strdup(tag, -1); msa->ngr++; } sre_strcat(&(msa->gr[tagidx][sqidx]), -1, value, -1); return; } /* Function: MSAVerifyParse() * Date: SRE, Sat Jun 5 14:24:24 1999 [Madison, 1999 worm mtg] * * Purpose: Last function called after a multiple alignment is * parsed. Checks that parse was successful; makes sure * required information is present; makes sure required * information is consistent. Some fields that are * only use during parsing may be freed (sqlen, for * example). * * Some fields in msa may be modified (msa->alen is set, * for example). * * Args: msa - the multiple alignment * sqname, aseq must be set * nseq must be correct * alen need not be set; will be set here. * wgt will be set here if not already set * * Returns: (void) * Will Die() here with diagnostics on error. * * Example: */ void MSAVerifyParse(MSA *msa) { int idx; if (msa->nseq == 0) Die("Parse error: no sequences were found for alignment %s", msa->name != NULL ? msa->name : ""); msa->alen = msa->sqlen[0]; /* We can rely on msa->sqname[] being valid for any index, * because of the way the line parsers always store any name * they add to the index. */ for (idx = 0; idx < msa->nseq; idx++) { /* aseq is required. */ if (msa->aseq[idx] == NULL) Die("Parse error: No sequence for %s in alignment %s", msa->sqname[idx], msa->name != NULL ? msa->name : ""); /* either all weights must be set, or none of them */ if ((msa->flags & MSA_SET_WGT) && msa->wgt[idx] == -1.0) Die("Parse error: some weights are set, but %s doesn't have one in alignment %s", msa->sqname[idx], msa->name != NULL ? msa->name : ""); /* all aseq must be same length. */ if (msa->sqlen[idx] != msa->alen) Die("Parse error: sequence %s: length %d, expected %d in alignment %s", msa->sqname[idx], msa->sqlen[idx], msa->alen, msa->name != NULL ? msa->name : ""); /* if SS is present, must have length right */ if (msa->ss != NULL && msa->ss[idx] != NULL && msa->sslen[idx] != msa->alen) Die("Parse error: #=GR SS annotation for %s: length %d, expected %d in alignment %s", msa->sqname[idx], msa->sslen[idx], msa->alen, msa->name != NULL ? msa->name : ""); /* if SA is present, must have length right */ if (msa->sa != NULL && msa->sa[idx] != NULL && msa->salen[idx] != msa->alen) Die("Parse error: #=GR SA annotation for %s: length %d, expected %d in alignment %s", msa->sqname[idx], msa->salen[idx], msa->alen, msa->name != NULL ? msa->name : ""); } /* if cons SS is present, must have length right */ if (msa->ss_cons != NULL && strlen(msa->ss_cons) != msa->alen) Die("Parse error: #=GC SS_cons annotation: length %d, expected %d in alignment %s", strlen(msa->ss_cons), msa->alen, msa->name != NULL ? msa->name : ""); /* if cons SA is present, must have length right */ if (msa->sa_cons != NULL && strlen(msa->sa_cons) != msa->alen) Die("Parse error: #=GC SA_cons annotation: length %d, expected %d in alignment %s", strlen(msa->sa_cons), msa->alen, msa->name != NULL ? msa->name : ""); /* if RF is present, must have length right */ if (msa->rf != NULL && strlen(msa->rf) != msa->alen) Die("Parse error: #=GC RF annotation: length %d, expected %d in alignment %s", strlen(msa->rf), msa->alen, msa->name != NULL ? msa->name : ""); /* Check that all or no weights are set */ if (!(msa->flags & MSA_SET_WGT)) FSet(msa->wgt, msa->nseq, 1.0); /* default weights */ /* Clean up a little from the parser */ if (msa->sqlen != NULL) { free(msa->sqlen); msa->sqlen = NULL; } if (msa->sslen != NULL) { free(msa->sslen); msa->sslen = NULL; } if (msa->salen != NULL) { free(msa->salen); msa->salen = NULL; } return; } /* Function: MSAFileOpen() * Date: SRE, Tue May 18 13:22:01 1999 [St. Louis] * * Purpose: Open an alignment database file and prepare * for reading one alignment, or sequentially * in the (rare) case of multiple MSA databases * (e.g. Stockholm format). * * Args: filename - name of file to open * if "-", read stdin * if it ends in ".gz", read from pipe to gunzip -dc * format - format of file (e.g. MSAFILE_STOCKHOLM) * env - environment variable for path (e.g. BLASTDB) * * Returns: opened MSAFILE * on success. * NULL on failure: * usually, because the file doesn't exist; * for gzip'ed files, may also mean that gzip isn't in the path. */ MSAFILE * MSAFileOpen(char *filename, int format, char *env) { MSAFILE *afp; afp = MallocOrDie(sizeof(MSAFILE)); if (strcmp(filename, "-") == 0) { afp->f = stdin; afp->do_stdin = TRUE; afp->do_gzip = FALSE; afp->fname = sre_strdup("[STDIN]", -1); afp->ssi = NULL; /* can't index stdin because we can't seek*/ } #ifndef SRE_STRICT_ANSI /* popen(), pclose() aren't portable to non-POSIX systems; disable */ else if (Strparse("^.*\\.gz$", filename, 0)) { char cmd[256]; /* Note that popen() will return "successfully" * if file doesn't exist, because gzip works fine * and prints an error! So we have to check for * existence of file ourself. */ if (! FileExists(filename)) Die("%s: file does not exist", filename); if (strlen(filename) + strlen("gzip -dc ") >= 256) Die("filename > 255 char in MSAFileOpen()"); sprintf(cmd, "gzip -dc %s", filename); if ((afp->f = popen(cmd, "r")) == NULL) return NULL; afp->do_stdin = FALSE; afp->do_gzip = TRUE; afp->fname = sre_strdup(filename, -1); /* we can't index a .gz file, because we can't seek in a pipe afaik */ afp->ssi = NULL; } #endif /*SRE_STRICT_ANSI*/ else { char *ssifile; char *dir; /* When we open a file, it may be either in the current * directory, or in the directory indicated by the env * argument - and we have to construct the SSI filename accordingly. */ if ((afp->f = fopen(filename, "r")) != NULL) { ssifile = MallocOrDie(sizeof(char) * (strlen(filename) + 5)); sprintf(ssifile, "%s.ssi", filename); } else if ((afp->f = EnvFileOpen(filename, env, &dir)) != NULL) { char *full; full = FileConcat(dir, filename); ssifile = MallocOrDie(sizeof(char) * (strlen(full) + strlen(filename) + 5)); sprintf(ssifile, "%s.ssi", full); free(dir); } else return NULL; afp->do_stdin = FALSE; afp->do_gzip = FALSE; afp->fname = sre_strdup(filename, -1); afp->ssi = NULL; /* Open the SSI index file. If it doesn't exist, or * it's corrupt, or some error happens, afp->ssi stays NULL. */ SSIOpen(ssifile, &(afp->ssi)); free(ssifile); } /* Invoke autodetection if we haven't already been told what * to expect. */ if (format == MSAFILE_UNKNOWN) { if (afp->do_stdin == TRUE || afp->do_gzip) Die("Can't autodetect alignment file format from a stdin or gzip pipe"); format = MSAFileFormat(afp); if (format == MSAFILE_UNKNOWN) Die("Can't determine format of multiple alignment file %s", afp->fname); } afp->format = format; afp->linenumber = 0; afp->buf = NULL; afp->buflen = 0; return afp; } /* Function: MSAFilePositionByKey() * MSAFilePositionByIndex() * MSAFileRewind() * * Date: SRE, Tue Nov 9 19:02:54 1999 [St. Louis] * * Purpose: Family of functions for repositioning in * open MSA files; analogous to a similarly * named function series in HMMER's hmmio.c. * * Args: afp - open alignment file * offset - disk offset in bytes * key - key to look up in SSI indices * idx - index of alignment. * * Returns: 0 on failure. * 1 on success. * If called on a non-fseek()'able file (e.g. a gzip'ed * or pipe'd alignment), returns 0 as a failure flag. */ int MSAFileRewind(MSAFILE *afp) { if (afp->do_gzip || afp->do_stdin) return 0; rewind(afp->f); return 1; } int MSAFilePositionByKey(MSAFILE *afp, char *key) { int fh; /* filehandle is ignored */ SSIOFFSET offset; /* offset of the key alignment */ if (afp->ssi == NULL) return 0; if (SSIGetOffsetByName(afp->ssi, key, &fh, &offset) != 0) return 0; if (SSISetFilePosition(afp->f, &offset) != 0) return 0; return 1; } int MSAFilePositionByIndex(MSAFILE *afp, int idx) { int fh; /* filehandled is passed but ignored */ SSIOFFSET offset; /* disk offset of desired alignment */ if (afp->ssi == NULL) return 0; if (SSIGetOffsetByNumber(afp->ssi, idx, &fh, &offset) != 0) return 0; if (SSISetFilePosition(afp->f, &offset) != 0) return 0; return 1; } /* Function: MSAFileRead() * Date: SRE, Fri May 28 16:01:43 1999 [St. Louis] * * Purpose: Read the next msa from an open alignment file. * This is a wrapper around format-specific calls. * * Args: afp - open alignment file * * Returns: next alignment, or NULL if out of alignments */ MSA * MSAFileRead(MSAFILE *afp) { MSA *msa = NULL; switch (afp->format) { case MSAFILE_STOCKHOLM: msa = ReadStockholm(afp); break; case MSAFILE_MSF: msa = ReadMSF(afp); break; case MSAFILE_A2M: msa = ReadA2M(afp); break; case MSAFILE_CLUSTAL: msa = ReadClustal(afp); break; case MSAFILE_SELEX: msa = ReadSELEX(afp); break; case MSAFILE_PHYLIP: msa = ReadPhylip(afp); break; default: Die("MSAFILE corrupted: bad format index"); } return msa; } /* Function: MSAFileClose() * Date: SRE, Tue May 18 14:05:28 1999 [St. Louis] * * Purpose: Close an open MSAFILE. * * Args: afp - ptr to an open MSAFILE. * * Returns: void */ void MSAFileClose(MSAFILE *afp) { #ifndef SRE_STRICT_ANSI /* gzip functionality only on POSIX systems */ if (afp->do_gzip) pclose(afp->f); #endif if (! afp->do_stdin) fclose(afp->f); if (afp->buf != NULL) free(afp->buf); if (afp->ssi != NULL) SSIClose(afp->ssi); if (afp->fname != NULL) free(afp->fname); free(afp); } char * MSAFileGetLine(MSAFILE *afp) { char *s; if ((s = sre_fgets(&(afp->buf), &(afp->buflen), afp->f)) == NULL) return NULL; afp->linenumber++; return afp->buf; } void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline) { switch (outfmt) { case MSAFILE_A2M: WriteA2M(fp, msa); break; case MSAFILE_CLUSTAL: WriteClustal(fp, msa); break; case MSAFILE_MSF: WriteMSF(fp, msa); break; case MSAFILE_PHYLIP: WritePhylip(fp, msa); break; case MSAFILE_SELEX: WriteSELEX(fp, msa); break; case MSAFILE_STOCKHOLM: if (do_oneline) WriteStockholmOneBlock(fp, msa); else WriteStockholm(fp, msa); break; default: Die("can't write. no such alignment format %d\n", outfmt); } } /* Function: MSAGetSeqidx() * Date: SRE, Wed May 19 15:08:25 1999 [St. Louis] * * Purpose: From a sequence name, return seqidx appropriate * for an MSA structure. * * 1) try to guess the index. (pass -1 if you can't guess) * 2) Look up name in msa's hashtable. * 3) If it's a new name, store in msa's hashtable; * expand allocs as needed; * save sqname. * * Args: msa - alignment object * name - a sequence name * guess - a guess at the right index, or -1 if no guess. * * Returns: seqidx */ int MSAGetSeqidx(MSA *msa, char *name, int guess) { int seqidx; /* can we guess? */ if (guess >= 0 && guess < msa->nseq && strcmp(name, msa->sqname[guess]) == 0) return guess; /* else, a lookup in the index */ if ((seqidx = GKIKeyIndex(msa->index, name)) >= 0) return seqidx; /* else, it's a new name */ seqidx = GKIStoreKey(msa->index, name); if (seqidx >= msa->nseqalloc) MSAExpand(msa); msa->sqname[seqidx] = sre_strdup(name, -1); msa->nseq++; return seqidx; } /* Function: MSAFromAINFO() * Date: SRE, Mon Jun 14 11:22:24 1999 [St. Louis] * * Purpose: Convert the old aseq/ainfo alignment structure * to new MSA structure. Enables more rapid conversion * of codebase to the new world order. * * Args: aseq - [0..nseq-1][0..alen-1] alignment * ainfo - old-style optional info * * Returns: MSA * */ MSA * MSAFromAINFO(char **aseq, AINFO *ainfo) { MSA *msa; int i, j; msa = MSAAlloc(ainfo->nseq, ainfo->alen); for (i = 0; i < ainfo->nseq; i++) { strcpy(msa->aseq[i], aseq[i]); msa->wgt[i] = ainfo->wgt[i]; msa->sqname[i] = sre_strdup(ainfo->sqinfo[i].name, -1); msa->sqlen[i] = msa->alen; GKIStoreKey(msa->index, msa->sqname[i]); if (ainfo->sqinfo[i].flags & SQINFO_ACC) MSASetSeqAccession(msa, i, ainfo->sqinfo[i].acc); if (ainfo->sqinfo[i].flags & SQINFO_DESC) MSASetSeqDescription(msa, i, ainfo->sqinfo[i].desc); if (ainfo->sqinfo[i].flags & SQINFO_SS) { if (msa->ss == NULL) { msa->ss = MallocOrDie(sizeof(char *) * msa->nseqalloc); msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc); for (j = 0; j < msa->nseqalloc; j++) { msa->ss[j] = NULL; msa->sslen[j] = 0; } } MakeAlignedString(msa->aseq[i], msa->alen, ainfo->sqinfo[i].ss, &(msa->ss[i])); msa->sslen[i] = msa->alen; } if (ainfo->sqinfo[i].flags & SQINFO_SA) { if (msa->sa == NULL) { msa->sa = MallocOrDie(sizeof(char *) * msa->nseqalloc); msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc); for (j = 0; j < msa->nseqalloc; j++) { msa->sa[j] = NULL; msa->salen[j] = 0; } } MakeAlignedString(msa->aseq[i], msa->alen, ainfo->sqinfo[i].sa, &(msa->sa[i])); msa->salen[i] = msa->alen; } } /* note that sre_strdup() returns NULL when passed NULL */ msa->name = sre_strdup(ainfo->name, -1); msa->desc = sre_strdup(ainfo->desc, -1); msa->acc = sre_strdup(ainfo->acc, -1); msa->au = sre_strdup(ainfo->au, -1); msa->ss_cons = sre_strdup(ainfo->cs, -1); msa->rf = sre_strdup(ainfo->rf, -1); if (ainfo->flags & AINFO_TC) { msa->cutoff[MSA_CUTOFF_TC1] = ainfo->tc1; msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE; msa->cutoff[MSA_CUTOFF_TC2] = ainfo->tc2; msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE; } if (ainfo->flags & AINFO_NC) { msa->cutoff[MSA_CUTOFF_NC1] = ainfo->nc1; msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE; msa->cutoff[MSA_CUTOFF_NC2] = ainfo->nc2; msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE; } if (ainfo->flags & AINFO_GA) { msa->cutoff[MSA_CUTOFF_GA1] = ainfo->ga1; msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE; msa->cutoff[MSA_CUTOFF_GA2] = ainfo->ga2; msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE; } msa->nseq = ainfo->nseq; msa->alen = ainfo->alen; return msa; } /* Function: MSAFileFormat() * Date: SRE, Fri Jun 18 14:26:49 1999 [Sanger Centre] * * Purpose: (Attempt to) determine the format of an alignment file. * Since it rewinds the file pointer when it's done, * cannot be used on a pipe or gzip'ed file. Works by * calling SeqfileFormat() from sqio.c, then making sure * that the format is indeed an alignment. If the format * comes back as FASTA, it assumes that the format as A2M * (e.g. aligned FASTA). * * Args: fname - file to evaluate * * Returns: format code; e.g. MSAFILE_STOCKHOLM */ int MSAFileFormat(MSAFILE *afp) { int fmt; fmt = SeqfileFormat(afp->f); if (fmt == SQFILE_FASTA) fmt = MSAFILE_A2M; if (fmt != MSAFILE_UNKNOWN && ! IsAlignmentFormat(fmt)) Die("File %s does not appear to be an alignment file;\n\ rather, it appears to be an unaligned file in %s format.\n\ I'm expecting an alignment file in this context.\n", afp->fname, SeqfileFormat2String(fmt)); return fmt; } /* Function: MSAMingap() * Date: SRE, Mon Jun 28 18:57:54 1999 [on jury duty, St. Louis Civil Court] * * Purpose: Remove all-gap columns from a multiple sequence alignment * and its associated per-residue data. * * Args: msa - the alignment * * Returns: (void) */ void MSAMingap(MSA *msa) { int *useme; /* array of TRUE/FALSE flags for which columns to keep */ int apos; /* position in original alignment */ int idx; /* sequence index */ useme = MallocOrDie(sizeof(int) * msa->alen); for (apos = 0; apos < msa->alen; apos++) { for (idx = 0; idx < msa->nseq; idx++) if (! isgap(msa->aseq[idx][apos])) break; if (idx == msa->nseq) useme[apos] = FALSE; else useme[apos] = TRUE; } MSAShorterAlignment(msa, useme); free(useme); return; } /* Function: MSANogap() * Date: SRE, Wed Nov 17 09:59:51 1999 [St. Louis] * * Purpose: Remove all columns from a multiple sequence alignment that * contain any gaps -- used for filtering before phylogenetic * analysis. * * Args: msa - the alignment * * Returns: (void). The alignment is modified, so if you want to keep * the original for something, make a copy. */ void MSANogap(MSA *msa) { int *useme; /* array of TRUE/FALSE flags for which columns to keep */ int apos; /* position in original alignment */ int idx; /* sequence index */ useme = MallocOrDie(sizeof(int) * msa->alen); for (apos = 0; apos < msa->alen; apos++) { for (idx = 0; idx < msa->nseq; idx++) if (isgap(msa->aseq[idx][apos])) break; if (idx == msa->nseq) useme[apos] = TRUE; else useme[apos] = FALSE; } MSAShorterAlignment(msa, useme); free(useme); return; } /* Function: MSAShorterAlignment() * Date: SRE, Wed Nov 17 09:49:32 1999 [St. Louis] * * Purpose: Given an array "useme" (0..alen-1) of TRUE/FALSE flags, * where TRUE means "keep this column in the new alignment": * Remove all columns annotated as "FALSE" in the useme * array. * * Args: msa - the alignment. The alignment is changed, so * if you don't want the original screwed up, make * a copy of it first. * useme - TRUE/FALSE flags for columns to keep: 0..alen-1 * * Returns: (void) */ void MSAShorterAlignment(MSA *msa, int *useme) { int apos; /* position in original alignment */ int mpos; /* position in new alignment */ int idx; /* sequence index */ int i; /* markup index */ /* Since we're minimizing, we can overwrite, using already allocated * memory. */ for (apos = 0, mpos = 0; apos < msa->alen; apos++) { if (useme[apos] == FALSE) continue; /* shift alignment and associated per-column+per-residue markup */ if (mpos != apos) { for (idx = 0; idx < msa->nseq; idx++) { msa->aseq[idx][mpos] = msa->aseq[idx][apos]; if (msa->ss != NULL && msa->ss[idx] != NULL) msa->ss[idx][mpos] = msa->ss[idx][apos]; if (msa->sa != NULL && msa->sa[idx] != NULL) msa->sa[idx][mpos] = msa->sa[idx][apos]; for (i = 0; i < msa->ngr; i++) if (msa->gr[i][idx] != NULL) msa->gr[i][idx][mpos] = msa->gr[i][idx][apos]; } if (msa->ss_cons != NULL) msa->ss_cons[mpos] = msa->ss_cons[apos]; if (msa->sa_cons != NULL) msa->sa_cons[mpos] = msa->sa_cons[apos]; if (msa->rf != NULL) msa->rf[mpos] = msa->rf[apos]; for (i = 0; i < msa->ngc; i++) msa->gc[i][mpos] = msa->gc[i][apos]; } mpos++; } msa->alen = mpos; /* set new length */ /* null terminate everything */ for (idx = 0; idx < msa->nseq; idx++) { msa->aseq[idx][mpos] = '\0'; if (msa->ss != NULL && msa->ss[idx] != NULL) msa->ss[idx][mpos] = '\0'; if (msa->sa != NULL && msa->sa[idx] != NULL) msa->sa[idx][mpos] = '\0'; for (i = 0; i < msa->ngr; i++) if (msa->gr[i][idx] != NULL) msa->gr[i][idx][mpos] = '\0'; } if (msa->ss_cons != NULL) msa->ss_cons[mpos] = '\0'; if (msa->sa_cons != NULL) msa->sa_cons[mpos] = '\0'; if (msa->rf != NULL) msa->rf[mpos] = '\0'; for (i = 0; i < msa->ngc; i++) msa->gc[i][mpos] = '\0'; return; } /* Function: MSASmallerAlignment() * Date: SRE, Wed Jun 30 09:56:08 1999 [St. Louis] * * Purpose: Given an array "useme" of TRUE/FALSE flags for * each sequence in an alignment, construct * and return a new alignment containing only * those sequences that are flagged useme=TRUE. * * Used by routines such as MSAFilterAlignment() * and MSASampleAlignment(). * * Limitations: * Does not copy unparsed Stockholm markup. * * Does not make assumptions about meaning of wgt; * if you want the new wgt vector renormalized, do * it yourself with FNorm(new->wgt, new->nseq). * * Args: msa -- the original (larger) alignment * useme -- [0..nseq-1] array of TRUE/FALSE flags; TRUE means include * this seq in new alignment * ret_new -- RETURN: new alignment * * Returns: void * ret_new is allocated here; free with MSAFree() */ void MSASmallerAlignment(MSA *msa, int *useme, MSA **ret_new) { MSA *new; /* RETURN: new alignment */ int nnew; /* number of seqs in new msa (e.g. # of TRUEs) */ int oidx, nidx; /* old, new indices */ int i; nnew = 0; for (oidx = 0; oidx < msa->nseq; oidx++) if (useme[oidx]) nnew++; if (nnew == 0) { *ret_new = NULL; return; } new = MSAAlloc(nnew, 0); nidx = 0; for (oidx = 0; oidx < msa->nseq; oidx++) if (useme[oidx]) { new->aseq[nidx] = sre_strdup(msa->aseq[oidx], msa->alen); new->sqname[nidx] = sre_strdup(msa->sqname[oidx], msa->alen); GKIStoreKey(new->index, msa->sqname[oidx]); new->wgt[nidx] = msa->wgt[oidx]; if (msa->sqacc != NULL) MSASetSeqAccession(new, nidx, msa->sqacc[oidx]); if (msa->sqdesc != NULL) MSASetSeqDescription(new, nidx, msa->sqdesc[oidx]); if (msa->ss != NULL && msa->ss[oidx] != NULL) { if (new->ss == NULL) new->ss = MallocOrDie(sizeof(char *) * new->nseq); new->ss[nidx] = sre_strdup(msa->ss[oidx], -1); } if (msa->sa != NULL && msa->sa[oidx] != NULL) { if (new->sa == NULL) new->sa = MallocOrDie(sizeof(char *) * new->nseq); new->sa[nidx] = sre_strdup(msa->sa[oidx], -1); } nidx++; } new->nseq = nnew; new->alen = msa->alen; new->flags = msa->flags; new->type = msa->type; new->name = sre_strdup(msa->name, -1); new->desc = sre_strdup(msa->desc, -1); new->acc = sre_strdup(msa->acc, -1); new->au = sre_strdup(msa->au, -1); new->ss_cons = sre_strdup(msa->ss_cons, -1); new->sa_cons = sre_strdup(msa->sa_cons, -1); new->rf = sre_strdup(msa->rf, -1); for (i = 0; i < MSA_MAXCUTOFFS; i++) { new->cutoff[i] = msa->cutoff[i]; new->cutoff_is_set[i] = msa->cutoff_is_set[i]; } free(new->sqlen); new->sqlen = NULL; MSAMingap(new); *ret_new = new; return; } /***************************************************************** * Retrieval routines * * Access to MSA structure data is possible through these routines. * I'm not doing this because of object oriented design, though * it might work in my favor someday. * I'm doing this because lots of MSA data is optional, and * checking through the chain of possible NULLs is a pain. *****************************************************************/ char * MSAGetSeqAccession(MSA *msa, int idx) { if (msa->sqacc != NULL && msa->sqacc[idx] != NULL) return msa->sqacc[idx]; else return NULL; } char * MSAGetSeqDescription(MSA *msa, int idx) { if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) return msa->sqdesc[idx]; else return NULL; } char * MSAGetSeqSS(MSA *msa, int idx) { if (msa->ss != NULL && msa->ss[idx] != NULL) return msa->ss[idx]; else return NULL; } char * MSAGetSeqSA(MSA *msa, int idx) { if (msa->sa != NULL && msa->sa[idx] != NULL) return msa->sa[idx]; else return NULL; } /***************************************************************** * Information routines * * Access information about the MSA. *****************************************************************/ /* Function: MSAAverageSequenceLength() * Date: SRE, Sat Apr 6 09:41:34 2002 [St. Louis] * * Purpose: Return the average length of the (unaligned) sequences * in the MSA. * * Args: msa - the alignment * * Returns: average length */ float MSAAverageSequenceLength(MSA *msa) { int i; float avg; avg = 0.; for (i = 0; i < msa->nseq; i++) avg += (float) DealignedLength(msa->aseq[i]); if (msa->nseq == 0) return 0.; else return (avg / msa->nseq); } squid/msf.c0000640000175000017520000002777310463223377013064 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* msf.c * SRE, Sun Jul 11 16:17:32 1993 * * Import/export of GCG MSF multiple sequence alignment * formatted files. Designed using format specifications * kindly provided by Steve Smith of Genetics Computer Group. * * CVS $Id: msf.c,v 1.6 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include #include "squid.h" #include "msa.h" #ifdef TESTDRIVE_MSF /***************************************************************** * msf.c test driver: * cc -DTESTDRIVE_MSF -g -O2 -Wall -o test msf.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c sqio.c alignio.c selex.c interleaved.c types.c -lm * */ int main(int argc, char **argv) { MSAFILE *afp; MSA *msa; char *file; file = argv[1]; if ((afp = MSAFileOpen(file, MSAFILE_STOCKHOLM, NULL)) == NULL) Die("Couldn't open %s\n", file); while ((msa = ReadMSF(afp)) != NULL) { WriteMSF(stdout, msa); MSAFree(msa); } MSAFileClose(afp); exit(0); } /******************************************************************/ #endif /* testdrive_msf */ /* Function: ReadMSF() * Date: SRE, Tue Jun 1 08:07:22 1999 [St. Louis] * * Purpose: Parse an alignment read from an open MSF format * alignment file. (MSF is a single-alignment format.) * Return the alignment, or NULL if we've already * read the alignment. * * Args: afp - open alignment file * * Returns: MSA * - an alignment object * caller responsible for an MSAFree() * NULL if no more alignments * * Diagnostics: * Will Die() here with a (potentially) useful message * if a parsing error occurs. */ MSA * ReadMSF(MSAFILE *afp) { MSA *msa; char *s; int alleged_alen; int alleged_type; int alleged_checksum; char *tok; char *sp; int slen; int sqidx; char *name; char *seq; if (feof(afp->f)) return NULL; if ((s = MSAFileGetLine(afp)) == NULL) return NULL; /* The first line is the header. * This is a new-ish GCG feature. Don't count on it, so * we can be a bit more tolerant towards non-GCG software * generating "MSF" files. */ msa = MSAAlloc(10, 0); if (strncmp(s, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0) { msa->type = kAmino; if ((s = MSAFileGetLine(afp)) == NULL) return NULL; } else if (strncmp(s, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0) { msa->type = kRNA; if ((s = MSAFileGetLine(afp)) == NULL) return NULL; } /* Now we're in the free text comment section of the MSF file. * It ends when we see the "MSF: Type: Check: .." line. * This line must be present. */ do { if ((strstr(s, "..") != NULL && strstr(s, "MSF:") != NULL) && Strparse("^.+MSF: +([0-9]+) +Type: +([PNX]).+Check: +([0-9]+) +\\.\\.", s, 3)) { alleged_alen = atoi(sqd_parse[0]); switch (*(sqd_parse[1])) { case 'N' : alleged_type = kRNA; break; case 'P' : alleged_type = kAmino; break; case 'X' : alleged_type = kOtherSeq; break; default : alleged_type = kOtherSeq; } alleged_checksum = atoi(sqd_parse[3]); if (msa->type == kOtherSeq) msa->type = alleged_type; break; /* we're done with comment section. */ } if (! IsBlankline(s)) MSAAddComment(msa, s); } while ((s = MSAFileGetLine(afp)) != NULL); /* Now we're in the name section. * GCG has a relatively poorly documented feature: only sequences that * appear in this list will be read from the alignment section. Commenting * out sequences in the name list (by preceding them with "!") is * allowed as a means of manually defining subsets of sequences in * the alignment section. We can support this feature reasonably * easily because of the hash table for names in the MSA: we * only add names to the hash table when we see 'em in the name section. */ while ((s = MSAFileGetLine(afp)) != NULL) { while ((*s == ' ' || *s == '\t') && *s) s++; /* skip leading whitespace */ if (*s == '\n') continue; /* skip blank lines */ else if (*s == '!') MSAAddComment(msa, s); else if ((sp = strstr(s, "Name:")) != NULL) { /* We take the name and the weigh, and that's it */ sp += 5; tok = sre_strtok(&sp, " \t", &slen); /* */ sqidx = GKIStoreKey(msa->index, tok); if (sqidx >= msa->nseqalloc) MSAExpand(msa); msa->sqname[sqidx] = sre_strdup(tok, slen); msa->nseq++; if ((sp = strstr(sp, "Weight:")) == NULL) Die("No Weight: on line %d for %s in name section of MSF file %s\n", afp->linenumber, msa->sqname[sqidx], afp->fname); sp += 7; tok = sre_strtok(&sp, " \t", &slen); msa->wgt[sqidx] = atof(tok); msa->flags |= MSA_SET_WGT; } else if (strncmp(s, "//", 2) == 0) break; else { Die("Invalid line (probably %d) in name section of MSF file %s:\n%s\n", afp->linenumber, afp->fname, s); squid_errno = SQERR_FORMAT; /* NOT THREADSAFE */ return NULL; } } /* And now we're in the sequence section. * As discussed above, if we haven't seen a sequence name, then we * don't include the sequence in the alignment. * Also, watch out for coordinate-only lines. */ while ((s = MSAFileGetLine(afp)) != NULL) { sp = s; if ((name = sre_strtok(&sp, " \t", NULL)) == NULL) continue; if ((seq = sre_strtok(&sp, "\n", &slen)) == NULL) continue; /* The test for a coord line: digits starting both fields */ if (isdigit((int) *name) && isdigit((int) *seq)) continue; /* It's not blank, and it's not a coord line: must be sequence */ sqidx = GKIKeyIndex(msa->index, name); if (sqidx < 0) continue; /* not a sequence we recognize */ msa->sqlen[sqidx] = sre_strcat(&(msa->aseq[sqidx]), msa->sqlen[sqidx], seq, slen); } /* We've left blanks in the aseqs; take them back out. */ for (sqidx = 0; sqidx < msa->nseq; sqidx++) { if (msa->aseq[sqidx] == NULL) Die("Didn't find a sequence for %s in MSF file %s\n", msa->sqname[sqidx], afp->fname); for (s = sp = msa->aseq[sqidx]; *s != '\0'; s++) { if (*s == ' ' || *s == '\t') { msa->sqlen[sqidx]--; } else { *sp = *s; sp++; } } *sp = '\0'; } MSAVerifyParse(msa); /* verifies, and also sets alen and wgt. */ return msa; } /* Function: WriteMSF() * Date: SRE, Mon May 31 11:25:18 1999 [St. Louis] * * Purpose: Write an alignment in MSF format to an open file. * * Args: fp - file that's open for writing. * msa - alignment to write. * * Note that msa->type, usually optional, must be * set for WriteMSF to work. If it isn't, a fatal * error is generated. * * Returns: (void) */ void WriteMSF(FILE *fp, MSA *msa) { time_t now; /* current time as a time_t */ char date[64]; /* today's date in GCG's format "October 3, 1996 15:57" */ char **gcg_aseq; /* aligned sequences with gaps converted to GCG format */ char **gcg_sqname; /* sequence names with GCG-valid character sets */ int idx; /* counter for sequences */ char *s; /* pointer into sqname or seq */ int len; /* tmp variable for name lengths */ int namelen; /* maximum name length used */ int pos; /* position counter */ char buffer[51]; /* buffer for writing seq */ int i; /* another position counter */ /***************************************************************** * Make copies of sequence names and sequences. * GCG recommends that name characters should only contain * alphanumeric characters, -, or _ * Some GCG and GCG-compatible software is sensitive to this. * We silently convert all other characters to '_'. * * For sequences, GCG allows only ~ and . for gaps. * Otherwise, everthing is interpreted as a residue; * so squid's IUPAC-restricted chars are fine. ~ means * an external gap. . means an internal gap. *****************************************************************/ /* make copies that we can edit */ gcg_aseq = MallocOrDie(sizeof(char *) * msa->nseq); gcg_sqname = MallocOrDie(sizeof(char *) * msa->nseq); for (idx = 0; idx < msa->nseq; idx++) { gcg_aseq[idx] = sre_strdup(msa->aseq[idx], msa->alen); gcg_sqname[idx] = sre_strdup(msa->sqname[idx], -1); } /* alter names as needed */ for (idx = 0; idx < msa->nseq; idx++) for (s = gcg_sqname[idx]; *s != '\0'; s++) if (! isalnum((int) *s) && *s != '-' && *s != '_') *s = '_'; /* alter gap chars in seq */ for (idx = 0; idx < msa->nseq; idx++) { for (s = gcg_aseq[idx]; *s != '\0' && isgap(*s); s++) *s = '~'; for (; *s != '\0'; s++) if (isgap(*s)) *s = '.'; for (pos = msa->alen-1; pos > 0 && isgap(gcg_aseq[idx][pos]); pos--) gcg_aseq[idx][pos] = '~'; } /* calculate max namelen used */ namelen = 0; for (idx = 0; idx < msa->nseq; idx++) if ((len = strlen(msa->sqname[idx])) > namelen) namelen = len; /***************************************************** * Write the MSF header *****************************************************/ /* required file type line */ if (msa->type == kOtherSeq) msa->type = GuessAlignmentSeqtype(msa->aseq, msa->nseq); if (msa->type == kRNA) fprintf(fp, "!!NA_MULTIPLE_ALIGNMENT 1.0\n"); else if (msa->type == kDNA) fprintf(fp, "!!NA_MULTIPLE_ALIGNMENT 1.0\n"); else if (msa->type == kAmino) fprintf(fp, "!!AA_MULTIPLE_ALIGNMENT 1.0\n"); else if (msa->type == kOtherSeq) Die("WriteMSF(): couldn't guess whether that alignment is RNA or protein.\n"); else Die("Invalid sequence type %d in WriteMSF()\n", msa->type); /* free text comments */ if (msa->ncomment > 0) { for (idx = 0; idx < msa->ncomment; idx++) fprintf(fp, "%s\n", msa->comment[idx]); fprintf(fp, "\n"); } /* required checksum line */ now = time(NULL); if (strftime(date, 64, "%B %d, %Y %H:%M", localtime(&now)) == 0) Die("What time is it on earth? strftime() failed in WriteMSF().\n"); fprintf(fp, " %s MSF: %d Type: %c %s Check: %d ..\n", msa->name != NULL ? msa->name : "squid.msf", msa->alen, msa->type == kRNA ? 'N' : 'P', date, GCGMultchecksum(gcg_aseq, msa->nseq)); fprintf(fp, "\n"); /***************************************************** * Names/weights section *****************************************************/ for (idx = 0; idx < msa->nseq; idx++) { fprintf(fp, " Name: %-*.*s Len: %5d Check: %4d Weight: %.2f\n", namelen, namelen, gcg_sqname[idx], msa->alen, GCGchecksum(gcg_aseq[idx], msa->alen), msa->wgt[idx]); } fprintf(fp, "\n"); fprintf(fp, "//\n"); /***************************************************** * Write the sequences *****************************************************/ for (pos = 0; pos < msa->alen; pos += 50) { fprintf(fp, "\n"); /* Blank line between sequence blocks */ /* Coordinate line */ len = (pos + 50) > msa->alen ? msa->alen - pos : 50; if (len > 10) fprintf(fp, "%*s %-6d%*s%6d\n", namelen, "", pos+1, len + ((len-1)/10) - 12, "", pos + len); else fprintf(fp, "%*s %-6d\n", namelen, "", pos+1); for (idx = 0; idx < msa->nseq; idx++) { fprintf(fp, "%-*s ", namelen, gcg_sqname[idx]); /* get next line's worth of 50 from seq */ strncpy(buffer, gcg_aseq[idx] + pos, 50); buffer[50] = '\0'; /* draw the sequence line */ for (i = 0; i < len; i++) { if (! (i % 10)) fputc(' ', fp); fputc(buffer[i], fp); } fputc('\n', fp); } } Free2DArray((void **) gcg_aseq, msa->nseq); Free2DArray((void **) gcg_sqname, msa->nseq); return; } squid/phylip.c0000640000175000017520000001173510463223377013573 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* phylip.c * SRE, Mon Jun 14 14:08:33 1999 [St. Louis] * * Import/export of PHYLIP interleaved multiple sequence alignment * format files. * * Follows documentation at: * http://evolution.genetics.washington.edu/phylip/doc/sequence.html * for rev 3.6 of PHYLIP's molecular sequence analysis programs. * * CVS $Id: phylip.c,v 1.4 2004/07/29 00:23:27 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "msa.h" #ifdef TESTDRIVE_PHYLIP /***************************************************************** * phylip.c test driver: * */ int main(int argc, char **argv) { MSAFILE *afp; MSA *msa; char *file; file = argv[1]; if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL) Die("Couldn't open %s\n", file); printf("format %d\n", afp->format); while ((msa = ReadPhylip(afp)) != NULL) { WritePhylip(stdout, msa); MSAFree(msa); } MSAFileClose(afp); exit(0); } /******************************************************************/ #endif /* testdrive_phylip */ /* Function: ReadPhylip() * Date: SRE, Fri Jun 18 12:59:37 1999 [Sanger Centre] * * Purpose: Parse an alignment from an open Phylip format * alignment file. Phylip is a single-alignment format. * Return the alignment, or NULL if we have no data. * * Args: afp - open alignment file * * Returns: MSA * - an alignment object * Caller responsible for an MSAFree() * NULL if no more alignments */ MSA * ReadPhylip(MSAFILE *afp) { MSA *msa; char *s, *s1, *s2; char name[11]; /* seq name max len = 10 char */ int nseq, alen; int idx; /* index of current sequence */ int nblock; int i,j; if (feof(afp->f)) return NULL; /* Skip until we see a nonblank line; it's the header, * containing nseq/alen */ nseq = 0; alen = 0; while ((s = MSAFileGetLine(afp)) != NULL) { if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) Die("Failed to parse nseq/alen from first line of PHYLIP file %s\n", afp->fname); if (! IsInt(s1) || ! IsInt(s2)) Die("nseq and/or alen not an integer in first line of PHYLIP file %s\n", afp->fname); nseq = atoi(s1); alen = atoi(s2); break; } msa = MSAAlloc(nseq, 0); idx = 0; nblock = 0; while ((s = MSAFileGetLine(afp)) != NULL) { /* ignore blank lines. nonblank lines start w/ nonblank char */ if (isspace((int) *s)) continue; /* First block has seq names */ if (nblock == 0) { strncpy(name, s, 10); /* First ten chars are the name */ name[10] = '\0'; GKIStoreKey(msa->index, name); msa->sqname[idx] = sre_strdup(name, -1); s += 10; } /* Run through the buffer and strip any chars we don't recognize as * legal PHYLIP: especially, spaces. */ for (i = 0, j=0; s[i] != '\0'; i++) { if (isalpha(s[i]) || strchr("-?*", s[i]) != NULL) { s[j] = s[i]; j++; } } s[j] = '\0'; /* Concat the buffer onto our growing sequence. */ msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], s, j); idx++; if (idx == nseq) { idx = 0; nblock++; } } msa->nseq = nseq; MSAVerifyParse(msa); /* verifies; sets alen, wgt; frees sqlen[] */ if (msa->alen != alen) Die("First line said alignment would be alen=%d; read %d\n", alen, msa->alen); return msa; } /* Function: WritePhylip() * Date: SRE, Fri Jun 18 12:07:41 1999 [Sanger Centre] * * Purpose: Write an alignment in Phylip format to an open file. * * Args: fp - file that's open for writing. * msa - alignment to write. * * Returns: (void) */ void WritePhylip(FILE *fp, MSA *msa) { int idx; /* counter for sequences */ int cpl = 50; /* 50 seq char per line */ char buf[51]; /* buffer for writing seq */ int pos; int i; /* First line has nseq, alen */ fprintf(fp, " %d %d\n", msa->nseq, msa->alen); /* Alignment section. * PHYLIP is a multiblock format, blocks (optionally) separated * by blanks; names only attached to first block. Names are * restricted to ten char; we achieve this by simple truncation (!). * Gaps must be '-'. Seq chars should be upper case. */ for (pos = 0; pos < msa->alen; pos += cpl) { if (pos > 0) fprintf(fp, "\n"); for (idx = 0; idx < msa->nseq; idx++) { strncpy(buf, msa->aseq[idx] + pos, cpl); buf[cpl] = '\0'; for (i = 0; buf[i] != '\0'; i++) { if (islower(buf[i])) buf[i] = toupper(buf[i]); if (isgap(buf[i])) buf[i] = '-'; } if (pos > 0) fprintf(fp, "%s\n", buf); else fprintf(fp, "%-10.10s%s\n", msa->sqname[idx], buf); } } return; } squid/revcomp.c0000640000175000017520000000375410463223377013743 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* revcomp.c * * Reverse complement of a IUPAC character string * CVS $Id: revcomp.c,v 1.6 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" /* Function: revcomp() * * Purpose: Reverse complement seq; store in comp. * Can revcomp "in place" (revcomp(seq, seq)). * * Args: comp - destination for reverse complement of seq * seq - sequence to reverse complement * * Returns: NULL on failure; or a (useless) pointer to comp. */ char * revcomp(char *comp, char *seq) { char *s; char c; if (comp == NULL) return NULL; if (seq == NULL) return NULL; StrReverse(comp, seq); for (s = comp; *s != '\0'; s++) { c = *s; c = sre_toupper(c); switch (c) { case 'A': c = 'T'; break; case 'C': c = 'G'; break; case 'G': c = 'C'; break; case 'T': c = 'A'; break; case 'U': c = 'A'; break; case 'R': c = 'Y'; break; case 'Y': c = 'R'; break; case 'M': c = 'K'; break; case 'K': c = 'M'; break; case 'S': c = 'S'; break; case 'W': c = 'W'; break; case 'H': c = 'D'; break; case 'D': c = 'H'; break; case 'B': c = 'V'; break; case 'V': c = 'B'; break; default: break; /* anything else? leave it; it's prob a gap or an X */ } if (islower((int) *s)) c = (char) sre_tolower((int) c); *s = c; } return comp; } #ifdef REVCOMP_TESTDRIVER /* gcc -g -DREVCOMP_TESTDRIVER revcomp.c sre_string.c shuffle.c sre_math.c sre_ctype.c sqerror.c -lm */ int main(void) { float p[4] = {0.25, 0.25, 0.25, 0.25}; char *alphabet = "ACGT"; int len = 10; char *seq; seq = RandomSequence(alphabet, p, 4, len); printf("%s\n", seq); revcomp(seq, seq); printf("%s\n", seq); free(seq); exit(0); } #endif squid/revcomp_main.c0000640000175000017520000000513110463223377014736 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* main for revcomp * * revcomp - generate reverse complement of sequences * SRE, Thu Aug 5 17:36:57 1993 * CVS $Id: revcomp_main.c,v 1.7 2003/10/04 18:26:49 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" static char banner[] = "revcomp - reverse complement a nucleic acid sequence"; static char usage[] = "Usage: revcomp [-options] \n\ Reverse complement a nucleic acid sequence.\n\ Available options:\n\ -h : help; print version and usage info\n\ "; static char experts[] = "\ "; static struct opt_s OPTIONS[] = { { "-h", TRUE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *seqfile; /* name of sequence file */ SQFILE *dbfp; /* open sequence file */ int fmt; /* format of seqfile */ char *seq; /* sequence */ SQINFO sqinfo; /* additional sequence info */ char *rev; /* reverse complement */ int swap; char *optname; /* name of option found by Getopt() */ char *optarg; /* argument found by Getopt() */ int optind; /* index in argv[] */ /*********************************************** * Parse command line ***********************************************/ fmt = SQFILE_UNKNOWN; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 1) Die("%s\n", usage); seqfile = argv[optind]; if ((dbfp = SeqfileOpen(seqfile, fmt, NULL)) == NULL) Die("Failed to open sequence file %s for reading", seqfile); while (ReadSeq(dbfp, dbfp->format, &seq, &sqinfo)) { if ((rev = (char *) malloc ((sqinfo.len + 1) * sizeof(char))) == NULL) Die("malloc failed"); revcomp(rev, seq); if (sqinfo.flags & (SQINFO_START | SQINFO_STOP)) { swap = sqinfo.start; sqinfo.start = sqinfo.stop; sqinfo.stop = swap; } /* secondary structure of reverse strand is nonsense */ if (sqinfo.flags & SQINFO_SS) { sqinfo.flags = sqinfo.flags & ~SQINFO_SS; free(sqinfo.ss); } WriteSeq(stdout, SQFILE_FASTA, rev, &sqinfo); free(rev); FreeSequence(seq, &sqinfo); } SeqfileClose(dbfp); return 0; } squid/rk.c0000640000175000017520000000551310463223377012677 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* rk.c (originally from rnabob's patsearch.c) * * Contains a compiler and a search engine for Rabin-Karp * based primary sequence pattern searching on encoded * sequences. * * See Sedgewick, _Algorithms_, for a general discussion of * the Rabin-Karp algorithm. See the rkcomp or rkexec man * pages for specific details. * * CVS $Id: rk.c,v 1.3 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" /* seq encoding utilities and typedefs */ #include "rk.h" Hashseq rkcomp(char *probe) /* A,C,G,T/U, N probe string, 0-8 nt long */ { Hashseq hashprobe = 0; char coded[RK_HASHSIZE + 1]; int len; int i; /* check bounds violation on probe */ if ((len = strlen(probe)) > RK_HASHSIZE) return 0; /* encode the probe */ if (seqencode(coded, probe) == 0) return 0; /* pack the probe into a Hashseq */ for (i = 0; i < len; i++) { hashprobe <<= 4; hashprobe |= (Hashseq) coded[i]; } /* left adjust as needed */ for (; i < RK_HASHSIZE; i++) { hashprobe <<= 4; hashprobe |= (Hashseq) NTN; } /* return the compiled probe */ return hashprobe; } int rkseq(Hashseq hashprobe, /* up to 8 nt packed into the probe */ char *sequence) /* encoded sequence */ { long i; long pos = 0; Hashseq target = 0; /* initialize the target hashseq */ for (i = 0; i < RK_HASHSIZE; i++) { if (*(sequence + i) == NTEND) break; target <<= 4; target |= (Hashseq) (*(sequence + i)); } while (*(sequence + pos + RK_HASHSIZE -1) != NTEND) { #ifdef DEBUG printf("hashprobe: "); writehash(hashprobe); printf("\ttarget: "); writehash(target); printf("\nhashprobe & target: "); writehash(hashprobe & target); printf("\n"); #endif if ((hashprobe & target) == target) return ((int) pos); target <<= 4; target |= (Hashseq) (*(sequence + pos + RK_HASHSIZE)); pos++; } /* now we deal with an end effect */ for (i = 0; i < RK_HASHSIZE; i++) { target |= (Hashseq) NTN; if ((hashprobe & target) == target) return ((int) pos); target <<=4; pos++; } return(-1); } #ifdef DEBUG /* Debugging aids */ static void writehash(Hashseq hashseq) { int idx; int sym; if (hashseq/16) writehash(hashseq/16); sym = (int) (hashseq % 16); if (sym == 0) putchar('-'); else { for (idx = 0; sym != iupac[idx].code && idx < IUPACSYMNUM; idx++); if (idx > IUPACSYMNUM) printf("(%d)", sym); else putchar(iupac[idx].sym); } } #endif squid/selex.c0000640000175000017520000006473710463223377013420 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* selex.c * * SRE, Mon Jun 14 11:08:38 1999 * SELEX obsolete as the preferred HMMER/SQUID format * replaced by Stockholm format * selex support retained for backwards compatibility * kludged to use the MSA interface * * SRE, Mon Jan 30 14:41:49 1995: * #=SA side chain % surface accessibility annotation supported * * SRE, Tue Nov 9 17:40:50 1993: * major revision. #= special comments and aliinfo_s optional * alignment info support added. Support for #=CS (consensus * secondary structure), #=SS (individual secondary structure), * #=RF (reference coordinate system), #=SQ (per-sequence header info), * and #=AU ("author") added. * * Fri Dec 4 17:43:24 1992, SRE: * Reading and writing aligned sequences to/from disk files. * Implements a new, broader specification of SELEX format * and supercedes alignio.c. * * SELEX format is documented in Docs/formats.tex. **************************************************************************** * CVS $Id: selex.c,v 1.12 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include #include "squid.h" #include "msa.h" static int copy_alignment_line(char *aseq, int apos, int name_rcol, char *buffer, int lcol, int rcol, char gapsym); static void actually_write_selex(FILE *fp, MSA *msa, int cpl); static char commentsyms[] = "%#"; /* Function: ReadSELEX() * Date: SRE, Sun Jun 6 18:24:09 1999 [St. Louis] * * Purpose: Parse an alignment read from an open SELEX format * alignment file. (SELEX is a single alignment format). * Return the alignment, or NULL if we've already read the * alignment or there's no alignment data in the file. * * Limitations: SELEX is the only remaining multipass parser for * alignment files. It cannot read from gzip or from stdin. * It Die()'s here if you try. The reason for this * that SELEX allows space characters as gaps, so we don't * know the borders of an alignment block until we've seen * the whole block. I could rewrite to allow single-pass * parsing (by storing the whole block in memory) but * since SELEX is now legacy, why bother. * * Note that the interface is totally kludged: fastest * possible adaptation of old ReadSELEX() to the new * MSA interface. * * Args: afp - open alignment file * * Returns: MSA * - an alignment object * caller responsible for an MSAFree() * NULL if no alignment data. */ MSA * ReadSELEX(MSAFILE *afp) { MSA *msa; /* RETURN: mult seq alignment */ FILE *fp; /* ptr to opened seqfile */ char **aseqs; /* aligned seqs */ int num = 0; /* number of seqs read */ char buffer[LINEBUFLEN]; /* input buffer for lines */ char bufcpy[LINEBUFLEN]; /* strtok'able copy of buffer */ struct block_struc { /** alignment data for a block: */ int lcol; /* furthest left aligned sym */ int rcol; /* furthest right aligned sym */ } *blocks = NULL; int blocknum; /* number of blocks in file */ char *nptr; /* ptr to start of name on line */ char *sptr; /* ptr into sequence on line */ int currnum; /* num. seqs in given block */ int currblock; /* index for blocks */ int i; /* loop counter */ int seqidx; /* counter for seqs */ int alen; /* length of alignment */ int warn_names; /* becomes TRUE if names don't match between blocks */ int headnum; /* seqidx in per-sequence header info */ int currlen; int count; int have_cs = 0; int have_rf = 0; AINFO base_ainfo, *ainfo; /* hack: used to be passed ptr to AINFO */ /* Convert from MSA interface to what old ReadSELEX() did: * - copy our open fp, rather than opening file * - verify that we're not reading a gzip or stdin */ if (feof(afp->f)) return NULL; if (afp->do_gzip || afp->do_stdin) Die("Can't read a SELEX format alignment from a pipe, stdin, or gzip'ed file"); fp = afp->f; ainfo = &base_ainfo; /*************************************************** * First pass across file. * Count seqs, get names, determine column info * Determine what sorts of info are active in this file. ***************************************************/ InitAinfo(ainfo); /* get first line of the block * (non-comment, non-blank) */ do { if (fgets(buffer, LINEBUFLEN, fp) == NULL) { squid_errno = SQERR_NODATA; return 0; } strcpy(bufcpy, buffer); if (*buffer == '#') { if (strncmp(buffer, "#=CS", 4) == 0) have_cs = 1; else if (strncmp(buffer, "#=RF", 4) == 0) have_rf = 1; } } while ((nptr = strtok(bufcpy, WHITESPACE)) == NULL || (strchr(commentsyms, *nptr) != NULL)); blocknum = 0; warn_names = FALSE; while (!feof(fp)) { /* allocate for info about this block. */ if (blocknum == 0) blocks = (struct block_struc *) MallocOrDie (sizeof(struct block_struc)); else blocks = (struct block_struc *) ReallocOrDie (blocks, (blocknum+1) * sizeof(struct block_struc)); blocks[blocknum].lcol = LINEBUFLEN+1; blocks[blocknum].rcol = -1; currnum = 0; while (nptr != NULL) /* becomes NULL when this block ends. */ { /* First block only: save names */ if (blocknum == 0) { if (currnum == 0) ainfo->sqinfo = (SQINFO *) MallocOrDie (sizeof(SQINFO)); else ainfo->sqinfo = (SQINFO *) ReallocOrDie (ainfo->sqinfo, (currnum + 1) * sizeof(SQINFO)); ainfo->sqinfo[currnum].flags = 0; SetSeqinfoString(&(ainfo->sqinfo[currnum]), nptr, SQINFO_NAME); } else /* in each additional block: check names */ { if (strcmp(ainfo->sqinfo[currnum].name, nptr) != 0) warn_names = TRUE; } currnum++; /* check rcol, lcol */ if ((sptr = strtok(NULL, WHITESPACE)) != NULL) { /* is this the furthest left we've seen word 2 in this block? */ if (sptr - bufcpy < blocks[blocknum].lcol) blocks[blocknum].lcol = sptr - bufcpy; /* look for right side in buffer */ for (sptr = buffer + strlen(buffer) - 1; strchr(WHITESPACE, *sptr) != NULL; sptr --) /* do nothing */ ; if (sptr - buffer > blocks[blocknum].rcol) blocks[blocknum].rcol = sptr - buffer; } /* get the next line; blank line means end of block */ do { if (fgets(buffer, LINEBUFLEN, fp) == NULL) { nptr = NULL; break; } strcpy(bufcpy, buffer); if (strncmp(buffer, "#=SS", 4) == 0) ainfo->sqinfo[currnum-1].flags |= SQINFO_SS; else if (strncmp(buffer, "#=SA", 4) == 0) ainfo->sqinfo[currnum-1].flags |= SQINFO_SA; else if (strncmp(buffer, "#=CS", 4) == 0) have_cs = 1; else if (strncmp(buffer, "#=RF", 4) == 0) have_rf = 1; if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) break; } while (strchr(commentsyms, *nptr) != NULL); } /* check that number of sequences matches expected */ if (blocknum == 0) num = currnum; else if (currnum != num) Die("Parse error in ReadSELEX()"); blocknum++; /* get first line of next block * (non-comment, non-blank) */ do { if (fgets(buffer, LINEBUFLEN, fp) == NULL) { nptr = NULL; break; } strcpy(bufcpy, buffer); } while ((nptr = strtok(bufcpy, WHITESPACE)) == NULL || (strchr(commentsyms, *nptr) != NULL)); } /*************************************************** * Get ready for second pass: * figure out the length of the alignment * malloc space * rewind the file ***************************************************/ alen = 0; for (currblock = 0; currblock < blocknum; currblock++) alen += blocks[currblock].rcol - blocks[currblock].lcol + 1; rewind(fp); /* allocations. we can't use AllocateAlignment because of * the way we already used ainfo->sqinfo. */ aseqs = (char **) MallocOrDie (num * sizeof(char *)); if (have_cs) ainfo->cs = (char *) MallocOrDie ((alen+1) * sizeof(char)); if (have_rf) ainfo->rf = (char *) MallocOrDie ((alen+1) * sizeof(char)); for (i = 0; i < num; i++) { aseqs[i] = (char *) MallocOrDie ((alen+1) * sizeof(char)); if (ainfo->sqinfo[i].flags & SQINFO_SS) ainfo->sqinfo[i].ss = (char *) MallocOrDie ((alen+1) * sizeof(char)); if (ainfo->sqinfo[i].flags & SQINFO_SA) ainfo->sqinfo[i].sa = (char *) MallocOrDie ((alen+1) * sizeof(char)); } ainfo->alen = alen; ainfo->nseq = num; ainfo->wgt = (float *) MallocOrDie (sizeof(float) * num); FSet(ainfo->wgt, num, 1.0); /*************************************************** * Second pass across file. Parse header; assemble sequences ***************************************************/ /* We've now made a complete first pass over the file. We know how * many blocks it contains, we know the number of seqs in the first * block, and we know every block has the same number of blocks; * so we can be a bit more cavalier about error-checking as we * make the second pass. */ /* Look for header */ headnum = 0; for (;;) { if (fgets(buffer, LINEBUFLEN, fp) == NULL) Die("Parse error in ReadSELEX()"); strcpy(bufcpy, buffer); if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) continue; /* skip blank lines */ if (strcmp(nptr, "#=AU") == 0 && (sptr = strtok(NULL, "\n")) != NULL) ainfo->au = Strdup(sptr); else if (strcmp(nptr, "#=ID") == 0 && (sptr = strtok(NULL, "\n")) != NULL) ainfo->name = Strdup(sptr); else if (strcmp(nptr, "#=AC") == 0 && (sptr = strtok(NULL, "\n")) != NULL) ainfo->acc = Strdup(sptr); else if (strcmp(nptr, "#=DE") == 0 && (sptr = strtok(NULL, "\n")) != NULL) ainfo->desc = Strdup(sptr); else if (strcmp(nptr, "#=GA") == 0) { if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=GA line in ReadSELEX()"); ainfo->ga1 = atof(sptr); if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=GA line in ReadSELEX()"); ainfo->ga2 = atof(sptr); ainfo->flags |= AINFO_GA; } else if (strcmp(nptr, "#=TC") == 0) { if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=TC line in ReadSELEX()"); ainfo->tc1 = atof(sptr); if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=TC line in ReadSELEX()"); ainfo->tc2 = atof(sptr); ainfo->flags |= AINFO_TC; } else if (strcmp(nptr, "#=NC") == 0) { if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=NC line in ReadSELEX()"); ainfo->nc1 = atof(sptr); if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=NC line in ReadSELEX()"); ainfo->nc2 = atof(sptr); ainfo->flags |= AINFO_NC; } else if (strcmp(nptr, "#=SQ") == 0) /* per-sequence header info */ { /* first field is the name */ if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=SQ line in ReadSELEX()"); if (strcmp(sptr, ainfo->sqinfo[headnum].name) != 0) warn_names = TRUE; /* second field is the weight */ if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=SQ line in ReadSELEX()"); if (!IsReal(sptr)) Die("Parse error in #=SQ line in ReadSELEX(): weight is not a number"); ainfo->wgt[headnum] = atof(sptr); /* third field is database source id */ if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=SQ line in ReadSELEX(): incomplete line"); SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_ID); /* fourth field is database accession number */ if ((sptr = strtok(NULL, WHITESPACE)) == NULL) Die("Parse error in #=SQ line in ReadSELEX(): incomplete line"); SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_ACC); /* fifth field is start..stop::olen */ if ((sptr = strtok(NULL, ".:")) == NULL) Die("Parse error in #=SQ line in ReadSELEX(): incomplete line"); SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_START); if ((sptr = strtok(NULL, ".:")) == NULL) Die("Parse error in #=SQ line in ReadSELEX(): incomplete line"); SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_STOP); if ((sptr = strtok(NULL, ":\t ")) == NULL) Die("Parse error in #=SQ line in ReadSELEX(): incomplete line"); SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_OLEN); /* rest of line is optional description */ if ((sptr = strtok(NULL, "\n")) != NULL) SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_DESC); headnum++; } else if (strcmp(nptr, "#=CS") == 0) break; else if (strcmp(nptr, "#=RF") == 0) break; else if (strchr(commentsyms, *nptr) == NULL) break; /* non-comment, non-header */ } currlen = 0; for (currblock = 0 ; currblock < blocknum; currblock++) { /* parse the block */ seqidx = 0; while (nptr != NULL) { /* Consensus structure */ if (strcmp(nptr, "#=CS") == 0) { if (! copy_alignment_line(ainfo->cs, currlen, strlen(nptr)-1, buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.')) Die("Parse error in #=CS line in ReadSELEX()"); } /* Reference coordinates */ else if (strcmp(nptr, "#=RF") == 0) { if (! copy_alignment_line(ainfo->rf, currlen, strlen(nptr)-1, buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.')) Die("Parse error in #=RF line in ReadSELEX()"); } /* Individual secondary structure */ else if (strcmp(nptr, "#=SS") == 0) { if (! copy_alignment_line(ainfo->sqinfo[seqidx-1].ss, currlen, strlen(nptr)-1, buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.')) Die("Parse error in #=SS line in ReadSELEX()"); } /* Side chain % surface accessibility code */ else if (strcmp(nptr, "#=SA") == 0) { if (! copy_alignment_line(ainfo->sqinfo[seqidx-1].sa, currlen, strlen(nptr)-1, buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.')) Die("Parse error in #=SA line in ReadSELEX()"); } /* Aligned sequence; avoid unparsed machine comments */ else if (strncmp(nptr, "#=", 2) != 0) { if (! copy_alignment_line(aseqs[seqidx], currlen, strlen(nptr)-1, buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.')) Die("Parse error in alignment line in ReadSELEX()"); seqidx++; } /* get next line */ for (;;) { nptr = NULL; if (fgets(buffer, LINEBUFLEN, fp) == NULL) break; /* EOF */ strcpy(bufcpy, buffer); if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) break; /* blank */ if (strncmp(buffer, "#=", 2) == 0) break; /* machine comment */ if (strchr(commentsyms, *nptr) == NULL) break; /* data */ } } /* end of a block */ currlen += blocks[currblock].rcol - blocks[currblock].lcol + 1; /* get line 1 of next block */ for (;;) { if (fgets(buffer, LINEBUFLEN, fp) == NULL) break; /* no data */ strcpy(bufcpy, buffer); if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) continue; /* blank */ if (strncmp(buffer, "#=", 2) == 0) break; /* machine comment */ if (strchr(commentsyms, *nptr) == NULL) break; /* non-comment */ } } /* end of the file */ /* Lengths in sqinfo are for raw sequence (ungapped), * and SS, SA are 0..rlen-1 not 0..alen-1. * Only the seqs with structures come out of here with lengths set. */ for (seqidx = 0; seqidx < num; seqidx++) { int apos, rpos; /* secondary structures */ if (ainfo->sqinfo[seqidx].flags & SQINFO_SS) { for (apos = rpos = 0; apos < alen; apos++) if (! isgap(aseqs[seqidx][apos])) { ainfo->sqinfo[seqidx].ss[rpos] = ainfo->sqinfo[seqidx].ss[apos]; rpos++; } ainfo->sqinfo[seqidx].ss[rpos] = '\0'; } /* Surface accessibility */ if (ainfo->sqinfo[seqidx].flags & SQINFO_SA) { for (apos = rpos = 0; apos < alen; apos++) if (! isgap(aseqs[seqidx][apos])) { ainfo->sqinfo[seqidx].sa[rpos] = ainfo->sqinfo[seqidx].sa[apos]; rpos++; } ainfo->sqinfo[seqidx].sa[rpos] = '\0'; } } /* NULL-terminate all the strings */ if (ainfo->rf != NULL) ainfo->rf[alen] = '\0'; if (ainfo->cs != NULL) ainfo->cs[alen] = '\0'; for (seqidx = 0; seqidx < num; seqidx++) aseqs[seqidx][alen] = '\0'; /* find raw sequence lengths for sqinfo */ for (seqidx = 0; seqidx < num; seqidx++) { count = 0; for (sptr = aseqs[seqidx]; *sptr != '\0'; sptr++) if (!isgap(*sptr)) count++; ainfo->sqinfo[seqidx].len = count; ainfo->sqinfo[seqidx].flags |= SQINFO_LEN; } /*************************************************** * Garbage collection and return ***************************************************/ free(blocks); if (warn_names) Warn("sequences may be in different orders in blocks of %s?", afp->fname); /* Convert back to MSA structure. (Wasteful kludge.) */ msa = MSAFromAINFO(aseqs, ainfo); MSAVerifyParse(msa); FreeAlignment(aseqs, ainfo); return msa; } /* Function: WriteSELEX() * Date: SRE, Mon Jun 14 13:13:14 1999 [St. Louis] * * Purpose: Write a SELEX file in multiblock format. * * Args: fp - file that's open for writing * msa - multiple sequence alignment object * * Returns: (void) */ void WriteSELEX(FILE *fp, MSA *msa) { actually_write_selex(fp, msa, 50); /* 50 char per block */ } /* Function: WriteSELEXOneBlock() * Date: SRE, Mon Jun 14 13:14:56 1999 [St. Louis] * * Purpose: Write a SELEX alignment file in Pfam's single-block * format style. A wrapper for actually_write_selex(). * * Args: fp - file that's open for writing * msa- alignment to write * * Returns: (void) */ void WriteSELEXOneBlock(FILE *fp, MSA *msa) { actually_write_selex(fp, msa, msa->alen); /* one big block */ } /* Function: actually_write_selex() * Date: SRE, Mon Jun 14 12:54:46 1999 [St. Louis] * * Purpose: Write an alignment in SELEX format to an open * file. This is the function that actually does * the work. The API's WriteSELEX() and * WriteSELEXOneBlock() are wrappers. * * Args: fp - file that's open for writing * msa - alignment to write * cpl - characters to write per line in alignment block * * Returns: (void) */ static void actually_write_selex(FILE *fp, MSA *msa, int cpl) { int i; int len = 0; int namewidth; char *buf; int currpos; buf = malloc(sizeof(char) * (cpl+101)); /* 100 chars allowed for name, etc. */ /* Figure out how much space we need for name + markup * to keep the alignment in register, for easier human viewing -- * even though Stockholm format doesn't care about visual * alignment. */ namewidth = 0; for (i = 0; i < msa->nseq; i++) if ((len = strlen(msa->sqname[i])) > namewidth) namewidth = len; if (namewidth < 6) namewidth = 6; /* minimum space for markup tags */ /* Free text comments */ for (i = 0; i < msa->ncomment; i++) fprintf(fp, "# %s\n", msa->comment[i]); if (msa->ncomment > 0) fprintf(fp, "\n"); /* Per-file annotation */ if (msa->name != NULL) fprintf(fp, "#=ID %s\n", msa->name); if (msa->acc != NULL) fprintf(fp, "#=AC %s\n", msa->acc); if (msa->desc != NULL) fprintf(fp, "#=DE %s\n", msa->desc); if (msa->au != NULL) fprintf(fp, "#=AU %s\n", msa->au); /* Thresholds are hacky. Pfam has two. Rfam has one. */ if (msa->cutoff_is_set[MSA_CUTOFF_GA1] && msa->cutoff_is_set[MSA_CUTOFF_GA2]) fprintf(fp, "#=GA %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_GA1], msa->cutoff[MSA_CUTOFF_GA2]); else if (msa->cutoff_is_set[MSA_CUTOFF_GA1]) fprintf(fp, "#=GA %.1f\n", msa->cutoff[MSA_CUTOFF_GA1]); if (msa->cutoff_is_set[MSA_CUTOFF_NC1] && msa->cutoff_is_set[MSA_CUTOFF_NC2]) fprintf(fp, "#=NC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_NC1], msa->cutoff[MSA_CUTOFF_NC2]); else if (msa->cutoff_is_set[MSA_CUTOFF_NC1]) fprintf(fp, "#=NC %.1f\n", msa->cutoff[MSA_CUTOFF_NC1]); if (msa->cutoff_is_set[MSA_CUTOFF_TC1] && msa->cutoff_is_set[MSA_CUTOFF_TC2]) fprintf(fp, "#=TC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_TC1], msa->cutoff[MSA_CUTOFF_TC2]); else if (msa->cutoff_is_set[MSA_CUTOFF_TC1]) fprintf(fp, "#=TC %.1f\n", msa->cutoff[MSA_CUTOFF_TC1]); /* Per-sequence annotation */ for (i = 0; i < msa->nseq; i++) fprintf(fp, "#=SQ %-*.*s %6.4f %s %s %d..%d::%d %s\n", namewidth, namewidth, msa->sqname[i], msa->wgt[i], "-", /* MSA has no ID field */ (msa->sqacc != NULL && msa->sqacc[i] != NULL) ? msa->sqacc[i] : "-", 0, 0, 0, /* MSA has no start, stop, olen field */ (msa->sqdesc != NULL && msa->sqdesc[i] != NULL) ? msa->sqdesc[i] : "-"); fprintf(fp, "\n"); /* Alignment section: */ for (currpos = 0; currpos < msa->alen; currpos += cpl) { if (currpos > 0) fprintf(fp, "\n"); if (msa->ss_cons != NULL) { strncpy(buf, msa->ss_cons + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=CS", buf); } if (msa->rf != NULL) { strncpy(buf, msa->rf + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=RF", buf); } for (i = 0; i < msa->nseq; i++) { strncpy(buf, msa->aseq[i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, msa->sqname[i], buf); if (msa->ss != NULL && msa->ss[i] != NULL) { strncpy(buf, msa->ss[i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=SS", buf); } if (msa->sa != NULL && msa->sa[i] != NULL) { strncpy(buf, msa->sa[i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=SA", buf); } } } free(buf); } /* Function: copy_alignment_line() * * Purpose: Given a line from an alignment file, and bounds lcol,rcol * on what part of it may be sequence, save the alignment into * aseq starting at position apos. * * name_rcol is set to the rightmost column this aseqs's name * occupies; if name_rcol >= lcol, we have a special case in * which the name intrudes into the sequence zone. */ static int copy_alignment_line(char *aseq, int apos, int name_rcol, char *buffer, int lcol, int rcol, char gapsym) { char *s1, *s2; int i; s1 = aseq + apos; s2 = buffer; /* be careful that buffer doesn't end before lcol! */ for (i = 0; i < lcol; i++) if (*s2) s2++; for (i = lcol; i <= rcol; i++) { if (*s2 == '\t') { Warn("TAB characters will corrupt a SELEX alignment! Please remove them first."); return 0; } if (name_rcol >= i) /* name intrusion special case: pad left w/ gaps */ *s1 = gapsym; /* short buffer special case: pad right w/ gaps */ else if (*s2 == '\0' || *s2 == '\n') *s1 = gapsym; else if (*s2 == ' ') /* new: disallow spaces as gap symbols */ *s1 = gapsym; else /* normal case: copy buffer into aseq */ *s1 = *s2; s1++; if (*s2) s2++; } return 1; } /* Function: DealignAseqs() * * Given an array of (num) aligned sequences aseqs, * strip the gaps. Store the raw sequences in a new allocated array. * * Caller is responsible for free'ing the memory allocated to * rseqs. * * Returns 1 on success. Returns 0 and sets squid_errno on * failure. */ int DealignAseqs(char **aseqs, int num, char ***ret_rseqs) { char **rseqs; /* de-aligned sequence array */ int idx; /* counter for sequences */ int depos; /* position counter for dealigned seq*/ int apos; /* position counter for aligned seq */ int seqlen; /* length of aligned seq */ /* alloc space */ rseqs = (char **) MallocOrDie (num * sizeof(char *)); /* main loop */ for (idx = 0; idx < num; idx++) { seqlen = strlen(aseqs[idx]); /* alloc space */ rseqs[idx] = (char *) MallocOrDie ((seqlen + 1) * sizeof(char)); /* strip gaps */ depos = 0; for (apos = 0; aseqs[idx][apos] != '\0'; apos++) if (!isgap(aseqs[idx][apos])) { rseqs[idx][depos] = aseqs[idx][apos]; depos++; } rseqs[idx][depos] = '\0'; } *ret_rseqs = rseqs; return 1; } /* Function: IsSELEXFormat() * * Return TRUE if filename may be in SELEX format. * * Accuracy is sacrificed for speed; a TRUE return does * *not* guarantee that the file will pass the stricter * error-checking of ReadSELEX(). All it checks is that * the first 500 non-comment lines of a file are * blank, or if there's a second "word" on the line * it looks like sequence (i.e., it's not kOtherSeq). * * Returns TRUE or FALSE. */ int IsSELEXFormat(char *filename) { FILE *fp; /* ptr to open sequence file */ char buffer[LINEBUFLEN]; char *sptr; /* ptr to first word */ int linenum; if ((fp = fopen(filename, "r")) == NULL) { squid_errno = SQERR_NOFILE; return 0; } linenum = 0; while (linenum < 500 && fgets(buffer, LINEBUFLEN, fp) != NULL) { linenum++; /* dead giveaways for extended SELEX */ if (strncmp(buffer, "#=AU", 4) == 0) goto DONE; else if (strncmp(buffer, "#=ID", 4) == 0) goto DONE; else if (strncmp(buffer, "#=AC", 4) == 0) goto DONE; else if (strncmp(buffer, "#=DE", 4) == 0) goto DONE; else if (strncmp(buffer, "#=GA", 4) == 0) goto DONE; else if (strncmp(buffer, "#=TC", 4) == 0) goto DONE; else if (strncmp(buffer, "#=NC", 4) == 0) goto DONE; else if (strncmp(buffer, "#=SQ", 4) == 0) goto DONE; else if (strncmp(buffer, "#=SS", 4) == 0) goto DONE; else if (strncmp(buffer, "#=CS", 4) == 0) goto DONE; else if (strncmp(buffer, "#=RF", 4) == 0) goto DONE; /* a comment? */ if (strchr(commentsyms, *buffer) != NULL) continue; /* a blank line? */ if ((sptr = strtok(buffer, WHITESPACE)) == NULL) continue; /* a one-word line (name only) is possible, though rare */ if ((sptr = strtok(NULL, "\n")) == NULL) continue; if (Seqtype(sptr) == kOtherSeq) {fclose(fp); return 0;} } DONE: fclose(fp); return 1; } squid/seqencode.c0000640000175000017520000000611410463223377014227 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* seqencode.c * * Routines for creating and manipulating encoded sequence strings. * CVS $Id: seqencode.c,v 1.4 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" /* seqcmp() returns 0 if s1 == s2 mismatch number otherwise */ int seqcmp(char *s1, char *s2, int allow) { int mmat = 0; while ((*s1 != NTEND) && (*s2 != NTEND) && (mmat <= allow)) { if (!(ntmatch(*s1, *s2))) mmat++;; s1++; s2++; } while ((*s1++ != NTEND) && (mmat <= allow)) mmat++; return(mmat); } /* seqncmp() same as seqcmp but it looks at, at most, n positions */ int seqncmp(char *s1, char *s2, int n, int allow) { int mmat = 0; while ((*s2 != NTEND) && (n-- != 0)) { if ((!(ntmatch(*s1, *s2))) && (++mmat > allow)) return(mmat); s1++; s2++; } while ((n-- != 0) && (*s1++ != NTEND) && (mmat <= allow)) mmat++; return (mmat); } /* seqencode() given a character text string str (A,C,G,T), convert to an encoded seq string; return 1 for success, 0 if fail */ int seqencode(char *codeseq, /* pre-allocated space for answer */ char *str) /* character string to convert */ { char *ptr; int idx; ptr = codeseq; while (*str != '\0') { if (islower((int) (*str))) *str = (char) toupper((int) (*str)); for (idx = 0; *str != iupac[idx].sym && idx <= IUPACSYMNUM; idx++) ; if (idx > IUPACSYMNUM) { *ptr = (char) NTEND; return 0; } else *ptr = iupac[idx].code; ptr++; str++; } *ptr = NTEND; return 1; } int coded_revcomp(char *comp, char *seq) { long bases; char *bckp, *fwdp; int idx; long pos; bases = strlen(seq); fwdp = comp; bckp = seq + bases -1; for (pos = 0; pos < bases; pos++) { for (idx = 0; *bckp != iupac[idx].code && idx < IUPACSYMNUM; idx++); if (idx > IUPACSYMNUM) { *fwdp = NTEND; return 0; } else *fwdp = iupac[idx].comp; fwdp++; bckp--; } *fwdp = NTEND; return(1); } int seqdecode(char *str, char *codeseq) { int idx; int pos; pos = 0; while (*codeseq != NTEND) { for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++) ; if (idx > IUPACSYMNUM) { str[pos] = 'X'; return 0; } else str[pos] = iupac[idx].sym; codeseq++; pos++; } str[pos] = '\0'; return 1; } int seqndecode( char *str, /* pre-allocated string to write into */ char *codeseq, /* sequence to decode */ int n) /* how many bases to decode */ { int idx; int pos = 0; while (--n >= 0) { for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++); if (idx > IUPACSYMNUM) { str[pos] = 'X'; return 0; } else str[pos] = iupac[idx].sym; codeseq++; pos++; } str[pos] = '\0'; return 1; } squid/seqsplit_main.c0000640000175000017520000002067310463223377015137 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* seqsplit_main.c * SRE, Mon Sep 25 11:43:58 2000 * * Split sequences into smaller chunks of defined size and overlap; * output a FASTA file. * * Limitations: * still working in 32 bits -- no sequence can be more than 2 GB * in size. * CVS $Id: seqsplit_main.c,v 1.9 2004/08/05 01:28:51 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "msa.h" static char banner[] = "seqsplit - split seqs into chunks of defined size and overlap"; static char usage[] = "\ Usage: seqsplit [-options] \n\ Available options:\n\ -h : help; display usage and version\n\ -o : output the new FASTA file to \n\ "; static char experts[] = "\ --fragfile : save one-line-per-frag coord summary file to \n\ --informat : specify sequence file format \n\ --length : set max length of each unique seq frag to \n\ --overlap : set overlap length to (total frag size = length+overlap)\n\ --shortnames : use short \"frag1\" names, not \"/-\"\n\ "; static struct opt_s OPTIONS[] = { { "-h", TRUE, sqdARG_NONE }, { "-o", TRUE, sqdARG_STRING }, { "--fragfile", FALSE, sqdARG_STRING }, { "--informat", FALSE, sqdARG_STRING }, { "--length", FALSE, sqdARG_INT }, { "--overlap", FALSE, sqdARG_INT }, { "--shortnames", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) static char *set_description(char *source, int start, int end, char *origdesc); static char *set_name(char *origname, int start, int end, int do_shortnames, int fragnum); int main(int argc, char **argv) { char *seqfile; /* name of sequence file */ char *outfile; /* name of output file */ SQFILE *dbfp; /* open sequence file */ FILE *ofp; /* open output file */ int fmt; /* format of seqfile */ char *seq; /* sequence */ SQINFO sqinfo; /* extra info about sequence */ char *seqfrag; /* space for a seq fragment */ int fraglength; /* length of unique seq per frag */ int overlap; /* length of overlap. frags are fraglength+overlap*/ char *sqname; /* renamed fragment, w/ coord info */ char *desc; /* new desc line */ int num; /* number of this fragment */ int pos; /* position in a sequence */ int len; /* length of a fragment */ int nseqs; /* total number of input sequences */ int nsplit; /* number of seqs that get split */ int nnewfrags; /* total number of new fragments */ int ntot; /* total number of seqs in new file */ int do_shortnames; /* TRUE to do short code names */ char *fragfile; /* fragment summary out file, or NULL */ FILE *fragfp; char *optname; char *optarg; int optind; /*********************************************** * Parse command line ***********************************************/ fmt = SQFILE_UNKNOWN; /* default: autodetect */ fraglength = 100000; overlap = 1000; outfile = NULL; do_shortnames = FALSE; fragfile = NULL; fragfp = NULL; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-o") == 0) outfile = optarg; else if (strcmp(optname, "--fragfile") == 0) fragfile = optarg; else if (strcmp(optname, "--length") == 0) fraglength = atoi(optarg); else if (strcmp(optname, "--overlap") == 0) overlap = atoi(optarg); else if (strcmp(optname, "--shortnames") == 0) do_shortnames = TRUE; else if (strcmp(optname, "--informat") == 0) { fmt = String2SeqfileFormat(optarg); if (fmt == SQFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 1) Die("%s\n", usage); seqfile = argv[argc-1]; seqfrag = MallocOrDie(sizeof(char) * (fraglength+overlap+1)); seqfrag[fraglength+overlap] = '\0'; /* Try to work around inability to autodetect from a pipe or .gz: * assume FASTA format */ if (fmt == SQFILE_UNKNOWN && (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) fmt = SQFILE_FASTA; /*********************************************** * Read the file. ***********************************************/ if (outfile == NULL) ofp = stdout; else { if ((ofp = fopen(outfile, "w")) == NULL) Die("Failed to open output sequence file %s for writing", outfile); } if (fragfile != NULL) { if ((fragfp = fopen(fragfile, "w")) == NULL) Die("Failed to open frag summary file %s for writing", fragfile); } if ((dbfp = SeqfileOpen(seqfile, fmt, NULL)) == NULL) Die("Failed to open sequence file %s for reading", seqfile); nseqs = nsplit = nnewfrags = ntot = 0; while (ReadSeq(dbfp, dbfp->format, &seq, &sqinfo)) { nseqs++; if (sqinfo.len <= fraglength+overlap) { ntot++; if (do_shortnames) { sqname = set_name(sqinfo.name, 1, sqinfo.len, do_shortnames, ntot); desc = set_description(sqinfo.name, 1, sqinfo.len, sqinfo.flags & SQINFO_DESC ? sqinfo.desc : NULL); } else { sqname = sre_strdup(sqinfo.name, -1); if (sqinfo.flags & SQINFO_DESC) desc = sre_strdup(sqinfo.desc, -1); else desc = NULL; } WriteSimpleFASTA(ofp, seq, sqname, desc); if (fragfp != NULL) fprintf(fragfp, "%s\t%s\t%d\t%d\n", sqname, sqinfo.name, 1, sqinfo.len); if (desc != NULL) free(desc); free(sqname); continue; } num = 1; nsplit++; for (pos = 0; pos < sqinfo.len; pos += fraglength) { if (sqinfo.len - pos <= overlap) continue; /* remaining length: seqinfo.len-pos+1 * fragment length: fraglength */ ntot++; if (sqinfo.len - pos < fraglength+overlap) strcpy(seqfrag, seq+pos); else strncpy(seqfrag, seq+pos, fraglength+overlap); len = strlen(seqfrag); if (do_shortnames) { sqname = set_name(sqinfo.name, pos+1, pos+len, do_shortnames, ntot); desc = set_description(sqinfo.name, pos+1, pos+len, sqinfo.flags & SQINFO_DESC ? sqinfo.desc : NULL); } else { sqname = set_name(sqinfo.name, pos+1, pos+len, do_shortnames, num); if (sqinfo.flags & SQINFO_DESC) desc = sre_strdup(sqinfo.desc, -1); else desc = NULL; } WriteSimpleFASTA(ofp, seqfrag, sqname, desc); if (fragfp != NULL) fprintf(fragfp, "%s\t%s\t%d\t%d\n", sqname, sqinfo.name, pos+1, pos+len); if (desc != NULL) free(desc); free(sqname); nnewfrags++; num ++; } FreeSequence(seq, &sqinfo); } SeqfileClose(dbfp); if (outfile != NULL) fclose(ofp); if (fragfile != NULL) fclose(fragfp); printf("Total # of seqs: %d\n", nseqs); printf("Affected by splitting: %d\n", nsplit); printf("New # of seqs: %d\n", nseqs-nsplit + nnewfrags); return 0; } static char * set_description(char *source, int start, int end, char *origdesc) { int len; char *new; len = 7; /* for [:..] \0 */ if (source != NULL) { len += strlen(source); len += start > 0 ? ceil(log10(start+1)) : 1; /* itoa length */ len += end > 0 ? ceil(log10(end+1)) : 1; } if (origdesc != NULL) len += strlen(origdesc); if (source != NULL) { new = MallocOrDie(sizeof(char) * len); sprintf(new, "[%s:%d..%d] %s", source, start, end, origdesc == NULL ? "" : origdesc); } else if (origdesc != NULL) { new = sre_strdup(origdesc, -1); } else new = NULL; return new; } static char * set_name(char *origname, int start, int end, int do_shortnames, int fragnum) { int len; char *new; if (do_shortnames) { len = 5; /* frag \0 */ len += fragnum > 0 ? ceil(log10(fragnum+1)) : 1; new = MallocOrDie(sizeof(char) * len); sprintf(new, "frag%d", fragnum); } else { len = strlen(origname) + 8; len += fragnum > 0 ? ceil(log10(fragnum+1)) : 1; len += start > 0 ? ceil(log10(start+1)) : 1; /* itoa length */ len += end > 0 ? ceil(log10(end+1)) : 1; new = MallocOrDie(sizeof(char) * len); sprintf(new, "%s/frag%d/%d-%d", origname, fragnum, start, end); } return new; } squid/seqstat_main.c0000640000175000017520000001477110463223377014761 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* seqstat_main.c * Wed Aug 10 15:47:14 1994 * * Look at a sequence file, determine some simple statistics. * CVS $Id: seqstat_main.c,v 1.13 2004/06/16 14:43:01 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "msa.h" static char banner[] = "seqstat - show some simple statistics on a sequence file"; static char usage[] = "\ Usage: seqstat [-options] \n\ Available options:\n\ -a : report per-sequence info, not just a summary\n\ -h : help; display usage and version\n\ "; static char experts[] = "\ --gccomp : with -a, include GC composition in report (DNA/RNA only)\n\ --informat : specify sequence file format \n\ --quiet : suppress verbose header (used in regression testing)\n\ "; static struct opt_s OPTIONS[] = { { "-a", TRUE, sqdARG_NONE }, { "-h", TRUE, sqdARG_NONE }, { "--gccomp", FALSE, sqdARG_NONE }, { "--informat", FALSE, sqdARG_STRING }, { "--quiet", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) static float gc_composition(char *seq); int main(int argc, char **argv) { char *seqfile; /* name of sequence file */ SQFILE *dbfp; /* open sequence file */ int fmt; /* format of seqfile */ char *seq; /* sequence */ SQINFO sqinfo; /* extra info about sequence */ int nseqs; long long small; /* smallest length */ long long large; /* largest length */ long long total; /* total length */ int type; /* kAmino, kDNA, kRNA, or kOtherSeq */ int allreport; /* TRUE to do a short table for each sequence */ int be_quiet; /* TRUE to suppress header */ int do_gccomp; /* TRUE to include GC composition in per-seq report */ float gc; /* fractional gc composition, 0..1 */ char *optname; char *optarg; int optind; /*********************************************** * Parse command line ***********************************************/ fmt = SQFILE_UNKNOWN; /* default: autodetect format */ allreport = FALSE; /* default: file summary only */ be_quiet = FALSE; /* show header info by default */ type = kOtherSeq; /* just to silence gcc uninit warning */ do_gccomp = FALSE; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-a") == 0) allreport = TRUE; else if (strcmp(optname, "--quiet") == 0) be_quiet = TRUE; else if (strcmp(optname, "--gccomp") == 0) do_gccomp = TRUE; else if (strcmp(optname, "--informat") == 0) { fmt = String2SeqfileFormat(optarg); if (fmt == SQFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 1) Die("%s\n", usage); seqfile = argv[argc-1]; if (! be_quiet) SqdBanner(stdout, banner); /* Try to work around inability to autodetect from a pipe or .gz: * assume FASTA format */ if (fmt == SQFILE_UNKNOWN && (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) fmt = SQFILE_FASTA; /*********************************************** * Read the file. ***********************************************/ if ((dbfp = SeqfileOpen(seqfile, fmt, NULL)) == NULL) Die("Failed to open sequence file %s for reading", seqfile); if (allreport) { printf(" %-15s %-5s %s%s\n", " NAME", "LEN", do_gccomp? " f_GC " : "", "DESCRIPTION"); printf(" --------------- ----- %s-----------\n", do_gccomp ? "----- " : ""); } nseqs = 0; small = -1; large = -1; total = 0L; while (ReadSeq(dbfp, dbfp->format, &seq, &sqinfo)) { if (nseqs == 0) type = Seqtype(seq); if (do_gccomp) gc = gc_composition(seq); if (allreport) { if (do_gccomp) { printf("* %-15s %5d %.3f %-50.50s\n", sqinfo.name, sqinfo.len, gc, sqinfo.flags & SQINFO_DESC ? sqinfo.desc : ""); } else { printf("* %-15s %5d %-50.50s\n", sqinfo.name, sqinfo.len, sqinfo.flags & SQINFO_DESC ? sqinfo.desc : ""); } } if (small == -1 || sqinfo.len < small) small = (long long) sqinfo.len; if (large == -1 || sqinfo.len > large) large = (long long) sqinfo.len; total += (long long) sqinfo.len; nseqs++; FreeSequence(seq, &sqinfo); } if (allreport) puts(""); printf("Format: %s\n", SeqfileFormat2String(dbfp->format)); printf("Type (of 1st seq): "); switch (type) { case kDNA: puts("DNA"); break; case kRNA: puts("RNA"); break; case kAmino: puts("Protein"); break; case kOtherSeq: puts("Unknown"); break; default: Die("oops."); } printf("Number of sequences: %d\n", nseqs); printf("Total # residues: %lld\n", total); printf("Smallest: %lld\n", small); printf("Largest: %lld\n", large); printf("Average length: %.1f\n", (float) total / (float) nseqs); SeqfileClose(dbfp); return 0; } /* Function: gc_composition() * Date: SRE, Mon Apr 23 10:01:48 2001 [St. Louis] * * Purpose: Calculate the fractional GC composition of * an input RNA or DNA sequence. Deals appropriately * with IUPAC degeneracy. Case-insensitive. * Ignores gap symbols. Other unexpected characters * make it die with an error (protein, for instance). * * Args: seq - the DNA or RNA sequence * * Returns: fractional GC composition, 0-1 */ static float gc_composition(char *seq) { int c; float total; float gc; gc = total = 0.; for (; *seq != '\0'; seq++) { c = toupper((int) *seq); if (isgap(c)) continue; total += 1.0; switch (c) { case 'C': case 'G': case 'S': gc += 1.0; break; case 'A': case 'T': case 'U': case 'W': gc += 0.0; break; case 'N': case 'R': case 'Y': case 'M': case 'K': gc += 0.5; break; case 'H': case 'D': gc += 0.3333; break; case 'B': case 'V': gc += 0.6667; break; default: Die("unrecognized nucleic acid character %c in sequence", c); } } return (gc/total); } squid/sfetch_main.c0000640000175000017520000003667510463223377014560 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sfetch_main.c, Fri Dec 25 14:22:17 1992, SRE * * sfetch -- a program to extract subsequences from a sequence database * Renamed from "getseq" SRE, Tue Jan 19 10:47:42 1999 (GCG clash) * * CVS $Id: sfetch_main.c,v 1.18 2004/06/16 14:46:04 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "msa.h" #include "ssi.h" static char banner[] = "sfetch - retrieve a specified sequence from a file"; static char usage[] = "\ Usage: sfetch [-options] \n\ or: sfetch [-options] .\n\ (The second version fetches the first seq in the file.)\n\ Get a sequence from a database.\n\ Available options:\n\ -a : name is an accession number, not a key\n\ -d : get sequence from \n\ -D : instead, get sequence from main database\n\ -h : help; print version and usage info\n\ -r : rename the fragment \n\ -f : from which residue (1..N)\n\ -t : to which residue (1..N)\n\ -o : direct output to \n\ -F : use output format of ; see below for\n\ list. Default is original format of database.\n\ \n\ Available output formats include:\n\ fasta\n\ genbank\n\ embl\n\ gcg\n\ pir\n\ raw\n\n\ Available databases are: (if $env variables are set correctly)\n\ -Dsw $SWDIR SwissProt\n\ -Dpir $PIRDIR PIR\n\ -Dem $EMBLDIR EMBL\n\ -Dgb $GBDIR GenBank\n\ -Dwp $WORMDIR WormPep\n\ -Dowl $OWLDIR OWL\n"; static char experts[] = "\ --informat : specify input sequence file format \n\ "; static struct opt_s OPTIONS[] = { { "-a", TRUE, sqdARG_NONE }, { "-d", TRUE, sqdARG_STRING }, { "-f", TRUE, sqdARG_INT }, { "-h", TRUE, sqdARG_NONE }, { "-o", TRUE, sqdARG_STRING }, { "-r", TRUE, sqdARG_STRING }, { "-t", TRUE, sqdARG_INT }, { "-D", TRUE, sqdARG_STRING }, { "-F", TRUE, sqdARG_STRING }, { "--informat", FALSE, sqdARG_STRING }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) /* dbenv maps command line database selection to an environment * variable, from which the database directory is obtained. */ static struct dbenv_s { char *dbname; /* name of database, as used on command line */ char *ssiname; /* name of SSI index file to look for */ char *envname; /* environment var to get directory path from*/ char *entryend; /* string signifying end of entry */ int addend; /* TRUE if entryend line is part of entry */ } dbenv[] = { { "sw", "swiss.ssi", "SWDIR", "//", TRUE}, { "pir", "pir.ssi", "PIRDIR", "///", TRUE}, { "em", "embl.ssi", "EMBLDIR", "//", TRUE}, { "gb", "genbank.ssi","GBDIR", "//", TRUE}, { "wp", "wormpep.ssi","WORMDIR", ">", FALSE}, { "owl", "owl.ssi", "OWLDIR", ">", FALSE}, /* use FASTA OWL version */ }; #define NUMDBS (sizeof(dbenv) / sizeof(struct dbenv_s)) int main(int argc, char **argv) { char *dbname; /* master database to search */ char *seqfile; /* name of sequence file to read */ char *ssifile; /* name of SSI index file (if one exists) */ SQFILE *seqfp; /* pointer to open sequence file */ char *getname; /* name of sequence to get from */ int from; /* starting residue, 1..N */ int to; /* ending residue, 1..N */ char *outfile; /* name of file to put output to */ FILE *outfp; /* file pointer to put output to */ int format; /* format of seqfile */ int outfmt; /* output format */ char *seq; /* current working sequence */ SQINFO sqinfo; char *frag; /* extracted subsequence */ int source_start; /* start of seq on original source 1..N */ int source_stop; /* end of seq on original source 1..N */ int source_orient; /* sign of parent: -1 revcomp, +1 normal*/ char *ss; /* secondary structure representation */ SSIFILE *ssi; /* open SSI index file */ SSIOFFSET ssi_offset; /* disk offset for locating sequence */ int used_ssi; /* TRUE if SSI file was used (don't scan) */ int status; /* status returned by an SSI call */ char *rename; /* new name to give fragment */ int reverse_complement; /* do we have to reverse complement? */ int getall; int getfirst; /* TRUE to extract from the first seq, w/o looking at name */ char *outformat; /* output format string */ int by_accession; /* TRUE if name is accession number not key */ int dbidx; char *optname; char *optarg; int optind; /*********************************************** * Parse the command line ***********************************************/ /* initializations and defaults */ format = SQFILE_UNKNOWN; /* autodetect default, overridden by --informat or SSI files */ reverse_complement = 0; getall = TRUE; getfirst= FALSE; dbname = NULL; dbidx = -1; seqfile = NULL; from = -1; to = -1; /* flag that says do the whole thing */ outfile = NULL; getname = NULL; rename = NULL; outformat = NULL; by_accession = FALSE; used_ssi = FALSE; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-a") == 0) { by_accession = TRUE; } else if (strcmp(optname, "-d") == 0) { seqfile = optarg; } else if (strcmp(optname, "-f") == 0) { from = atoi(optarg); getall = FALSE; } else if (strcmp(optname, "-t") == 0) { to = atoi(optarg); getall = FALSE; } else if (strcmp(optname, "-r") == 0) { rename = optarg; } else if (strcmp(optname, "-o") == 0) { outfile = optarg; } else if (strcmp(optname, "-D") == 0) { dbname = optarg; } else if (strcmp(optname, "-F") == 0) { outformat = optarg; } else if (strcmp(optname, "--informat") == 0) { format = String2SeqfileFormat(optarg); if (format == SQFILE_UNKNOWN) Die("unrecognized input sequence file format \"%s\"", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 1) Die("Incorrect number of command line arguments.\n%s\n", usage); getname = argv[optind]; if (strcmp(getname, ".") == 0) getfirst = TRUE; if (getfirst && seqfile == NULL) Die("You need to specify -d to retrieve a first sequence.\n%s", usage); /* Try to work around inability to autodetect from a pipe or .gz: * assume FASTA format */ if (seqfile != NULL && format == SQFILE_UNKNOWN && (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) format = SQFILE_FASTA; /*********************************************** * Get name of file to look through, and disk offset, * using SSI file if one exists. Three possibilities: * 1) Look in main DB, which has SSI index in the directory * 2) Look in a file, which has associated SSI index * 3) Look in an unindexed file ***********************************************/ if (dbname != NULL && seqfile != NULL) Die("Can't fetch from *both* a database %s and a file %s\n%s", dbname, seqfile, usage); if (dbname == NULL && seqfile == NULL) { /* try to guess SwissProt, stupidly, but usually works */ if (strchr(getname, '_') != NULL) dbname = Strdup("sw"); else Die("You have to specify either a database or a seqfile\n%s", usage); } if (dbname != NULL) /* Main database. SSI index mandatory. */ { char *dbdir; char *dbfile; int fh; /* find which db this is */ for (dbidx = 0; dbidx < NUMDBS; dbidx++) if (strcmp(dbenv[dbidx].dbname, dbname) == 0) break; if (dbidx == NUMDBS) Die("No such main database %s\n%s", dbname, usage); /* get directory name */ if ((dbdir = getenv(dbenv[dbidx].envname)) == NULL) Die("Environment variable %s is not set.\n%s", dbenv[dbidx].envname, usage); /* open ssi file */ ssifile = (char *) MallocOrDie ((strlen(dbdir) + strlen(dbenv[dbidx].ssiname) + 2) * sizeof(char)); sprintf(ssifile, "%s/%s", dbdir, dbenv[dbidx].ssiname); if ((status = SSIOpen(ssifile, &ssi)) != 0) Die("Failed to open SSI index file %s in directory %s\n%s", dbenv[dbidx].ssiname, dbdir, usage); /* get seqfile name, file format, and offset */ if ((status = SSIGetOffsetByName(ssi, getname, &fh, &ssi_offset)) != 0) Die("Failed to find key %s in SSI file %s", getname, ssifile); if ((status = SSIFileInfo(ssi, fh, &dbfile, &format)) != 0) Die("SSI error: %s", SSIErrorString(status)); free(ssifile); /* set up proper seqfile, with path */ seqfile = (char *) MallocOrDie ((strlen(dbdir) + strlen(dbfile) + 2) * sizeof(char)); sprintf(seqfile, "%s/%s", dbdir, dbfile); used_ssi = TRUE; SSIClose(ssi); } else if (! getfirst) /* Sequence file. SSI index optional. */ { char *dbfile; int fh; ssifile = (char *) MallocOrDie ((strlen(seqfile) + 5) * sizeof(char)); sprintf(ssifile, "%s.ssi", seqfile); if ((status = SSIOpen(ssifile, &ssi)) == 0) { SQD_DPRINTF1(("Opened SSI index %s...\n", ssifile)); if ((status = SSIGetOffsetByName(ssi, getname, &fh, &ssi_offset)) != 0) Die("Failed to find key %s in SSI file %s", getname, ssifile); if ((status = SSIFileInfo(ssi, fh, &dbfile, &format)) != 0) Die("SSI error: %s", SSIErrorString(status)); /* Set up seqfile name - possibly replacing what the user gave us in -d, because she may have been referring to an SSI file that indexes multiple sequence files. ... but be careful we preserve the path! */ if ((seqfile = FileSameDirectory(ssifile, dbfile)) == NULL) Die("SSI file %s and dbfile %s are in different locations?!", ssifile, dbfile); SSIClose(ssi); used_ssi = TRUE; } free(ssifile); } /*********************************************** * Open database file ***********************************************/ if ((seqfp = SeqfileOpen(seqfile, format, NULL)) == NULL) Die("Failed to open sequence database file %s\n%s\n", seqfile, usage); if (used_ssi) SeqfilePosition(seqfp, &ssi_offset); /*********************************************** * Open output file ***********************************************/ /* Determine output format. Default: use same as input. Override: -F option. */ outfmt = seqfp->format; if (outformat != NULL) { outfmt = String2SeqfileFormat(outformat); if (outfmt == SQFILE_UNKNOWN) Die("Unknown output format %s\n%s", outformat, usage); if (IsAlignmentFormat(outfmt)) Die("Can't output a single sequence in an alignment format (%s)\n", outformat); } /* open output file for writing; use stdout by default */ if (outfile == NULL) outfp = stdout; else if ((outfp = fopen(outfile, "w")) == NULL) Die("cannot open %s for output\n", outfile); /*********************************************** * Main loop ***********************************************/ /* If this is a simple fetch of the complete sequence * in native format, and we've been positioned in the file * by an SSI index file, we can just read right from the file, * partially bypassing the ReadSeq() API, and probably * putting our fingers a little too deep into the seqfp object. */ if (getall && used_ssi && outfmt == format && dbname != NULL) { char *buf = NULL; int buflen = 0; int endlen; if (dbidx == -1) Die("That's weird. No database index available."); endlen = strlen(dbenv[dbidx].entryend); fputs(seqfp->buf, outfp); /* always do first line */ /* fputs("\n", outfp); */ /* buf has its /n */ while (sre_fgets(&buf, &buflen, seqfp->f) != NULL) { if (strncmp(buf, dbenv[dbidx].entryend, endlen) == 0) { if (dbenv[dbidx].addend) fputs(buf, outfp); break; } fputs(buf, outfp); } if (buf != NULL) free(buf); } else /* else, the hard way with ReadSeq */ { seq = NULL; frag = NULL; while (ReadSeq(seqfp, format, &seq, &sqinfo)) { if (used_ssi) /* SSI file puts us right on our seq. */ break; else if (getfirst) /* Use the first seq in the file. */ break; else if (by_accession && (sqinfo.flags & SQINFO_ACC) && strcmp(sqinfo.acc, getname) == 0) break; else if (strcmp(sqinfo.name, getname) == 0) break; FreeSequence(seq, &sqinfo); seq = NULL; } if (seq == NULL) Die("failed to extract the subsequence %s\n%s", getname, usage); if (getall) { from = 1; to = sqinfo.len; } else if (from == -1) from = 1; else if (to == -1) to = sqinfo.len; if (to > sqinfo.len || from > sqinfo.len) Warn("Extracting beyond the length of the sequence"); if (to < 1 || from < 1) Warn("Extracting beyond the beginning of the sequence"); /* check for reverse complement */ if (to != -1 && from > to) { int swapfoo; /* temp variable for swapping coords */ reverse_complement = TRUE; swapfoo = from; from = to; to = swapfoo; } if (to > sqinfo.len) to = sqinfo.len; if (from < 1) from = 1; if ((frag = (char *) calloc (to-from+2, sizeof(char))) == NULL) Die("memory error\n"); if (strncpy(frag, seq+from-1, to-from+1) == NULL) Die("strncpy() failed\n"); if (sqinfo.flags & SQINFO_SS) { if ((ss = (char *) calloc (to-from+2, sizeof(char))) == NULL) Die("memory error\n"); if (strncpy(ss, sqinfo.ss+from-1, to-from+1) == NULL) Die("strncpy() failed\n"); free(sqinfo.ss); sqinfo.ss = ss; } if (reverse_complement) { char *revfrag; /* temp variable for reverse complement */ int swapfoo; /* temp variable for swapping coords back */ if ((revfrag = calloc ( to-from+2, sizeof(char))) == NULL) Die("memory failure\n"); revcomp(revfrag, frag); free(frag); frag = revfrag; swapfoo = from; from = to; to = swapfoo; /* reverse complement nullifies secondary structure */ if (sqinfo.flags & SQINFO_SS) { free(sqinfo.ss); sqinfo.flags &= ~SQINFO_SS; } } if (! (sqinfo.flags & SQINFO_ID)) SetSeqinfoString(&sqinfo, sqinfo.name, SQINFO_ID); if (! (sqinfo.flags & SQINFO_OLEN)) { sqinfo.olen = sqinfo.len; sqinfo.flags |= SQINFO_OLEN; } sqinfo.len = (to > from) ? to-from+1 : from-to+1; sqinfo.flags |= SQINFO_LEN; if (rename != NULL) SetSeqinfoString(&sqinfo, rename, SQINFO_NAME); source_start = (sqinfo.flags & SQINFO_START) ? sqinfo.start : 1; source_stop = (sqinfo.flags & SQINFO_STOP) ? sqinfo.stop : sqinfo.len; source_orient= (source_stop > source_start) ? 1 : -1; sqinfo.start = source_start + (from- 1) * source_orient; sqinfo.stop = source_start + (to - 1) * source_orient; sqinfo.flags |= SQINFO_START | SQINFO_STOP; WriteSeq(outfp, outfmt, frag, &sqinfo); free(frag); FreeSequence(seq, &sqinfo); } if (outfile != NULL) printf("Fragment written to file %s\n", outfile); SeqfileClose(seqfp); fclose(outfp); return(0); } squid/shuffle.c0000640000175000017520000004423110463223377013717 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* shuffle.c * * Routines for randomizing sequences. * * All routines are alphabet-independent (DNA, protein, RNA, whatever); * they assume that input strings are purely alphabetical [a-zA-Z], and * will return strings in all upper case [A-Z]. * * The maximum string length is whatever the machine's "int" can count * to; on most modern 32-bit machines, that's ~2 GB. Largest human chromosome * is ~246 MB. * * All return 1 on success, and 0 on failure; 0 status invariably * means the input string was not alphabetical. * * StrShuffle() - shuffled string, preserve mono-symbol composition. * StrDPShuffle() - shuffled string, preserve mono- and di-symbol composition. * * StrMarkov0() - random string, same zeroth order Markov properties. * StrMarkov1() - random string, same first order Markov properties. * * StrReverse() - simple reversal of string * StrRegionalShuffle() - mono-symbol shuffled string in regional windows * * There are also similar routines for shuffling alignments: * * AlignmentShuffle() - alignment version of StrShuffle(). * AlignmentBootstrap() - sample with replacement; a bootstrap dataset. * QRNAShuffle() - shuffle a pairwise alignment, preserving all gap positions. * * CVS $Id: shuffle.c,v 1.9 2004/06/30 15:35:21 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "sre_random.h" /* Function: StrShuffle() * * Purpose: Returns a shuffled version of s2, in s1. * (s1 and s2 can be identical, to shuffle in place.) * * Args: s1 - allocated space for shuffled string. * s2 - string to shuffle. * * Return: 1 on success. */ int StrShuffle(char *s1, char *s2) { int len; int pos; char c; if (s1 != s2) strcpy(s1, s2); for (len = strlen(s1); len > 1; len--) { pos = CHOOSE(len); c = s1[pos]; s1[pos] = s1[len-1]; s1[len-1] = c; } return 1; } /* Function: StrDPShuffle() * Date: SRE, Fri Oct 29 09:15:17 1999 [St. Louis] * * Purpose: Returns a shuffled version of s2, in s1. * (s1 and s2 may be identical; i.e. a string * may be shuffled in place.) The shuffle is a * "doublet-preserving" (DP) shuffle. Both * mono- and di-symbol composition are preserved. * * Done by searching for a random Eulerian * walk on a directed multigraph. * Reference: S.F. Altschul and B.W. Erickson, Mol. Biol. * Evol. 2:526-538, 1985. Quoted bits in my comments * are from Altschul's outline of the algorithm. * * Args: s1 - RETURN: the string after it's been shuffled * (space for s1 allocated by caller) * s2 - the string to be shuffled * * Returns: 0 if string can't be shuffled (it's not all [a-zA-z] * alphabetic. * 1 on success. */ int StrDPShuffle(char *s1, char *s2) { int len; int pos; /* a position in s1 or s2 */ int x,y; /* indices of two characters */ char **E; /* edge lists: E[0] is the edge list from vertex A */ int *nE; /* lengths of edge lists */ int *iE; /* positions in edge lists */ int n; /* tmp: remaining length of an edge list to be shuffled */ char sf; /* last character in s2 */ char Z[26]; /* connectivity in last edge graph Z */ int keep_connecting; /* flag used in Z connectivity algorithm */ int is_eulerian; /* flag used for when we've got a good Z */ /* First, verify that the string is entirely alphabetic. */ len = strlen(s2); for (pos = 0; pos < len; pos++) if (! isalpha((int) s2[pos])) return 0; /* "(1) Construct the doublet graph G and edge ordering E * corresponding to S." * * Note that these also imply the graph G; and note, * for any list x with nE[x] = 0, vertex x is not part * of G. */ E = MallocOrDie(sizeof(char *) * 26); nE = MallocOrDie(sizeof(int) * 26); for (x = 0; x < 26; x++) { E[x] = MallocOrDie(sizeof(char) * (len-1)); nE[x] = 0; } x = toupper((int) s2[0]) - 'A'; for (pos = 1; pos < len; pos++) { y = toupper((int) s2[pos]) - 'A'; E[x][nE[x]] = y; nE[x]++; x = y; } /* Now we have to find a random Eulerian edge ordering. */ sf = toupper((int) s2[len-1]) - 'A'; is_eulerian = 0; while (! is_eulerian) { /* "(2) For each vertex s in G except s_f, randomly select * one edge from the s edge list of E(S) to be the * last edge of the s list in a new edge ordering." * * select random edges and move them to the end of each * edge list. */ for (x = 0; x < 26; x++) { if (nE[x] == 0 || x == sf) continue; pos = CHOOSE(nE[x]); y = E[x][pos]; E[x][pos] = E[x][nE[x]-1]; E[x][nE[x]-1] = y; } /* "(3) From this last set of edges, construct the last-edge * graph Z and determine whether or not all of its * vertices are connected to s_f." * * a probably stupid algorithm for looking at the * connectivity in Z: iteratively sweep through the * edges in Z, and build up an array (confusing called Z[x]) * whose elements are 1 if x is connected to sf, else 0. */ for (x = 0; x < 26; x++) Z[x] = 0; Z[(int) sf] = keep_connecting = 1; while (keep_connecting) { keep_connecting = 0; for (x = 0; x < 26; x++) { y = E[x][nE[x]-1]; /* xy is an edge in Z */ if (Z[x] == 0 && Z[y] == 1) /* x is connected to sf in Z */ { Z[x] = 1; keep_connecting = 1; } } } /* if any vertex in Z is tagged with a 0, it's * not connected to sf, and we won't have a Eulerian * walk. */ is_eulerian = 1; for (x = 0; x < 26; x++) { if (nE[x] == 0 || x == sf) continue; if (Z[x] == 0) { is_eulerian = 0; break; } } /* "(4) If any vertex is not connected in Z to s_f, the * new edge ordering will not be Eulerian, so return to * (2). If all vertices are connected in Z to s_f, * the new edge ordering will be Eulerian, so * continue to (5)." * * e.g. note infinite loop while is_eulerian is FALSE. */ } /* "(5) For each vertex s in G, randomly permute the remaining * edges of the s edge list of E(S) to generate the s * edge list of the new edge ordering E(S')." * * Essentially a StrShuffle() on the remaining nE[x]-1 elements * of each edge list; unfortunately our edge lists are arrays, * not strings, so we can't just call out to StrShuffle(). */ for (x = 0; x < 26; x++) for (n = nE[x] - 1; n > 1; n--) { pos = CHOOSE(n); y = E[x][pos]; E[x][pos] = E[x][n-1]; E[x][n-1] = y; } /* "(6) Construct sequence S', a random DP permutation of * S, from E(S') as follows. Start at the s_1 edge list. * At each s_i edge list, add s_i to S', delete the * first edge s_i,s_j of the edge list, and move to * the s_j edge list. Continue this process until * all edge lists are exhausted." */ iE = MallocOrDie(sizeof(int) * 26); for (x = 0; x < 26; x++) iE[x] = 0; pos = 0; x = toupper((int) s2[0]) - 'A'; while (1) { s1[pos++] = 'A' + x; /* add s_i to S' */ y = E[x][iE[x]]; iE[x]++; /* "delete" s_i,s_j from edge list */ x = y; /* move to s_j edge list. */ if (iE[x] == nE[x]) break; /* the edge list is exhausted. */ } s1[pos++] = 'A' + sf; s1[pos] = '\0'; /* Reality checks. */ if (x != sf) Die("hey, you didn't end on s_f."); if (pos != len) Die("hey, pos (%d) != len (%d).", pos, len); /* Free and return. */ Free2DArray((void **) E, 26); free(nE); free(iE); return 1; } /* Function: StrMarkov0() * Date: SRE, Fri Oct 29 11:08:31 1999 [St. Louis] * * Purpose: Returns a random string s1 with the same * length and zero-th order Markov properties * as s2. * * s1 and s2 may be identical, to randomize s2 * in place. * * Args: s1 - allocated space for random string * s2 - string to base s1's properties on. * * Returns: 1 on success; 0 if s2 doesn't look alphabetical. */ int StrMarkov0(char *s1, char *s2) { int len; int pos; int c[26]; /* symbol counts */ float p[26]; /* symbol probabilities */ int x; /* First, verify that the string is entirely alphabetic. */ len = strlen(s2); for (pos = 0; pos < len; pos++) if (! isalpha((int) s2[pos])) return 0; /* Collect zeroth order counts and convert to frequencies. * You can't count directly into p, because of limited * numeric range of a float. */ for (x = 0; x < 26; x++) c[x] = 0; for (pos = 0; pos < len; pos++) c[(int)(toupper((int) s2[pos]) - 'A')] ++; for (x = 0; x < 26; x++) p[x] = (float) c[x]; FNorm(p, 26); /* Generate a random string using those p's. */ for (pos = 0; pos < len; pos++) s1[pos] = FChoose(p, 26) + 'A'; s1[pos] = '\0'; return 1; } /* Function: StrMarkov1() * Date: SRE, Fri Oct 29 11:22:20 1999 [St. Louis] * * Purpose: Returns a random string s1 with the same * length and first order Markov properties * as s2. * * s1 and s2 may be identical, to randomize s2 * in place. * * Args: s1 - allocated space for random string * s2 - string to base s1's properties on. * * Returns: 1 on success; 0 if s2 doesn't look alphabetical. */ int StrMarkov1(char *s1, char *s2) { int len; int pos; int x,y; int i; /* initial symbol */ int c[26][26]; /* symbol counts */ float p[26][26]; /* symbol probabilities */ /* First, verify that the string is entirely alphabetic. */ len = strlen(s2); for (pos = 0; pos < len; pos++) if (! isalpha((int) s2[pos])) return 0; /* Collect first order counts and convert to frequencies. */ for (x = 0; x < 26; x++) for (y = 0; y < 26; y++) c[x][y] = 0; i = x = toupper((int) s2[0]) - 'A'; for (pos = 1; pos < len; pos++) { y = toupper((int) s2[pos]) - 'A'; c[x][y] ++; x = y; } for (x = 0; x < 26; x++) { for (y = 0; y < 26; y++) p[x][y] = (float) c[x][y]; FNorm(p[x], 26); } /* Generate a random string using those p's. */ x = i; s1[0] = x + 'A'; for (pos = 1; pos < len; pos++) { y = FChoose(p[x], 26); s1[pos] = y + 'A'; x = y; } s1[pos] = '\0'; return 1; } /* Function: StrReverse() * Date: SRE, Thu Nov 20 10:54:52 1997 [St. Louis] * * Purpose: Returns a reversed version of s2, in s1. * (s1 and s2 can be identical, to reverse in place) * * Args: s1 - allocated space for reversed string. * s2 - string to reverse. * * Return: 1. */ int StrReverse(char *s1, char *s2) { int len; int pos; char c; len = strlen(s2); for (pos = 0; pos < len/2; pos++) { /* swap ends */ c = s2[len-pos-1]; s1[len-pos-1] = s2[pos]; s1[pos] = c; } if (len%2) { s1[pos] = s2[pos]; } /* copy middle residue in odd-len s2 */ s1[len] = '\0'; return 1; } /* Function: StrRegionalShuffle() * Date: SRE, Thu Nov 20 11:02:34 1997 [St. Louis] * * Purpose: Returns a regionally shuffled version of s2, in s1. * (s1 and s2 can be identical to regionally * shuffle in place.) See [Pearson88]. * * Args: s1 - allocated space for regionally shuffled string. * s2 - string to regionally shuffle * w - window size (typically 10 or 20) * * Return: 1. */ int StrRegionalShuffle(char *s1, char *s2, int w) { int len; char c; int pos; int i, j; if (s1 != s2) strcpy(s1, s2); len = strlen(s1); for (i = 0; i < len; i += w) for (j = MIN(len-1, i+w-1); j > i; j--) { pos = i + CHOOSE(j-i); c = s1[pos]; s1[pos] = s1[j]; s1[j] = c; } return 1; } /* Function: AlignmentShuffle() * Date: SRE, Sun Apr 22 18:37:15 2001 [St. Louis] * * Purpose: Returns a shuffled version of ali2, in ali1. * (ali1 and ali2 can be identical, to shuffle * in place.) The alignment columns are shuffled, * preserving % identity within the columns. * * Args: ali1 - allocated space for shuffled alignment * [0..nseq-1][0..alen-1] * ali2 - alignment to be shuffled * nseq - number of sequences in the alignment * alen - length of alignment, in columns. * * Returns: int */ int AlignmentShuffle(char **ali1, char **ali2, int nseq, int alen) { int i; int pos; char c; if (ali1 != ali2) { for (i = 0; i < nseq; i++) strcpy(ali1[i], ali2[i]); } for (i = 0; i < nseq; i++) ali1[i][alen] = '\0'; for (; alen > 1; alen--) { pos = CHOOSE(alen); for (i = 0; i < nseq; i++) { c = ali1[i][pos]; ali1[i][pos] = ali1[i][alen-1]; ali1[i][alen-1] = c; } } return 1; } /* Function: AlignmentBootstrap() * Date: SRE, Sun Apr 22 18:49:14 2001 [St. Louis] * * Purpose: Returns a bootstrapped alignment sample in ali1, * constructed from ali2 by sampling columns with * replacement. * * Unlike the other shuffling routines, ali1 and * ali2 cannot be the same. ali2 is left unchanged. * ali1 must be a properly allocated space for an * alignment the same size as ali2. * * Args: ali1 - allocated space for bootstrapped alignment * [0..nseq-1][0..alen-1] * ali2 - alignment to be bootstrapped * nseq - number of sequences in the alignment * alen - length of alignment, in columns. * * Returns: 1 on success. */ int AlignmentBootstrap(char **ali1, char **ali2, int nseq, int alen) { int pos; int col; int i; for (pos = 0; pos < alen; pos++) { col = CHOOSE(alen); for (i = 0; i < nseq; i++) ali1[i][pos] = ali2[i][col]; } for (i = 0; i < nseq; i++) ali1[i][alen] = '\0'; return 1; } /* Function: QRNAShuffle() * Date: SRE, Mon Dec 10 10:14:12 2001 [St. Louis] * * Purpose: Shuffle a pairwise alignment x,y while preserving the * position of gaps; return the shuffled alignment in xs, * ys. * * Works by doing three separate * shuffles, of (1) columns with residues in both * x and y, (2) columns with residue in x and gap in y, * and (3) columns with gap in x and residue in y. * * xs,x and ys,y may be identical: that is, to shuffle * an alignment "in place", destroying the original * alignment, just call: * QRNAShuffle(x,y,x,y); * * Args: xs, ys: allocated space for shuffled pairwise ali of x,y [L+1] * x, y: pairwise alignment to be shuffled [0..L-1] * * Returns: 1 on success, 0 on failure. * The shuffled alignment is returned in xs, ys. */ int QRNAShuffle(char *xs, char *ys, char *x, char *y) { int L; int *xycol, *xcol, *ycol; int nxy, nx, ny; int i; int pos, c; char xsym, ysym; if (xs != x) strcpy(xs, x); if (ys != y) strcpy(ys, y); /* First, construct three arrays containing lists of the column positions * of the three types of columns. (If a column contains gaps in both x and y, * we've already simply copied it to the shuffled sequence.) */ L = strlen(x); xycol = MallocOrDie(sizeof(int) * L); xcol = MallocOrDie(sizeof(int) * L); ycol = MallocOrDie(sizeof(int) * L); nxy = nx = ny = 0; for (i = 0; i < L; i++) { if (isgap(x[i]) && isgap(y[i])) { continue; } else if (! isgap(x[i]) && ! isgap(y[i])) { xycol[nxy] = i; nxy++; } else if (isgap(x[i])) { ycol[ny] = i; ny++; } else if (isgap(y[i])) { xcol[nx] = i; nx++; } } /* Second, shuffle the sequences indirectly, via shuffling these arrays. * Yow, careful with those indices, and with order of the statements... */ for (; nxy > 1; nxy--) { pos = CHOOSE(nxy); xsym = xs[xycol[pos]]; ysym = ys[xycol[pos]]; c = xycol[pos]; xs[xycol[pos]] = xs[xycol[nxy-1]]; ys[xycol[pos]] = ys[xycol[nxy-1]]; xycol[pos] = xycol[nxy-1]; xs[xycol[nxy-1]] = xsym; ys[xycol[nxy-1]] = ysym; xycol[pos] = xycol[nxy-1]; } for (; nx > 1; nx--) { pos = CHOOSE(nx); xsym = xs[xcol[pos]]; ysym = ys[xcol[pos]]; c = xcol[pos]; xs[xcol[pos]] = xs[xcol[nx-1]]; ys[xcol[pos]] = ys[xcol[nx-1]]; xcol[pos] = xcol[nx-1]; xs[xcol[nx-1]] = xsym; ys[xcol[nx-1]] = ysym; xcol[nx-1] = c; } for (; ny > 1; ny--) { pos = CHOOSE(ny); xsym = xs[ycol[pos]]; ysym = ys[ycol[pos]]; c = ycol[pos]; xs[ycol[pos]] = xs[ycol[ny-1]]; ys[ycol[pos]] = ys[ycol[ny-1]]; ycol[pos] = ycol[ny-1]; xs[ycol[ny-1]] = xsym; ys[ycol[ny-1]] = ysym; ycol[ny-1] = c; } free(xycol); free(xcol); free(ycol); return 1; } #ifdef TESTDRIVER /* * cc -g -o testdriver -DTESTDRIVER -L. shuffle.c -lsquid -lm */ int main(int argc, char **argv) { char s1[100]; char s2[100]; sre_srandom(42); strcpy(s2, "GGGGGGGGGGCCCCCCCCCC"); /* strcpy(s2, "AGACATAAAGTTCCGTACTGCCGGGAT"); */ StrDPShuffle(s1, s2); printf("DPshuffle: %s\n", s1); StrMarkov0(s1,s2); printf("Markov 0 : %s\n", s1); StrMarkov1(s1,s2); printf("Markov 1 : %s\n", s1); strcpy(s1, "ACGTACGT--------ACGTACGT----ACGTACGT"); strcpy(s2, "ACGTACGTACGTACGT------------ACGTACGT"); QRNAShuffle(s1,s2,s1,s2); printf("QRNA : %s\n", s1); printf(" : %s\n", s2); return 0; } #endif squid/shuffle_main.c0000640000175000017520000003060310463223377014721 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* main for shuffle * * shuffle - generate shuffled sequences * Mon Feb 26 16:56:08 1996 * * CVS $Id: shuffle_main.c,v 1.16 2004/03/30 21:40:01 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "sre_random.h" static char banner[] = "shuffle - generated shuffled (or otherwise randomized) sequence"; static char usage[] = "\ Usage: shuffle [-options] \n\ Available options:\n\ -h : help; print version and usage info\n\ -n : make samples per input seq (default 1)\n\ -o : save shuffled sequences to file \n\ -t : truncate/delete inputs to fixed length \n\ \n\ Default: shuffle each input randomly, preserving mono-symbol composition.\n\ Other choices (exclusive; can't use more than one) :\n\ -d : shuffle but preserve both mono- and di-symbol composition\n\ -0 : generate with same 0th order Markov properties as each input\n\ -1 : generate with same 1st order Markov properties as each input\n\ -l : make iid sequences of same number and length as inputs\n\ -r : reverse inputs\n\ -w : regionally shuffle inputs in window size \n\ -i : make [-n] iid seqs of length [-t] of type [--dna|--amino];\n\ when -i is set, no argument is used\n\ "; static char experts[] = "\ --alignment : is an alignment; shuffle the columns\n\ --amino : synthesize protein sequences [default] (see -i, -l)\n\ --dna : synthesize DNA sequences (see -i, -l))\n\ --informat : specify sequence file format \n\ --nodesc : remove sequence description lines\n\ --qrna : is a QRNA/FASTA pairwise alignment file;\n\ shuffle the pairwise alignments, preserving gap position\n\ --seed : set random number seed to \n\ "; static struct opt_s OPTIONS[] = { { "-0", TRUE, sqdARG_NONE }, /* 0th order Markov */ { "-1", TRUE, sqdARG_NONE }, /* 1st order Markov */ { "-d", TRUE, sqdARG_NONE }, /* digram shuffle */ { "-h", TRUE, sqdARG_NONE }, /* help */ { "-i", TRUE, sqdARG_NONE }, /* make iid seq of set length */ { "-l", TRUE, sqdARG_NONE }, /* make iid seq of same length */ { "-n", TRUE, sqdARG_INT }, /* number of shuffles per input seq */ { "-o", TRUE, sqdARG_STRING }, /* file to save to */ { "-r", TRUE, sqdARG_NONE }, /* reverse seq rather than shuffle */ { "-t", TRUE, sqdARG_INT }, /* truncation of inputs to fixed len */ { "-w", TRUE, sqdARG_INT }, /* do regional shuffling */ { "--alignment",FALSE, sqdARG_NONE }, /* input is alignment; shuff cols */ { "--amino", FALSE, sqdARG_NONE }, /* make iid protein seqs [default]*/ { "--dna", FALSE, sqdARG_NONE }, /* make iid DNA seqs */ { "--informat", FALSE, sqdARG_STRING }, /* remove desc lines */ { "--nodesc", FALSE, sqdARG_NONE }, /* remove desc lines */ { "--qrna", FALSE, sqdARG_NONE }, /* pairwise alignment shuffler */ { "--seed", FALSE, sqdARG_INT }, /* set the random number seed */ }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) static void shuffle_alignment_file(FILE *ofp, char *afile, int fmt); int main(int argc, char **argv) { char *seqfile; /* name of sequence file */ SQFILE *dbfp; /* open sequence file */ int fmt; /* format of seqfile */ char *seq; /* sequence */ char sqname[32]; /* name of an iid sequence */ SQINFO sqinfo; /* additional sequence info */ char *shuff; /* shuffled sequence */ int num; /* number to generate */ int seed; /* random number generator seed */ int i; int w; /* window size for regional shuffle (or 0) */ int truncation; /* fixed length for truncation option (or 0) */ int no_desc; /* TRUE to remove description lines */ enum { /* shuffling strategy */ DO_SHUFFLE, DO_DPSHUFFLE, DO_MARKOV0, DO_MARKOV1, DO_REVERSE, DO_REGIONAL, DO_IID_SAMELEN, DO_IID_FIXEDLEN} strategy; int do_dna; /* TRUE to make DNA iid seqs, not protein */ int do_alignment; /* TRUE to shuffle alignment columns */ int do_qrna; /* TRUE for pairwise alignment shuffling mode */ char *outfile; /* name of save file (default NULL) */ FILE *ofp; /* open output file (default stdout) */ char *optname; /* option name */ char *optarg; /* option argument (or NULL) */ int optind; /* index of next argv[] */ /*********************************************** * Parse command line ***********************************************/ fmt = SQFILE_UNKNOWN; /* autodetect file format by default */ num = 0; seed = (int) time ((time_t *) NULL); w = 0; truncation = 0; strategy = DO_SHUFFLE; no_desc = FALSE; do_dna = FALSE; do_alignment = FALSE; do_qrna = FALSE; outfile = NULL; ofp = stdout; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-0") == 0) strategy = DO_MARKOV0; else if (strcmp(optname, "-1") == 0) strategy = DO_MARKOV1; else if (strcmp(optname, "-d") == 0) strategy = DO_DPSHUFFLE; else if (strcmp(optname, "-n") == 0) num = atoi(optarg); else if (strcmp(optname, "-o") == 0) outfile = optarg; else if (strcmp(optname, "-w") == 0) {strategy = DO_REGIONAL; w = atoi(optarg); } else if (strcmp(optname, "-i") == 0) strategy = DO_IID_FIXEDLEN; else if (strcmp(optname, "-l") == 0) strategy = DO_IID_SAMELEN; else if (strcmp(optname, "-r") == 0) strategy = DO_REVERSE; else if (strcmp(optname, "-t") == 0) truncation = atoi(optarg); else if (strcmp(optname, "--alignment")== 0) do_alignment = TRUE; else if (strcmp(optname, "--amino") == 0) do_dna = FALSE; else if (strcmp(optname, "--dna") == 0) do_dna = TRUE; else if (strcmp(optname, "--nodesc") == 0) no_desc = TRUE; else if (strcmp(optname, "--qrna") == 0) do_qrna = TRUE; else if (strcmp(optname, "--seed") == 0) seed = atoi(optarg); else if (strcmp(optname, "--informat") == 0) { fmt = String2SeqfileFormat(optarg); if (fmt == SQFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (outfile != NULL) { if ((ofp = fopen(outfile,"w")) == NULL) Die("Failed to open output file %s", outfile); } /***************************************************************** * Special case, 1: IID sequence generation. * -i option is special, because it synthesizes, rather than * shuffles. Doesn't take a seqfile argument; * requires -n, -t; and doesn't use the same code logic as the * other shuffling strategies. Note that we misuse/overload the * -t "truncation length" option to set our fixed length for * generating iid sequence. *****************************************************************/ if (strategy == DO_IID_FIXEDLEN) { if (num == 0 || truncation == 0) Die("-i (i.i.d. sequence generation) requires -n,-t to be set\n%s\n", usage); if (argc-optind != 0) Die("-i (i.i.d. sequence generation) takes no seqfile argument\n%s\n", usage); sre_srandom(seed); for (i = 0; i < num; i++) { if (do_dna) shuff = RandomSequence(DNA_ALPHABET, dnafq, 4, truncation); else shuff = RandomSequence(AMINO_ALPHABET, aafq, 20, truncation); /* pedantic note: sqname has room for 31 char + \0, so * there's room for 24 digits - a 32-bit integer can only run up * to 10 digits, and a 64-bit integer to 20, so we don't worry * about the following sprintf() overrunning its bounds. */ sprintf(sqname, "randseq%d", i); WriteSimpleFASTA(ofp, shuff, sqname, NULL); free(shuff); } return 0; } /***************************************************************** * Check command line *****************************************************************/ if (argc - optind != 1) Die("Incorrect number of command line arguments\n%s\n", usage); seqfile = argv[optind]; if (num == 0) num = 1; /* set default shuffle number per sequence */ sre_srandom(seed); /* Try to work around inability to autodetect from a pipe or .gz: * assume FASTA format */ if (fmt == SQFILE_UNKNOWN && (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) fmt = SQFILE_FASTA; /***************************************************************** * Special case, 2: Multiple alignment shuffling *****************************************************************/ if (do_alignment) { shuffle_alignment_file(ofp, seqfile, fmt); if (outfile != NULL) fclose(ofp); return 0; } /***************************************************************** * Main logic of the shuffling program: * expect one seqfile argument *****************************************************************/ if ((dbfp = SeqfileOpen(seqfile, fmt, NULL)) == NULL) Die("Failed to open sequence file %s for reading", seqfile); if (do_qrna && dbfp->format != SQFILE_FASTA) Die("--qrna option requires that %s is in QRNA/FASTA format", seqfile); while (ReadSeq(dbfp, dbfp->format, &seq, &sqinfo)) { /* Another special case: QRNA mode */ if (do_qrna) { char *seq2; SQINFO sqinfo2; if (! ReadSeq(dbfp, dbfp->format, &seq2, &sqinfo2)) Die("Failed to read an aligned partner for sequence %s", sqinfo.name); if (strlen(seq) != strlen(seq2)) Die("Length of %s is not the same as %s\n", sqinfo.name, sqinfo2.name); QRNAShuffle(seq, seq2, seq, seq2); WriteSeq(ofp, SQFILE_FASTA, seq, &sqinfo); WriteSeq(ofp, SQFILE_FASTA, seq2, &sqinfo2); FreeSequence(seq, &sqinfo); FreeSequence(seq2, &sqinfo2); continue; } /* back to the main logic... */ shuff = (char *) MallocOrDie ((sqinfo.len + 1) * sizeof(char)); if (no_desc) strcpy(sqinfo.desc, ""); /* If we're truncating seq, do it now. */ if (truncation > 0) { int start; if (sqinfo.len < truncation) { free(shuff); FreeSequence(seq, &sqinfo); continue; } start = CHOOSE(sqinfo.len - truncation + 1); strncpy(shuff, seq+start, truncation); shuff[truncation] = '\0'; strcpy(seq, shuff); sqinfo.len = truncation; } for (i = 0; i < num; i++) { switch (strategy) { case DO_SHUFFLE: StrShuffle(shuff, seq); break; case DO_DPSHUFFLE: StrDPShuffle(shuff, seq); break; case DO_MARKOV0: StrMarkov0(shuff, seq); break; case DO_MARKOV1: StrMarkov1(shuff, seq); break; case DO_REVERSE: StrReverse(shuff, seq); break; case DO_REGIONAL: StrRegionalShuffle(shuff, seq, w); break; case DO_IID_SAMELEN: free(shuff); if (do_dna) shuff = RandomSequence(DNA_ALPHABET, dnafq, 20, sqinfo.len); else shuff = RandomSequence(AMINO_ALPHABET, aafq, 20, sqinfo.len); break; default: Die("choked on a bad enum; tragic."); } WriteSeq(ofp, SQFILE_FASTA, shuff, &sqinfo); } if (shuff != NULL) free(shuff); FreeSequence(seq, &sqinfo); } SeqfileClose(dbfp); if (outfile != NULL) fclose(ofp); return 0; } static void shuffle_alignment_file(FILE *ofp, char *afile, int fmt) { MSAFILE *afp; MSA *msa; if ((afp = MSAFileOpen(afile, fmt, NULL)) == NULL) Die("Alignment file %s could not be opened for reading", afile); while ((msa = MSAFileRead(afp)) != NULL) { /* shuffle in place */ AlignmentShuffle(msa->aseq, msa->aseq, msa->nseq, msa->alen); /* write in same format we read in */ MSAFileWrite(ofp, msa, afp->format, FALSE); MSAFree(msa); } MSAFileClose(afp); } squid/sindex_main.c0000640000175000017520000001607710463223377014570 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sindex_main.c, SRE, Fri Feb 16 08:38:39 2001 [St. Louis] * * sindex -- create SSI index of sequence file(s) for sfetch * * CVS $Id: sindex_main.c,v 1.8 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "msa.h" #include "ssi.h" static char banner[] = "sindex - create SSI index of sequence file(s) for sfetch"; static char usage[] = "\ Usage: sindex [-options] ...\n\ Available options:\n\ -h : help; print version and usage info.\n\ -o : output the SSI index to file named \n\ "; static char experts[] = "\ --64 : force index mode to 64-bit, even on small files\n\ --external : force index compilation to use external (on-disk) sorting\n\ --informat : specify input sequence file format \n\ --pfamseq : index a FASTA file with >(name) (accession) (desc)\n\ "; struct opt_s OPTIONS[] = { { "-h", TRUE, sqdARG_NONE }, { "-o", TRUE, sqdARG_STRING }, { "--64", FALSE, sqdARG_NONE }, { "--external", FALSE, sqdARG_NONE }, { "--informat", FALSE, sqdARG_STRING }, { "--pfamseq", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *file; /* name of a sequence file */ SQFILE *sfp; /* open sequence file */ int format; /* forced sequence file format, if any */ int mode; /* SSI_OFFSET_I32 or SSI_OFFSET_I64 */ int idx; /* counter over files */ int status; /* return status from an SSI call */ SSIINDEX *ssi; /* the index we're creating */ char *ssifile; /* file name for the SSI index */ int fh; /* handle on current file */ char *seq; /* a sequence read from the file */ SQINFO sqinfo; /* info on the sequence */ int do_pfamseq; /* TRUE to index name and accession in a FASTA*/ int do_external; /* TRUE to force external sorting */ char *optname; char *optarg; int optind; /*********************************************** * Parse the command line ***********************************************/ /* initializations and defaults */ format = SQFILE_UNKNOWN; /* autodetecting format is the default */ mode = SSI_OFFSET_I32; /* default = 32 bit mode */ ssifile = NULL; /* default: set SSI file name as .ssi */ do_pfamseq = FALSE; /* default: don't hack FASTA parsing, duh */ do_external = FALSE; /* default: use in-memory sorting if possible */ while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-o") == 0) ssifile = sre_strdup(optarg, -1); else if (strcmp(optname, "--64") == 0) mode = SSI_OFFSET_I64; else if (strcmp(optname, "--external") == 0) do_external = TRUE; else if (strcmp(optname, "--pfamseq") == 0) do_pfamseq = TRUE; else if (strcmp(optname, "--informat") == 0) { format = String2SeqfileFormat(optarg); if (format == SQFILE_UNKNOWN) Die("unrecognized input sequence file format \"%s\"", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind < 1) Die("Incorrect number of command line arguments.\n%s\n", usage); /***************************************************************** * Get set up... *****************************************************************/ /* Determine whether we'll index in 32-bit or 64-bit mode. * 32-bit is default, but 64-bit trumps; if any file needs 64-bit, * we index them all that way. */ for (idx = optind; idx < argc; idx++) { file = argv[idx]; if ((status = SSIRecommendMode(file)) == -1) Die("Couldn't stat %s - file doesn't exist, or is too big", file); if (status == SSI_OFFSET_I64) mode = SSI_OFFSET_I64; } if (ssifile == NULL) { ssifile = sre_strdup(file, -1); sre_strcat(&ssifile, -1, ".ssi", -1); } if ((ssi = SSICreateIndex(mode)) == NULL) Die("Couldn't allocate/initialize the new SSI index\n"); if (do_external) SSIForceExternalSort(ssi); /***************************************************************** * Go through the files one at a time and compile index. *****************************************************************/ for (idx = optind; idx < argc; idx++) { file = argv[idx]; printf("Working on file %s... \t", file); fflush(stdout); if ((sfp = SeqfileOpenForIndexing(file, format, NULL, mode)) == NULL) Die("Failed to open sequence file %s for reading", file); if ((status = SSIAddFileToIndex(ssi, file, sfp->format, &fh)) != 0) Die("SSI error: %s\n", SSIErrorString(status)); while (ReadSeq(sfp, sfp->format, &seq, &sqinfo)) { if ((status = SSIAddPrimaryKeyToIndex(ssi, sqinfo.name, fh, &(sfp->r_off), &(sfp->d_off), sqinfo.len)) != 0) Die("SSI error: %s\n", SSIErrorString(status)); #if DEBUGLEVEL >= 2 if (mode == SSI_OFFSET_I32) SQD_DPRINTF2(("Added primary key %s: r_off=%lu, d_off=%lu len=%d\n", sqinfo.name, sfp->r_off.off.i32, sfp->d_off.off.i32, sqinfo.len)); else SQD_DPRINTF2(("Added primary key %s: r_off=%llu, d_off=%llu len=%d\n", sqinfo.name, sfp->r_off.off.i64, sfp->d_off.off.i64, sqinfo.len)); #endif if (sqinfo.flags & SQINFO_ID) { if ((status = SSIAddSecondaryKeyToIndex(ssi, sqinfo.id, sqinfo.name)) != 0) Die("SSI error: %s\n", SSIErrorString(status)); } if (sqinfo.flags & SQINFO_ACC) { if ((status = SSIAddSecondaryKeyToIndex(ssi, sqinfo.acc, sqinfo.name)) != 0) Die("SSI error: %s\n", SSIErrorString(status)); } if (do_pfamseq && sfp->format == SQFILE_FASTA && sqinfo.desc != NULL) { char *acc, *s; s = sqinfo.desc; acc = sre_strtok(&s, " \t", NULL); if (acc != NULL) { if ((status = SSIAddSecondaryKeyToIndex(ssi, acc, sqinfo.name)) != 0) Die("SSI error: %s\n", SSIErrorString(status)); } } FreeSequence(seq, &sqinfo); } if (sfp->bpl > 0 && sfp->rpl > 0) { if ((status = SSISetFileForSubseq(ssi, fh, sfp->bpl, sfp->rpl)) != 0) Die("SSI error: %s\n", SSIErrorString(status)); printf("FAST_SUBSEQ set...\t"); } else printf(" \t"); SeqfileClose(sfp); printf("[done]\n"); } printf("Sorting and writing index to SSI file %s...\t", ssifile); fflush(stdout); if ((status = SSIWriteIndex(ssifile, ssi)) != 0) Die("SSIWriteIndex() failed: %s", SSIErrorString(status)); printf("[done]\n"); printf("%s:\n", ssifile); printf("Mode: %s\n", mode == SSI_OFFSET_I32 ? "32-bit" : "64-bit"); printf("Files: %d\n", ssi->nfiles); printf("Primary keys: %d\n", ssi->nprimary); printf("Secondary keys: %d\n", ssi->nsecondary); SSIFreeIndex(ssi); free(ssifile); return 0; } squid/sqerror.c0000640000175000017520000000374210463223377013762 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sqerror.c * * error handling for the squid library * CVS $Id: sqerror.c,v 1.6 2003/05/26 16:21:50 eddy Exp $ */ #include "squidconf.h" #include "squid.h" #include #include #include int squid_errno; /* a global errno equivalent */ /* Function: Die() * * Purpose: Print an error message and die. The arguments * are formatted exactly like arguments to printf(). * * Return: None. Exits the program. */ /* VARARGS0 */ void Die(char *format, ...) { va_list argp; /* format the error mesg */ fprintf(stderr, "\nFATAL: "); va_start(argp, format); vfprintf(stderr, format, argp); va_end(argp); fprintf(stderr, "\n"); fflush(stderr); /* exit */ exit(1); } /* Function: Warn() * * Purpose: Print an error message and return. The arguments * are formatted exactly like arguments to printf(). * * Return: (void) */ /* VARARGS0 */ void Warn(char *format, ...) { va_list argp; /* format the error mesg */ fprintf(stderr, "WARNING: "); va_start(argp, format); vfprintf(stderr, format, argp); va_end(argp); fprintf(stderr, "\n"); fflush(stderr); } /* Function: Panic() * * Purpose: Die from a lethal error that's not my problem, * but instead a failure of a StdC/POSIX call that * shouldn't fail. Call perror() to get the * errno flag, then die. * * Usually called by the PANIC macro which adds * the __FILE__ and __LINE__ information; see * structs.h. * * Inspired by code in Donald Lewine's book, _POSIX * Programmer's Guide_. */ void Panic(char *file, int line) { (void) fprintf(stderr, "\nPANIC [%s line %d] ", file, line); (void) perror("Unusual error"); exit(EXIT_FAILURE); } squid/sqio.c0000640000175000017520000016054210463223377013242 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* File: sqio.c * From: ureadseq.c in Don Gilbert's sequence i/o package * * Reads and writes nucleic/protein sequence in various * formats. Data files may have multiple sequences. * * Heavily modified from READSEQ package * Copyright (C) 1990 by D.G. Gilbert * Biology Dept., Indiana University, Bloomington, IN 47405 * email: gilbertd@bio.indiana.edu * Thanks Don! * * SRE: Modifications as noted. Fri Jul 3 09:44:54 1992 * Packaged for squid, Thu Oct 1 10:07:11 1992 * ANSI conversion in full swing, Mon Jul 12 12:22:21 1993 * * CVS $Id: sqio.c,v 1.34 2004/10/08 12:14:21 eddy Exp $ * ***************************************************************** * Basic API for single sequence reading: * * SQFILE *sqfp; * char *seqfile; * int format; - see squid.h for formats; example: SQFILE_FASTA * char *seq; * SQINFO sqinfo; * * if ((sqfp = SeqfileOpen(seqfile, format, "BLASTDB")) == NULL) * Die("Failed to open sequence database file %s\n%s\n", seqfile, usage); * while (ReadSeq(sqfp, sqfp->format, &seq, &sqinfo)) { * do_stuff; * FreeSequence(seq, &sqinfo); * } * SeqfileClose(sqfp); * ***************************************************************** */ #include "squidconf.h" #include #include #include #include #ifndef SEEK_SET #include #endif #include "squid.h" #include "msa.h" #include "ssi.h" static void SeqfileGetLine(SQFILE *V); #define kStartLength 500 static char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*"; static char *primenuc = "ACGTUN"; static char *protonly = "EFIPQZ"; static SQFILE *seqfile_open(char *filename, int format, char *env, int ssimode); /* Function: SeqfileOpen() * * Purpose : Open a sequence database file and prepare for reading * sequentially. * * Args: filename - name of file to open * format - format of file * env - environment variable for path (e.g. BLASTDB) * ssimode - -1, SSI_OFFSET_I32, or SSI_OFFSET_I64 * * Returns opened SQFILE ptr, or NULL on failure. */ SQFILE * SeqfileOpen(char *filename, int format, char *env) { return seqfile_open(filename, format, env, -1); } SQFILE * SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode) { return seqfile_open(filename, format, env, ssimode); } static SQFILE * seqfile_open(char *filename, int format, char *env, int ssimode) { SQFILE *dbfp; dbfp = (SQFILE *) MallocOrDie (sizeof(SQFILE)); dbfp->ssimode = ssimode; dbfp->rpl = -1; /* flag meaning "unset" */ dbfp->lastrpl = 0; dbfp->maxrpl = 0; dbfp->bpl = -1; /* flag meaning "unset" */ dbfp->lastbpl = 0; dbfp->maxbpl = 0; /* Open our file handle. * Three possibilities: * 1. normal file open * 2. filename = "-"; read from stdin * 3. filename = "*.gz"; read thru pipe from gzip * If we're reading from stdin or a pipe, we can't reliably * back up, so we can't do two-pass parsers like the interleaved alignment * formats. */ if (strcmp(filename, "-") == 0) { dbfp->f = stdin; dbfp->do_stdin = TRUE; dbfp->do_gzip = FALSE; dbfp->fname = sre_strdup("[STDIN]", -1); } #ifndef SRE_STRICT_ANSI /* popen(), pclose() aren't portable to non-POSIX systems; disable */ else if (Strparse("^.*\\.gz$", filename, 0)) { char cmd[256]; /* Note that popen() will return "successfully" * if file doesn't exist, because gzip works fine * and prints an error! So we have to check for * existence of file ourself. */ if (! FileExists(filename)) Die("%s: file does not exist", filename); if (strlen(filename) + strlen("gzip -dc ") >= 256) Die("filename > 255 char in SeqfileOpen()"); sprintf(cmd, "gzip -dc %s", filename); if ((dbfp->f = popen(cmd, "r")) == NULL) return NULL; dbfp->do_stdin = FALSE; dbfp->do_gzip = TRUE; dbfp->fname = sre_strdup(filename, -1); } #endif /*SRE_STRICT_ANSI*/ else { if ((dbfp->f = fopen(filename, "r")) == NULL && (dbfp->f = EnvFileOpen(filename, env, NULL)) == NULL) return NULL; dbfp->do_stdin = FALSE; dbfp->do_gzip = FALSE; dbfp->fname = sre_strdup(filename, -1); } /* Invoke autodetection if we haven't already been told what * to expect. */ if (format == SQFILE_UNKNOWN) { if (dbfp->do_stdin == TRUE || dbfp->do_gzip) Die("Can't autodetect sequence file format from a stdin or gzip pipe"); format = SeqfileFormat(dbfp->f); if (format == SQFILE_UNKNOWN) Die("Can't determine format of sequence file %s", dbfp->fname); } /* The hack for sequential access of an interleaved alignment file: * read the alignment in, we'll copy sequences out one at a time. */ dbfp->msa = NULL; dbfp->afp = NULL; dbfp->format = format; dbfp->linenumber = 0; dbfp->buf = NULL; dbfp->buflen = 0; if (IsAlignmentFormat(format)) { /* We'll be reading from the MSA interface. Copy our data * to the MSA afp's structure. */ dbfp->afp = MallocOrDie(sizeof(MSAFILE)); dbfp->afp->f = dbfp->f; /* just a ptr, don't close */ dbfp->afp->do_stdin = dbfp->do_stdin; dbfp->afp->do_gzip = dbfp->do_gzip; dbfp->afp->fname = dbfp->fname; /* just a ptr, don't free */ dbfp->afp->format = dbfp->format; /* e.g. format */ dbfp->afp->linenumber = dbfp->linenumber; /* e.g. 0 */ dbfp->afp->buf = NULL; dbfp->afp->buflen = 0; if ((dbfp->msa = MSAFileRead(dbfp->afp)) == NULL) Die("Failed to read any alignment data from file %s", dbfp->fname); /* hack: overload/reuse msa->lastidx; indicates next seq to return upon a ReadSeq() call */ dbfp->msa->lastidx = 0; return dbfp; } /* Load the first line. */ SeqfileGetLine(dbfp); return dbfp; } /* Function: SeqfilePosition() * * Purpose: Move to a particular offset in a seqfile. * Will not work on alignment files. */ void SeqfilePosition(SQFILE *sqfp, SSIOFFSET *offset) { if (sqfp->do_stdin || sqfp->do_gzip || IsAlignmentFormat(sqfp->format)) Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); if (SSISetFilePosition(sqfp->f, offset) != 0) Die("SSISetFilePosition failed, but that shouldn't happen."); SeqfileGetLine(sqfp); } /* Function: SeqfileRewind() * * Purpose: Set a sequence file back to the first sequence. * * Won't work on alignment files. Although it would * seem that it could (just set msa->lastidx back to 0), * that'll fail on "multiple multiple" alignment file formats * (e.g. Stockholm). */ void SeqfileRewind(SQFILE *sqfp) { if (sqfp->do_stdin || sqfp->do_gzip) Die("SeqfileRewind() failed: in a nonrewindable data file or stream"); rewind(sqfp->f); SeqfileGetLine(sqfp); } /* Function: SeqfileLineParameters() * Date: SRE, Thu Feb 15 17:00:41 2001 [St. Louis] * * Purpose: After all the sequences have been read from the file, * but before closing it, retrieve overall bytes-per-line and * residues-per-line info. If non-zero, these mean that * the file contains homogeneous sequence line lengths (except * the last line in each record). * * If either of bpl or rpl is determined to be inhomogeneous, * both are returned as 0. * * Args: *sqfp - an open but fully read sequence file * ret_bpl - RETURN: bytes per line, or 0 if inhomogeneous * ret_rpl - RETURN: residues per line, or 0 if inhomogenous. * * Returns: void */ void SeqfileLineParameters(SQFILE *V, int *ret_bpl, int *ret_rpl) { if (V->rpl > 0 && V->maxrpl == V->rpl && V->bpl > 0 && V->maxbpl == V->bpl) { *ret_bpl = V->bpl; *ret_rpl = V->rpl; } else { *ret_bpl = 0; *ret_rpl = 0; } } void SeqfileClose(SQFILE *sqfp) { /* note: don't test for sqfp->msa being NULL. Now that * we're holding afp open and allowing access to multi-MSA * databases (e.g. Stockholm format, Pfam), msa ends * up being NULL when we run out of alignments. */ if (sqfp->afp != NULL) { if (sqfp->msa != NULL) MSAFree(sqfp->msa); if (sqfp->afp->buf != NULL) free(sqfp->afp->buf); free(sqfp->afp); } #ifndef SRE_STRICT_ANSI /* gunzip functionality only on POSIX systems */ if (sqfp->do_gzip) pclose(sqfp->f); #endif else if (! sqfp->do_stdin) fclose(sqfp->f); if (sqfp->buf != NULL) free(sqfp->buf); if (sqfp->fname != NULL) free(sqfp->fname); free(sqfp); } /* Function: SeqfileGetLine() * Date: SRE, Tue Jun 22 09:15:49 1999 [Sanger Centre] * * Purpose: read a line from a sequence file into V->buf * If the fgets() is NULL, sets V->buf[0] to '\0'. * * Args: V * * Returns: void */ static void SeqfileGetLine(SQFILE *V) { if (V->ssimode >= 0) if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->ssioffset))) Die("SSIGetFilePosition() failed"); if (sre_fgets(&(V->buf), &(V->buflen), V->f) == NULL) *(V->buf) = '\0'; V->linenumber++; } void FreeSequence(char *seq, SQINFO *sqinfo) { if (seq != NULL) free(seq); if (sqinfo->flags & SQINFO_SS) free(sqinfo->ss); if (sqinfo->flags & SQINFO_SA) free(sqinfo->sa); } int SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag) { int len; int pos; /* silently ignore NULL. */ if (sptr == NULL) return 1; while (*sptr == ' ') sptr++; /* ignore leading whitespace */ for (pos = strlen(sptr)-1; pos >= 0; pos--) if (! isspace((int) sptr[pos])) break; sptr[pos+1] = '\0'; /* ignore trailing whitespace */ switch (flag) { case SQINFO_NAME: if (*sptr != '-') { strncpy(sqinfo->name, sptr, SQINFO_NAMELEN-1); sqinfo->name[SQINFO_NAMELEN-1] = '\0'; sqinfo->flags |= SQINFO_NAME; } break; case SQINFO_ID: if (*sptr != '-') { strncpy(sqinfo->id, sptr, SQINFO_NAMELEN-1); sqinfo->id[SQINFO_NAMELEN-1] = '\0'; sqinfo->flags |= SQINFO_ID; } break; case SQINFO_ACC: if (*sptr != '-') { strncpy(sqinfo->acc, sptr, SQINFO_NAMELEN-1); sqinfo->acc[SQINFO_NAMELEN-1] = '\0'; sqinfo->flags |= SQINFO_ACC; } break; case SQINFO_DESC: if (*sptr != '-') { if (sqinfo->flags & SQINFO_DESC) /* append? */ { len = strlen(sqinfo->desc); if (len < SQINFO_DESCLEN-2) /* is there room? */ { strncat(sqinfo->desc, " ", SQINFO_DESCLEN-1-len); len++; strncat(sqinfo->desc, sptr, SQINFO_DESCLEN-1-len); } } else /* else copy */ strncpy(sqinfo->desc, sptr, SQINFO_DESCLEN-1); sqinfo->desc[SQINFO_DESCLEN-1] = '\0'; sqinfo->flags |= SQINFO_DESC; } break; case SQINFO_START: if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; } sqinfo->start = atoi(sptr); if (sqinfo->start != 0) sqinfo->flags |= SQINFO_START; break; case SQINFO_STOP: if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; } sqinfo->stop = atoi(sptr); if (sqinfo->stop != 0) sqinfo->flags |= SQINFO_STOP; break; case SQINFO_OLEN: if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; } sqinfo->olen = atoi(sptr); if (sqinfo->olen != 0) sqinfo->flags |= SQINFO_OLEN; break; default: Die("Invalid flag %d to SetSeqinfoString()", flag); } return 1; } void SeqinfoCopy(SQINFO *sq1, SQINFO *sq2) { sq1->flags = sq2->flags; if (sq2->flags & SQINFO_NAME) strcpy(sq1->name, sq2->name); if (sq2->flags & SQINFO_ID) strcpy(sq1->id, sq2->id); if (sq2->flags & SQINFO_ACC) strcpy(sq1->acc, sq2->acc); if (sq2->flags & SQINFO_DESC) strcpy(sq1->desc, sq2->desc); if (sq2->flags & SQINFO_LEN) sq1->len = sq2->len; if (sq2->flags & SQINFO_START) sq1->start = sq2->start; if (sq2->flags & SQINFO_STOP) sq1->stop = sq2->stop; if (sq2->flags & SQINFO_OLEN) sq1->olen = sq2->olen; if (sq2->flags & SQINFO_TYPE) sq1->type = sq2->type; if (sq2->flags & SQINFO_SS) sq1->ss = Strdup(sq2->ss); if (sq2->flags & SQINFO_SA) sq1->sa = Strdup(sq2->sa); } /* Function: ToDNA() * * Purpose: Convert a sequence to DNA. * U --> T */ void ToDNA(char *seq) { for (; *seq != '\0'; seq++) { if (*seq == 'U') *seq = 'T'; else if (*seq == 'u') *seq = 't'; } } /* Function: ToRNA() * * Purpose: Convert a sequence to RNA. * T --> U */ void ToRNA(char *seq) { for (; *seq != '\0'; seq++) { if (*seq == 'T') *seq = 'U'; else if (*seq == 't') *seq = 'u'; } } /* Function: ToIUPAC() * * Purpose: Convert X's, o's, other junk in a nucleic acid sequence to N's, * to comply with IUPAC code. If is_aseq is TRUE, will allow gap * characters though, so we can call ToIUPAC() on aligned seqs. * * NUCLEOTIDES is defined in squid.h as: * "ACGTUNRYMKSWHBVDacgtunrymkswhbvd" * gap chars allowed by isgap() are defined in squid.h as: * " ._-~" * * WU-BLAST's pressdb will * choke on X's, for instance, necessitating conversion * of certain genome centers' data. * * Because this always converts to upper case N, * call this function *before* forcing any case conversion * (e.g. in sreformat). */ void ToIUPAC(char *seq, int is_aseq) { if (is_aseq) { for (; *seq != '\0'; seq++) if (strchr(NUCLEOTIDES, *seq) == NULL && ! isgap(*seq)) *seq = 'N'; } else { for (; *seq != '\0'; seq++) if (strchr(NUCLEOTIDES, *seq) == NULL) *seq = 'N'; } } /* Function: ToSimplyN() * Incept: SRE, Mon Jan 19 17:52:02 2004 [St. Louis] * * Purpose: Like ToIUPAC(), but convert anything that's not * unambiguous nucleotide sequence to an N. Some RNA * folding programs disallow IUPAC codes, and require * N for any unknown base. * * Because this always converts to upper case N, * call this function *before* forcing any case conversion * (e.g. in sreformat). * * Args: seq - sequence to convert * is_aseq - if TRUE, sequence is an aligned seq, and gaps * are left untouched. Otherwise, even gap characters * are converted to N's. * * Returns: (void) * The seq is changed in place. */ void ToSimplyN(char *seq, int is_aseq) { if (is_aseq) { for (; *seq != '\0'; seq++) if (strchr("ACGTUacgtu", *seq) == NULL && ! isgap(*seq)) *seq = 'N'; } else { for (; *seq != '\0'; seq++) if (strchr("ACGTUacgtu", *seq) == NULL) *seq = 'N'; } } /* Function: addseq() * * Purpose: Add a line of sequence to the growing string in V. * * In the seven supported unaligned formats, all sequence * lines may contain whitespace that must be filtered out; * four formats (PIR, EMBL, Genbank, GCG) include coordinates * that must be filtered out. Thus an (!isdigit && !isspace) * test on each character before we accept it. */ static void addseq(char *s, struct ReadSeqVars *V) { char *s0; char *sq; int rpl; /* valid residues per line */ int bpl; /* characters per line */ if (V->ssimode == -1) { /* Normal mode: keeping the seq */ /* Make sure we have enough room. We know that s is <= buflen, * so just make sure we've got room for a whole new buflen worth * of sequence. */ if (V->seqlen + V->buflen > V->maxseq) { V->maxseq += MAX(V->buflen, kStartLength); V->seq = ReallocOrDie (V->seq, V->maxseq+1); } sq = V->seq + V->seqlen; while (*s != 0) { if (! isdigit((int) *s) && ! isspace((int) *s)) { *sq = *s; sq++; } s++; } V->seqlen = sq - V->seq; } else /* else: indexing mode, discard the seq */ { s0 = s; rpl = 0; while (*s != 0) { if (! isdigit((int) *s) && ! isspace((int) *s)) { rpl++; } s++; } V->seqlen += rpl; bpl = s - s0; /* Keep track of the global rpl, bpl for the file. * This is overly complicated because we have to * allow the last line of each record (e.g. the last addseq() call * on each sequence) to have a different length - and sometimes * we'll have one-line sequence records, too. Thus we only * do something with the global V->rpl when we have *passed over* * a line - we keep the last line's rpl in last_rpl. And because * a file might consist entirely of single-line records, we keep * a third guy, maxrpl, that tells us the maximum rpl of any line * in the file. If we reach the end of file and rpl is still unset, * we'll set it to maxrpl. If we reach eof and rpl is set, but is * less than maxrpl, that's a weird case where a last line in some * record is longer than every other line. */ if (V->rpl != 0) { /* 0 means we already know rpl is invalid */ if (V->lastrpl > 0) { /* we're on something that's not the first line */ if (V->rpl > 0 && V->lastrpl != V->rpl) V->rpl = 0; else if (V->rpl == -1) V->rpl = V->lastrpl; } V->lastrpl = rpl; if (rpl > V->maxrpl) V->maxrpl = rpl; /* make sure we check max length of final lines */ } if (V->bpl != 0) { /* 0 means we already know bpl is invalid */ if (V->lastbpl > 0) { /* we're on something that's not the first line */ if (V->bpl > 0 && V->lastbpl != V->bpl) V->bpl = 0; else if (V->bpl == -1) V->bpl = V->lastbpl; } V->lastbpl = bpl; if (bpl > V->maxbpl) V->maxbpl = bpl; /* make sure we check max length of final lines */ } } /* end of indexing mode of addseq(). */ } static void readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) { int addend = 0; int done = 0; V->seqlen = 0; V->lastrpl = V->lastbpl = 0; if (addfirst) { if (V->ssimode >= 0) V->d_off = V->ssioffset; addseq(V->buf, V); } else if (V->ssimode >= 0) if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->d_off))) Die("SSIGetFilePosition() failed"); do { SeqfileGetLine(V); /* feof() alone is a bug; files not necessarily \n terminated */ if (*(V->buf) == '\0' && feof(V->f)) done = TRUE; done |= (*endTest)(V->buf, &addend); if (addend || !done) addseq(V->buf, V); } while (!done); } static int endPIR(char *s, int *addend) { *addend = 0; if ((strncmp(s, "///", 3) == 0) || (strncmp(s, "ENTRY", 5) == 0)) return 1; else return 0; } static void readPIR(struct ReadSeqVars *V) { char *sptr; /* load first line of entry */ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) { SeqfileGetLine(V); } if (feof(V->f)) return; if (V->ssimode >= 0) V->r_off = V->ssioffset; if ((sptr = strtok(V->buf + 15, "\n\t ")) != NULL) { SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); } do { SeqfileGetLine(V); if (!feof(V->f) && strncmp(V->buf, "TITLE", 5) == 0) SetSeqinfoString(V->sqinfo, V->buf+15, SQINFO_DESC); else if (!feof(V->f) && strncmp(V->buf, "ACCESSION", 9) == 0) { if ((sptr = strtok(V->buf+15, " \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); } } while (! feof(V->f) && (strncmp(V->buf,"SEQUENCE", 8) != 0)); SeqfileGetLine(V); /* skip next line, coords */ readLoop(0, endPIR, V); /* reading a real PIR-CODATA database file, we keep the source coords */ V->sqinfo->start = 1; V->sqinfo->stop = V->seqlen; V->sqinfo->olen = V->seqlen; V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN; /* get next line */ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) { SeqfileGetLine(V); } } static int endIG(char *s, int *addend) { *addend = 1; /* 1 or 2 occur in line w/ bases */ return((strchr(s,'1')!=NULL) || (strchr(s,'2')!=NULL)); } static void readIG(struct ReadSeqVars *V) { char *nm; /* position past ';' comments */ do { SeqfileGetLine(V); } while (! (feof(V->f) || ((*V->buf != 0) && (*V->buf != ';')) )); if (!feof(V->f)) { if ((nm = strtok(V->buf, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); readLoop(0, endIG, V); } while (!(feof(V->f) || ((*V->buf != '\0') && (*V->buf == ';')))) SeqfileGetLine(V); } static int endStrider(char *s, int *addend) { *addend = 0; return (strstr( s, "//") != NULL); } static void readStrider(struct ReadSeqVars *V) { char *nm; while ((!feof(V->f)) && (*V->buf == ';')) { if (strncmp(V->buf,"; DNA sequence", 14) == 0) { if ((nm = strtok(V->buf+16, ",\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); } SeqfileGetLine(V); } if (! feof(V->f)) readLoop(1, endStrider, V); /* load next line */ while ((!feof(V->f)) && (*V->buf != ';')) SeqfileGetLine(V); } static int endGB(char *s, int *addend) { *addend = 0; return ((strstr(s,"//") != NULL) || (strstr(s,"LOCUS") == s)); } static void readGenBank(struct ReadSeqVars *V) { char *sptr; int in_definition; /* We'll map three genbank identifiers onto names: * LOCUS -> sqinfo.name * ACCESSION -> sqinfo.acc [primary accession only] * VERSION -> sqinfo.id * We don't currently store the GI number, or secondary accessions. */ while (strncmp(V->buf, "LOCUS", 5) != 0) { SeqfileGetLine(V); } if (V->ssimode >= 0) V->r_off = V->ssioffset; if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); in_definition = FALSE; while (! feof(V->f)) { SeqfileGetLine(V); if (! feof(V->f) && strstr(V->buf, "DEFINITION") == V->buf) { if ((sptr = strtok(V->buf+12, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); in_definition = TRUE; } else if (! feof(V->f) && strstr(V->buf, "ACCESSION") == V->buf) { if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); in_definition = FALSE; } else if (! feof(V->f) && strstr(V->buf, "VERSION") == V->buf) { if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); in_definition = FALSE; } else if (strncmp(V->buf,"ORIGIN", 6) != 0) { if (in_definition) SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC); } else break; } readLoop(0, endGB, V); /* reading a real GenBank database file, we keep the source coords */ V->sqinfo->start = 1; V->sqinfo->stop = V->seqlen; V->sqinfo->olen = V->seqlen; V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN; while (!(feof(V->f) || ((*V->buf!=0) && (strstr(V->buf,"LOCUS") == V->buf)))) SeqfileGetLine(V); /* SRE: V->s now holds "//", so sequential reads are wedged: fixed Tue Jul 13 1993 */ while (!feof(V->f) && strstr(V->buf, "LOCUS ") != V->buf) SeqfileGetLine(V); } static int endGCGdata(char *s, int *addend) { *addend = 0; return (*s == '>'); } static void readGCGdata(struct ReadSeqVars *V) { int binary = FALSE; /* whether data are binary or not */ int blen = 0; /* length of binary sequence */ /* first line contains ">>>>" followed by name */ if (Strparse(">>>>([^ ]+) .+2BIT +Len: ([0-9]+)", V->buf, 2)) { binary = TRUE; SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME); blen = atoi(sqd_parse[2]); } else if (Strparse(">>>>([^ ]+) .+ASCII +Len: [0-9]+", V->buf, 1)) SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME); else Die("bogus GCGdata format? %s", V->buf); /* second line contains free text description */ SeqfileGetLine(V); SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC); if (binary) { /* allocate for blen characters +3... (allow for 3 bytes of slop) */ if (blen >= V->maxseq) { V->maxseq = blen; if ((V->seq = (char *) realloc (V->seq, sizeof(char)*(V->maxseq+4)))==NULL) Die("malloc failed"); } /* read (blen+3)/4 bytes from file */ if (fread(V->seq, sizeof(char), (blen+3)/4, V->f) < (size_t) ((blen+3)/4)) Die("fread failed"); V->seqlen = blen; /* convert binary code to seq */ GCGBinaryToSequence(V->seq, blen); } else readLoop(0, endGCGdata, V); while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>')))) SeqfileGetLine(V); } static int endPearson(char *s, int *addend) { *addend = 0; return(*s == '>'); } static void readPearson(struct ReadSeqVars *V) { char *sptr; if (V->ssimode >= 0) V->r_off = V->ssioffset; if (*V->buf != '>') Die("\ File %s does not appear to be in FASTA format at line %d.\n\ You may want to specify the file format on the command line.\n\ Usually this is done with an option --informat .\n", V->fname, V->linenumber); if ((sptr = strtok(V->buf+1, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); if ((sptr = strtok(NULL, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); readLoop(0, endPearson, V); while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>')))) { SeqfileGetLine(V); } } static int endEMBL(char *s, int *addend) { *addend = 0; /* Some people (Berlin 5S rRNA database, f'r instance) use * an extended EMBL format that attaches extra data after * the sequence -- watch out for that. We use the fact that * real EMBL sequence lines begin with five spaces. * * We can use this as the sole end test because readEMBL() will * advance to the next ID line before starting to read again. */ return (strncmp(s," ",5) != 0); /* return ((strstr(s,"//") != NULL) || (strstr(s,"ID ") == s)); */ } static void readEMBL(struct ReadSeqVars *V) { char *sptr; int i; /* make sure we have first line */ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) { SeqfileGetLine(V); } if (V->ssimode >= 0) V->r_off = V->ssioffset; if ((sptr = strtok(V->buf+5, "\n\t ")) != NULL) { SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); } do { SeqfileGetLine(V); if (!feof(V->f) && strstr(V->buf, "AC ") == V->buf) { if ((sptr = strtok(V->buf+5, "; \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); } else if (!feof(V->f) && strstr(V->buf, "DE ") == V->buf) { if ((sptr = strtok(V->buf+5, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); } } while (! feof(V->f) && strncmp(V->buf,"SQ",2) != 0); readLoop(0, endEMBL, V); /* Hack for Staden experiment files: convert - to N. * * You may not treat V->seq as a string yet; it is not null terminated * until we return and ReadSeq() polishes it off. * [bug #h25; xref STL7 p.121] */ if (V->ssimode == -1) /* if we're in ssi mode, we're not keeping the seq */ for (i = 0; i < V->seqlen; i++) if (V->seq[i] == '-') V->seq[i] = 'N'; /* reading a real EMBL database file, we keep the source coords */ V->sqinfo->start = 1; V->sqinfo->stop = V->seqlen; V->sqinfo->olen = V->seqlen; V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN; /* load next record's ID line */ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) { SeqfileGetLine(V); } } static int endZuker(char *s, int *addend) { *addend = 0; return( *s == '(' ); } static void readZuker(struct ReadSeqVars *V) { char *sptr; SeqfileGetLine(V); /*s == "seqLen seqid string..."*/ if ((sptr = strtok(V->buf+6, " \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); if ((sptr = strtok(NULL, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); readLoop(0, endZuker, V); while (!(feof(V->f) | ((*V->buf != '\0') & (*V->buf == '(')))) SeqfileGetLine(V); } static void readUWGCG(struct ReadSeqVars *V) { char *si; char *sptr; int done; V->seqlen = 0; /*writeseq: " %s Length: %d (today) Check: %d ..\n" */ /*drop above or ".." from id*/ if ((si = strstr(V->buf," Length: ")) != NULL) *si = 0; else if ((si = strstr(V->buf,"..")) != NULL) *si = 0; if ((sptr = strtok(V->buf, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); do { done = feof(V->f); SeqfileGetLine(V); if (! done) addseq(V->buf, V); } while (!done); } /* Function: ReadSeq() * * Purpose: Read next sequence from an open database file. * Return the sequence and associated info. * * Args: fp - open sequence database file pointer * format - format of the file (previously determined * by call to SeqfileFormat()). * Currently unused, since we carry it in V. * ret_seq - RETURN: sequence * sqinfo - RETURN: filled in w/ other information * * Limitations: uses squid_errno, so it's not threadsafe. * * Return: 1 on success, 0 on failure. * ret_seq and some field of sqinfo are allocated here, * The preferred call mechanism to properly free the memory is: * * SQINFO sqinfo; * char *seq; * * ReadSeq(fp, format, &seq, &sqinfo); * ... do something... * FreeSequence(seq, &sqinfo); */ int ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) { int gotuw; squid_errno = SQERR_OK; /* Here's the hack for sequential access of sequences from * the multiple sequence alignment formats */ if (IsAlignmentFormat(V->format)) { if (V->msa->lastidx >= V->msa->nseq) { /* out of data. try to read another alignment */ MSAFree(V->msa); if ((V->msa = MSAFileRead(V->afp)) == NULL) return 0; V->msa->lastidx = 0; } /* copy and dealign the appropriate aligned seq */ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen, V->msa->aseq[V->msa->lastidx], &(V->seq)); V->seqlen = strlen(V->seq); /* Extract sqinfo stuff for this sequence from the msa. * Tedious; code that should be cleaned. */ sqinfo->flags = 0; if (V->msa->sqname[V->msa->lastidx] != NULL) SetSeqinfoString(sqinfo, V->msa->sqname[V->msa->lastidx], SQINFO_NAME); if (V->msa->sqacc != NULL && V->msa->sqacc[V->msa->lastidx] != NULL) SetSeqinfoString(sqinfo, V->msa->sqacc[V->msa->lastidx], SQINFO_ACC); if (V->msa->sqdesc != NULL && V->msa->sqdesc[V->msa->lastidx] != NULL) SetSeqinfoString(sqinfo, V->msa->sqdesc[V->msa->lastidx], SQINFO_DESC); if (V->msa->ss != NULL && V->msa->ss[V->msa->lastidx] != NULL) { MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen, V->msa->ss[V->msa->lastidx], &(sqinfo->ss)); sqinfo->flags |= SQINFO_SS; } if (V->msa->sa != NULL && V->msa->sa[V->msa->lastidx] != NULL) { MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen, V->msa->sa[V->msa->lastidx], &(sqinfo->sa)); sqinfo->flags |= SQINFO_SA; } V->msa->lastidx++; } else { if (feof(V->f)) return 0; if (V->ssimode == -1) { /* normal mode */ V->seq = (char*) calloc (kStartLength+1, sizeof(char)); V->maxseq = kStartLength; } else { /* index mode: discarding seq */ V->seq = NULL; V->maxseq = 0; } V->seqlen = 0; V->sqinfo = sqinfo; V->sqinfo->flags = 0; switch (V->format) { case SQFILE_IG : readIG(V); break; case SQFILE_STRIDER : readStrider(V); break; case SQFILE_GENBANK : readGenBank(V); break; case SQFILE_FASTA : readPearson(V); break; case SQFILE_EMBL : readEMBL(V); break; case SQFILE_ZUKER : readZuker(V); break; case SQFILE_PIR : readPIR(V); break; case SQFILE_GCGDATA : readGCGdata(V); break; case SQFILE_GCG : do { /* skip leading comments on GCG file */ gotuw = (strstr(V->buf,"..") != NULL); if (gotuw) readUWGCG(V); SeqfileGetLine(V); } while (! feof(V->f)); break; case SQFILE_IDRAW: /* SRE: no attempt to read idraw postscript */ default: squid_errno = SQERR_FORMAT; free(V->seq); return 0; } if (V->seq != NULL) /* (yes, it can be NULL, in indexing mode) */ V->seq[V->seqlen] = '\0'; /* stick a string terminator on it */ } /* Cleanup */ sqinfo->len = V->seqlen; sqinfo->flags |= SQINFO_LEN; *ret_seq = V->seq; if (squid_errno == SQERR_OK) return 1; else return 0; } /* Function: SeqfileFormat() * Date: SRE, Tue Jun 22 10:58:58 1999 [Sanger Centre] * * Purpose: Determine format of an open file. * Returns format code. * Rewinds the file. * * Autodetects the following unaligned formats: * SQFILE_FASTA * SQFILE_GENBANK * SQFILE_EMBL * SQFILE_GCG * SQFILE_GCGDATA * SQFILE_PIR * Also autodetects the following alignment formats: * MSAFILE_STOCKHOLM * MSAFILE_MSF * MSAFILE_CLUSTAL * MSAFILE_SELEX * MSAFILE_PHYLIP * * Can't autodetect MSAFILE_A2M, calls it SQFILE_FASTA. * MSAFileFormat() does the opposite. * * Args: sfp - open SQFILE * * Return: format code, or SQFILE_UNKNOWN if unrecognized */ int SeqfileFormat(FILE *fp) { char *buf; int len; int fmt = SQFILE_UNKNOWN; int ndataline; char *bufcpy, *s, *s1, *s2; int has_junk; buf = NULL; len = 0; ndataline = 0; has_junk = FALSE; while (sre_fgets(&buf, &len, fp) != NULL) { if (IsBlankline(buf)) continue; /* Well-behaved formats identify themselves in first nonblank line. */ if (ndataline == 0) { if (strncmp(buf, ">>>>", 4) == 0 && strstr(buf, "Len: ")) { fmt = SQFILE_GCGDATA; goto DONE; } if (buf[0] == '>') { fmt = SQFILE_FASTA; goto DONE; } if (strncmp(buf, "!!AA_SEQUENCE", 13) == 0 || strncmp(buf, "!!NA_SEQUENCE", 13) == 0) { fmt = SQFILE_GCG; goto DONE; } if (strncmp(buf, "# STOCKHOLM 1.", 14) == 0) { fmt = MSAFILE_STOCKHOLM; goto DONE; } /* Examples of "CLUSTAL format": * ClustalW: "CLUSTAL W (1.81) multiple sequence alignment" * T-COFFEE: "CLUSTAL FORMAT for T-COFFEE Version_1.37, CPU=0.00 sec, SCORE=29, Nseq=7, Len=124" */ if (strncmp(buf, "CLUSTAL ", 8) == 0) { fmt = MSAFILE_CLUSTAL; goto DONE; } if (strncmp(buf, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0 || strncmp(buf, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0) { fmt = MSAFILE_MSF; goto DONE; } /* PHYLIP id: also just a good bet */ bufcpy = sre_strdup(buf, -1); s = bufcpy; if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) != NULL && (s2 = sre_strtok(&s, WHITESPACE, NULL)) != NULL && IsInt(s1) && IsInt(s2)) { free(bufcpy); fmt = MSAFILE_PHYLIP; goto DONE; } free(bufcpy); } /* We trust that other formats identify themselves soon. */ /* dead giveaways for extended SELEX */ if (strncmp(buf, "#=AU", 4) == 0 || strncmp(buf, "#=ID", 4) == 0 || strncmp(buf, "#=AC", 4) == 0 || strncmp(buf, "#=DE", 4) == 0 || strncmp(buf, "#=GA", 4) == 0 || strncmp(buf, "#=TC", 4) == 0 || strncmp(buf, "#=NC", 4) == 0 || strncmp(buf, "#=SQ", 4) == 0 || strncmp(buf, "#=SS", 4) == 0 || strncmp(buf, "#=CS", 4) == 0 || strncmp(buf, "#=RF", 4) == 0) { fmt = MSAFILE_SELEX; goto DONE; } if (strncmp(buf, "///", 3) == 0 || strncmp(buf, "ENTRY ", 6) == 0) { fmt = SQFILE_PIR; goto DONE; } /* a ha, diagnostic of an (old) MSF file */ if ((strstr(buf, "..") != NULL) && (strstr(buf, "MSF:") != NULL) && (strstr(buf, "Check:")!= NULL)) { fmt = MSAFILE_MSF; goto DONE; } /* unaligned GCG (must follow MSF test!) */ if (strstr(buf, " Check: ") != NULL && strstr(buf, "..") != NULL) { fmt = SQFILE_GCG; goto DONE; } if (strncmp(buf,"LOCUS ",6) == 0 || strncmp(buf,"ORIGIN ",6) == 0) { fmt = SQFILE_GENBANK; goto DONE; } if (strncmp(buf,"ID ",5) == 0 || strncmp(buf,"SQ ",5) == 0) { fmt = SQFILE_EMBL; goto DONE; } /* But past here, we're being desperate. A simple SELEX file is * very difficult to detect; we can only try to disprove it. */ s = buf; if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; /* skip blank lines */ if (strchr("#%", *s1) != NULL) continue; /* skip comment lines */ /* Disproof 1. Noncomment, nonblank lines in a SELEX file * must have at least two space-delimited fields (name/seq) */ if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) has_junk = TRUE; /* Disproof 2. * The sequence field should look like a sequence. */ if (s2 != NULL && Seqtype(s2) == kOtherSeq) has_junk = TRUE; ndataline++; if (ndataline == 300) break; /* only look at first 300 lines */ } if (ndataline == 0) Die("Sequence file contains no data"); /* If we've made it this far, we've run out of data, but there * was at least one line of it; check if we've * disproven SELEX. If not, cross our fingers, pray, and guess SELEX. */ if (has_junk == TRUE) fmt = SQFILE_UNKNOWN; else fmt = MSAFILE_SELEX; DONE: if (buf != NULL) free(buf); rewind(fp); return fmt; } /* Function: GCGBinaryToSequence() * * Purpose: Convert a GCG 2BIT binary string to DNA sequence. * 0 = C 1 = T 2 = A 3 = G * 4 nts/byte * * Args: seq - binary sequence. Converted in place to DNA. * len - length of DNA. binary is (len+3)/4 bytes */ int GCGBinaryToSequence(char *seq, int len) { int bpos; /* position in binary */ int spos; /* position in sequence */ char twobit; int i; for (bpos = (len-1)/4; bpos >= 0; bpos--) { twobit = seq[bpos]; spos = bpos*4; for (i = 3; i >= 0; i--) { switch (twobit & 0x3) { case 0: seq[spos+i] = 'C'; break; case 1: seq[spos+i] = 'T'; break; case 2: seq[spos+i] = 'A'; break; case 3: seq[spos+i] = 'G'; break; } twobit = twobit >> 2; } } seq[len] = '\0'; return 1; } /* Function: GCGchecksum() * Date: SRE, Mon May 31 11:13:21 1999 [St. Louis] * * Purpose: Calculate a GCG checksum for a sequence. * Code provided by Steve Smith of Genetics * Computer Group. * * Args: seq - sequence to calculate checksum for. * may contain gap symbols. * len - length of sequence (usually known, * so save a strlen() call) * * Returns: GCG checksum. */ int GCGchecksum(char *seq, int len) { int i; /* position in sequence */ int chk = 0; /* calculated checksum */ for (i = 0; i < len; i++) chk = (chk + (i % 57 + 1) * (sre_toupper((int) seq[i]))) % 10000; return chk; } /* Function: GCGMultchecksum() * * Purpose: GCG checksum for a multiple alignment: sum of * individual sequence checksums (including their * gap characters) modulo 10000. * * Implemented using spec provided by Steve Smith of * Genetics Computer Group. * * Args: seqs - sequences to be checksummed; aligned or not * nseq - number of sequences * * Return: the checksum, a number between 0 and 9999 */ int GCGMultchecksum(char **seqs, int nseq) { int chk = 0; int idx; for (idx = 0; idx < nseq; idx++) chk = (chk + GCGchecksum(seqs[idx], strlen(seqs[idx]))) % 10000; return chk; } /* Function: Seqtype() * * Purpose: Returns a (very good) guess about type of sequence: * kDNA, kRNA, kAmino, or kOtherSeq. * * Modified from, and replaces, Gilbert getseqtype(). */ int Seqtype(char *seq) { int saw; /* how many non-gap characters I saw */ char c; int po = 0; /* count of protein-only */ int nt = 0; /* count of t's */ int nu = 0; /* count of u's */ int na = 0; /* count of nucleotides */ int aa = 0; /* count of amino acids */ int no = 0; /* count of others */ /* Look at the first 300 non-gap characters */ for (saw = 0; *seq != '\0' && saw < 300; seq++) { c = sre_toupper((int) *seq); if (! isgap(c)) { if (strchr(protonly, c)) po++; else if (strchr(primenuc,c)) { na++; if (c == 'T') nt++; else if (c == 'U') nu++; } else if (strchr(aminos,c)) aa++; else if (isalpha((int) c)) no++; saw++; } } if (no > 0) return kOtherSeq; else if (po > 0) return kAmino; else if (na > aa) { if (nu > nt) return kRNA; else return kDNA; } else return kAmino; /* ooooh. risky. */ } /* Function: GuessAlignmentSeqtype() * Date: SRE, Wed Jul 7 09:42:34 1999 [St. Louis] * * Purpose: Try to guess whether an alignment is protein * or nucleic acid; return a code for the * type (kRNA, kDNA, or kAmino). * * Args: aseq - array of aligned sequences. (Could also * be an rseq unaligned sequence array) * nseq - number of aseqs * * Returns: kRNA, kDNA, kAmino; * kOtherSeq if inconsistency is detected. */ int GuessAlignmentSeqtype(char **aseq, int nseq) { int idx; int nrna = 0; int ndna = 0; int namino = 0; int nother = 0; for (idx = 0; idx < nseq; idx++) switch (Seqtype(aseq[idx])) { case kRNA: nrna++; break; case kDNA: ndna++; break; case kAmino: namino++; break; default: nother++; } /* Unambiguous decisions: */ if (nother) return kOtherSeq; if (namino == nseq) return kAmino; if (ndna == nseq) return kDNA; if (nrna == nseq) return kRNA; /* Ambiguous decisions: */ if (namino == 0) return kRNA; /* it's nucleic acid, but seems mixed RNA/DNA */ return kAmino; /* some amino acid seen; others probably short seqs, some of which may be entirely ACGT (ala,cys,gly,thr). We could be a little more sophisticated: U would be a giveaway that we're not in protein seqs */ } /* Function: WriteSimpleFASTA() * Date: SRE, Tue Nov 16 18:06:00 1999 [St. Louis] * * Purpose: Just write a FASTA format sequence to a file; * minimal interface, mostly for quick and dirty programs. * * Args: fp - open file handle (stdout, possibly) * seq - sequence to output * name - name for the sequence * desc - optional description line, or NULL. * * Returns: void */ void WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc) { char buf[61]; int len; int pos; len = strlen(seq); buf[60] = '\0'; fprintf(fp, ">%s %s\n", name, desc != NULL ? desc : ""); for (pos = 0; pos < len; pos += 60) { strncpy(buf, seq+pos, 60); fprintf(fp, "%s\n", buf); } } int WriteSeq(FILE *outf, int outform, char *seq, SQINFO *sqinfo) { int numline = 0; int lines = 0, spacer = 0, width = 50, tab = 0; int i, j, l, l1, ibase; char endstr[10]; char s[100]; /* buffer for sequence */ char ss[100]; /* buffer for structure */ int checksum = 0; int seqlen; int which_case; /* 0 = do nothing. 1 = upper case. 2 = lower case */ int dostruc; /* TRUE to print structure lines*/ which_case = 0; dostruc = FALSE; seqlen = (sqinfo->flags & SQINFO_LEN) ? sqinfo->len : strlen(seq); if (IsAlignmentFormat(outform)) Die("Tried to write an aligned format with WriteSeq() -- bad, bad."); strcpy( endstr,""); l1 = 0; checksum = GCGchecksum(seq, seqlen); switch (outform) { case SQFILE_UNKNOWN: /* no header, just sequence */ strcpy(endstr,"\n"); /* end w/ extra blank line */ break; case SQFILE_GENBANK: fprintf(outf,"LOCUS %s %d bp\n", sqinfo->name, seqlen); fprintf(outf,"ACCESSION %s\n", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "."); fprintf(outf,"DEFINITION %s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "."); fprintf(outf,"VERSION %s\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : "."); fprintf(outf,"ORIGIN \n"); spacer = 11; numline = 1; strcpy(endstr, "\n//"); break; case SQFILE_GCGDATA: fprintf(outf, ">>>>%s 9/95 ASCII Len: %d\n", sqinfo->name, seqlen); fprintf(outf, "%s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-"); break; case SQFILE_PIR: fprintf(outf, "ENTRY %s\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name); fprintf(outf, "TITLE %s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-"); fprintf(outf, "ACCESSION %s\n", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-"); fprintf(outf, "SUMMARY #Length %d #Checksum %d\n", sqinfo->len, checksum); fprintf(outf, "SEQUENCE\n"); fprintf(outf, " 5 10 15 20 25 30\n"); spacer = 2; /* spaces after every residue */ numline = 1; /* number lines w/ coords */ width = 30; /* 30 aa per line */ strcpy(endstr, "\n///"); break; case SQFILE_SQUID: fprintf(outf, "NAM %s\n", sqinfo->name); if (sqinfo->flags & (SQINFO_ID | SQINFO_ACC | SQINFO_START | SQINFO_STOP | SQINFO_OLEN)) fprintf(outf, "SRC %s %s %d..%d::%d\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : "-", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-", (sqinfo->flags & SQINFO_START) ? sqinfo->start : 0, (sqinfo->flags & SQINFO_STOP) ? sqinfo->stop : 0, (sqinfo->flags & SQINFO_OLEN) ? sqinfo->olen : 0); if (sqinfo->flags & SQINFO_DESC) fprintf(outf, "DES %s\n", sqinfo->desc); if (sqinfo->flags & SQINFO_SS) { fprintf(outf, "SEQ +SS\n"); dostruc = TRUE; /* print structure lines too */ } else fprintf(outf, "SEQ\n"); numline = 1; /* number seq lines w/ coords */ strcpy(endstr, "\n++"); break; case SQFILE_EMBL: fprintf(outf,"ID %s\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name); fprintf(outf,"AC %s\n", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-"); fprintf(outf,"DE %s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-"); fprintf(outf,"SQ %d BP\n", seqlen); strcpy(endstr, "\n//"); /* 11Oct90: bug fix*/ tab = 5; /** added 31jan91 */ spacer = 11; /** added 31jan91 */ break; case SQFILE_GCG: fprintf(outf,"%s\n", sqinfo->name); if (sqinfo->flags & SQINFO_ACC) fprintf(outf,"ACCESSION %s\n", sqinfo->acc); if (sqinfo->flags & SQINFO_DESC) fprintf(outf,"DEFINITION %s\n", sqinfo->desc); fprintf(outf," %s Length: %d (today) Check: %d ..\n", sqinfo->name, seqlen, checksum); spacer = 11; numline = 1; strcpy(endstr, "\n"); /* this is insurance to help prevent misreads at eof */ break; case SQFILE_STRIDER: /* ?? map ?*/ fprintf(outf,"; ### from DNA Strider ;-)\n"); fprintf(outf,"; DNA sequence %s, %d bases, %d checksum.\n;\n", sqinfo->name, seqlen, checksum); strcpy(endstr, "\n//"); break; /* SRE: Don had Zuker default to Pearson, which is not intuitive or helpful, since Zuker's MFOLD can't read Pearson format. More useful to use kIG */ case SQFILE_ZUKER: which_case = 1; /* MFOLD requires upper case. */ /*FALLTHRU*/ case SQFILE_IG: fprintf(outf,";%s %s\n", sqinfo->name, (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : ""); fprintf(outf,"%s\n", sqinfo->name); strcpy(endstr,"1"); /* == linear dna */ break; case SQFILE_RAW: /* Raw: no header at all. */ break; default : case SQFILE_FASTA: fprintf(outf,">%s %s\n", sqinfo->name, (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : ""); break; } if (which_case == 1) s2upper(seq); if (which_case == 2) s2lower(seq); width = MIN(width,100); for (i=0, l=0, ibase = 1, lines = 0; i < seqlen; ) { if (l1 < 0) l1 = 0; else if (l1 == 0) { if (numline) fprintf(outf,"%8d ",ibase); for (j=0; jflags & SQINFO_SS) ? sqinfo->ss[i] : '.'; l++; i++; l1++; /* don't count spaces for width*/ if (l1 == width || i == seqlen) { s[l] = ss[l] = '\0'; l = 0; l1 = 0; if (dostruc) { fprintf(outf, "%s\n", s); if (numline) fprintf(outf," "); for (j=0; jformat, &rseqs[num], &(sqinfo[num]))) { num++; if (num == numalloced) /* more seqs coming, alloc more room */ { numalloced += 16; rseqs = (char **) ReallocOrDie (rseqs, numalloced*sizeof(char *)); sqinfo = (SQINFO *) ReallocOrDie (sqinfo, numalloced * sizeof(SQINFO)); } } SeqfileClose(dbfp); *ret_rseqs = rseqs; *ret_sqinfo = sqinfo; *ret_num = num; return 1; } /* Function: String2SeqfileFormat() * Date: SRE, Sun Jun 27 15:25:54 1999 [TW 723 over Canadian Shield] * * Purpose: Convert a string (e.g. from command line option arg) * to a format code. Case insensitive. Return * MSAFILE_UNKNOWN/SQFILE_UNKNOWN if string is bad. * Uses codes defined in squid.h (unaligned formats) and * msa.h (aligned formats). * * Args: s - string to convert; e.g. "stockholm" * * Returns: format code; e.g. MSAFILE_STOCKHOLM. * Returns SQFILE_UNKNOWN (same as MSAFILE_UNKNOWN) if string is * not valid. */ int String2SeqfileFormat(char *s) { char *s2; int code = SQFILE_UNKNOWN; if (s == NULL) return SQFILE_UNKNOWN; s2 = sre_strdup(s, -1); s2upper(s2); if (strcmp(s2, "FASTA") == 0) code = SQFILE_FASTA; else if (strcmp(s2, "GENBANK") == 0) code = SQFILE_GENBANK; else if (strcmp(s2, "EMBL") == 0) code = SQFILE_EMBL; else if (strcmp(s2, "GCG") == 0) code = SQFILE_GCG; else if (strcmp(s2, "GCGDATA") == 0) code = SQFILE_GCGDATA; else if (strcmp(s2, "RAW") == 0) code = SQFILE_RAW; else if (strcmp(s2, "IG") == 0) code = SQFILE_IG; else if (strcmp(s2, "STRIDER") == 0) code = SQFILE_STRIDER; else if (strcmp(s2, "IDRAW") == 0) code = SQFILE_IDRAW; else if (strcmp(s2, "ZUKER") == 0) code = SQFILE_ZUKER; else if (strcmp(s2, "PIR") == 0) code = SQFILE_PIR; else if (strcmp(s2, "SQUID") == 0) code = SQFILE_SQUID; else if (strcmp(s2, "STOCKHOLM") == 0) code = MSAFILE_STOCKHOLM; else if (strcmp(s2, "SELEX") == 0) code = MSAFILE_SELEX; else if (strcmp(s2, "MSF") == 0) code = MSAFILE_MSF; else if (strcmp(s2, "CLUSTAL") == 0) code = MSAFILE_CLUSTAL; else if (strcmp(s2, "A2M") == 0) code = MSAFILE_A2M; else if (strcmp(s2, "PHYLIP") == 0) code = MSAFILE_PHYLIP; else if (strcmp(s2, "EPS") == 0) code = MSAFILE_EPS; free(s2); return code; } char * SeqfileFormat2String(int code) { switch (code) { case SQFILE_UNKNOWN: return "unknown"; case SQFILE_FASTA: return "FASTA"; case SQFILE_GENBANK: return "Genbank"; case SQFILE_EMBL: return "EMBL"; case SQFILE_GCG: return "GCG"; case SQFILE_GCGDATA: return "GCG data library"; case SQFILE_RAW: return "raw"; case SQFILE_IG: return "Intelligenetics"; case SQFILE_STRIDER: return "MacStrider"; case SQFILE_IDRAW: return "Idraw Postscript"; case SQFILE_ZUKER: return "Zuker"; case SQFILE_PIR: return "PIR"; case SQFILE_SQUID: return "SQUID"; case MSAFILE_STOCKHOLM: return "Stockholm"; case MSAFILE_SELEX: return "SELEX"; case MSAFILE_MSF: return "MSF"; case MSAFILE_CLUSTAL: return "Clustal"; case MSAFILE_A2M: return "a2m"; case MSAFILE_PHYLIP: return "Phylip"; case MSAFILE_EPS: return "EPS"; default: Die("Bad code passed to MSAFormat2String()"); } /*NOTREACHED*/ return NULL; } /* Function: MSAToSqinfo() * Date: SRE, Tue Jul 20 14:36:56 1999 [St. Louis] * * Purpose: Take an MSA and generate a SQINFO array suitable * for use in annotating the unaligned sequences. * Return the array. * * Permanent temporary code. sqinfo was poorly designed. * it must eventually be replaced, but the odds * of this happening soon are nil, so I have to deal. * * Args: msa - the alignment * * Returns: ptr to allocated sqinfo array. * Freeing is ghastly: free in each individual sqinfo[i] * with FreeSequence(NULL, &(sqinfo[i])), then * free(sqinfo). */ SQINFO * MSAToSqinfo(MSA *msa) { int idx; SQINFO *sqinfo; sqinfo = MallocOrDie(sizeof(SQINFO) * msa->nseq); for (idx = 0; idx < msa->nseq; idx++) { sqinfo[idx].flags = 0; SetSeqinfoString(&(sqinfo[idx]), msa->sqname[idx], SQINFO_NAME); SetSeqinfoString(&(sqinfo[idx]), MSAGetSeqAccession(msa, idx), SQINFO_ACC); SetSeqinfoString(&(sqinfo[idx]), MSAGetSeqDescription(msa, idx), SQINFO_DESC); if (msa->ss != NULL && msa->ss[idx] != NULL) { MakeDealignedString(msa->aseq[idx], msa->alen, msa->ss[idx], &(sqinfo[idx].ss)); sqinfo[idx].flags |= SQINFO_SS; } if (msa->sa != NULL && msa->sa[idx] != NULL) { MakeDealignedString(msa->aseq[idx], msa->alen, msa->sa[idx], &(sqinfo[idx].sa)); sqinfo[idx].flags |= SQINFO_SA; } sqinfo[idx].len = DealignedLength(msa->aseq[idx]); sqinfo[idx].flags |= SQINFO_LEN; } return sqinfo; } /* cc -o sqio_test -DA_QUIET_DAY -L. sqio.c -lsquid */ #ifdef A_QUIET_DAY #include "ssi.h" int main(int argc, char **argv) { FILE *fp; char *filename; char *buf; int len; int mode = 3; SSIOFFSET off; filename = argv[1]; if (mode == 1) { buf = malloc(sizeof(char) * 256); if ((fp = fopen(filename, "r")) == NULL) Die("open of %s failed", filename); while (fgets(buf, 255, fp) != NULL) ; fclose(fp); free(buf); } else if (mode == 2) { if ((fp = fopen(filename, "r")) == NULL) Die("open of %s failed", filename); buf = NULL; len = 0; while (sre_fgets(&buf, &len, fp) != NULL) SSIGetFilePosition(fp, SSI_OFFSET_I32, &off); fclose(fp); free(buf); } else if (mode == 3) { SQFILE *dbfp; SQINFO info; if ((dbfp = SeqfileOpen(filename, SQFILE_FASTA, NULL)) == NULL) Die("open of %s failed", filename); while (ReadSeq(dbfp, dbfp->format, &buf, &info)) { SSIGetFilePosition(dbfp->f, SSI_OFFSET_I32, &off); FreeSequence(buf, &info); } SeqfileClose(dbfp); } } #endif squid/squidcore.c0000640000175000017520000000313310463223377014255 0ustar naolivbiolinux/************************************************************ * @LICENSE@ ************************************************************/ /* squidcore.c * SRE, Sun Jun 20 17:19:04 1999 [Graeme's kitchen] * * Core functions for SQUID library. * CVS $Id: squidcore.c,v 1.4 2003/09/27 20:31:15 eddy Exp $ */ #include "squidconf.h" #include "squid.h" #include /* Function: SqdBanner() * Date: SRE, Sun Jun 20 17:19:41 1999 [Graeme's kitchen] * * Purpose: Print a package version and copyright banner. * Used by all the main()'s in squid. * * Expects to be able to pick up preprocessor #define's from squidconf.h: * symbol example * ------ -------------- * SQUID_VERSION "2.0.42" * SQUID_DATE "April 1999" * SQUID_COPYRIGHT "Copyright (C) 1992-1999 Washington University School of Medicine" * SQUID_LICENSE "Freely distributed under the GNU General Public License (GPL)." * * This gives us a general mechanism to update release information * without changing multiple points in the code. * * Args: fp - where to print it * banner - one-line program description, e.g.: * "foobar - make bars from foo with elan" * Returns: (void) */ void SqdBanner(FILE *fp, char *banner) { fprintf(fp, "%s\n", banner); fprintf(fp, "SQUID %s (%s)\n", SQUID_VERSION, SQUID_DATE); fprintf(fp, "%s\n", SQUID_COPYRIGHT); fprintf(fp, "%s\n", SQUID_LICENSE); fprintf(fp, "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n"); } squid/sre_ctype.c0000640000175000017520000000110410463223377014250 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sre_ctype.c * * For portability. Some systems have functions tolower, toupper * as macros (for instance, MIPS M-2000 RISC/os!) * * CVS $Id: sre_ctype.c,v 1.4 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include "squid.h" int sre_tolower(int c) { if (isupper(c)) return tolower(c); else return c; } int sre_toupper(int c) { if (islower(c)) return toupper(c); else return c; } squid/sre_math.c0000640000175000017520000001030510463223377014060 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sre_math.c * * Portability for and extensions to C math library. * RCS $Id: sre_math.c,v 1.16 2005/01/21 16:36:58 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" /* Function: Linefit() * * Purpose: Given points x[0..N-1] and y[0..N-1], fit to * a straight line y = a + bx. * a, b, and the linear correlation coefficient r * are filled in for return. * * Args: x - x values of data * y - y values of data * N - number of data points * ret_a - RETURN: intercept * ret_b - RETURN: slope * ret_r - RETURN: correlation coefficient * * Return: 1 on success, 0 on failure. */ int Linefit(float *x, float *y, int N, float *ret_a, float *ret_b, float *ret_r) { float xavg, yavg; float sxx, syy, sxy; int i; /* Calculate averages, xavg and yavg */ xavg = yavg = 0.0; for (i = 0; i < N; i++) { xavg += x[i]; yavg += y[i]; } xavg /= (float) N; yavg /= (float) N; sxx = syy = sxy = 0.0; for (i = 0; i < N; i++) { sxx += (x[i] - xavg) * (x[i] - xavg); syy += (y[i] - yavg) * (y[i] - xavg); sxy += (x[i] - xavg) * (y[i] - yavg); } *ret_b = sxy / sxx; *ret_a = yavg - xavg*(*ret_b); *ret_r = sxy / (sqrt(sxx) * sqrt(syy)); return 1; } /* Function: WeightedLinefit() * * Purpose: Given points x[0..N-1] and y[0..N-1] with * variances (measurement errors) var[0..N-1], * fit to a straight line y = mx + b. * * Method: Algorithm from Numerical Recipes in C, [Press88]. * * Return: (void) * ret_m contains slope; ret_b contains intercept */ void WeightedLinefit(float *x, float *y, float *var, int N, float *ret_m, float *ret_b) { int i; double s; double sx, sy; double sxx, sxy; double delta; double m, b; s = sx = sy = sxx = sxy = 0.; for (i = 0; i < N; i++) { s += 1./var[i]; sx += x[i] / var[i]; sy += y[i] / var[i]; sxx += x[i] * x[i] / var[i]; sxy += x[i] * y[i] / var[i]; } delta = s * sxx - (sx * sx); b = (sxx * sy - sx * sxy) / delta; m = (s * sxy - sx * sy) / delta; *ret_m = m; *ret_b = b; } /* 2D matrix operations */ float ** FMX2Alloc(int rows, int cols) { float **mx; int r; mx = (float **) MallocOrDie(sizeof(float *) * rows); mx[0] = (float *) MallocOrDie(sizeof(float) * rows * cols); for (r = 1; r < rows; r++) mx[r] = mx[0] + r*cols; return mx; } void FMX2Free(float **mx) { free(mx[0]); free(mx); } double ** DMX2Alloc(int rows, int cols) { double **mx; int r; mx = (double **) MallocOrDie(sizeof(double *) * rows); mx[0] = (double *) MallocOrDie(sizeof(double) * rows * cols); for (r = 1; r < rows; r++) mx[r] = mx[0] + r*cols; return mx; } void DMX2Free(double **mx) { free(mx[0]); free(mx); } /* Function: FMX2Multiply() * * Purpose: Matrix multiplication. * Multiply an m x p matrix A by a p x n matrix B, * giving an m x n matrix C. * Matrix C must be a preallocated matrix of the right * size. */ void FMX2Multiply(float **A, float **B, float **C, int m, int p, int n) { int i, j, k; for (i = 0; i < m; i++) for (j = 0; j < n; j++) { C[i][j] = 0.; for (k = 0; k < p; k++) C[i][j] += A[i][k] * B[k][j]; } } /* Function: FMX2Copy() * Incept: LSJ 14 Oct 2003 * incorp of HMMER eweights code; * SRE, Thu May 20 11:27:05 2004 [St. Louis] * * Purpose: Copy mx_src to mx_dest. * mx_src is m x n (rows x columns). * mx_dest is too, and must already be allocated. * * Args: mx_dest - new copy * mx_src - matrix to be copied * * Returns: (void) */ void FMX2Copy(float **mx_dest, float **mx_src, int m, int n) { int row; for (row = 0; row < m; row++) FCopy(mx_dest[row], mx_src[row], n); return; } squid/sre_random.c0000644000175000017520000002323210463223377014416 0ustar naolivbiolinux/* sre_random.c * * Portable random number generator, and sampling routines. * * SRE, Tue Oct 1 15:24:11 2002 [St. Louis] * CVS $Id: sre_random.c,v 1.4 2004/07/01 16:44:45 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "sre_random.h" static int sre_randseed = 42; /* default seed for sre_random() */ /* Function: sre_random() * * Purpose: Return a uniform deviate x, 0.0 <= x < 1.0. * * sre_randseed is a static variable, set * by sre_srandom(). When it is non-zero, * we re-seed. * * Implements L'Ecuyer's algorithm for combining output * of two linear congruential generators, plus a Bays-Durham * shuffle. This is essentially ran2() from Numerical Recipes, * sans their nonhelpful Rand/McNally-esque code obfuscation. * * Overflow errors are avoided by Schrage's algorithm: * az % m = a(z%q) - r(z/q) (+m if <0) * where q=m/a, r=m%a * * Requires that long int's have at least 32 bits. * This function uses statics and is NOT THREADSAFE. * * Reference: Press et al. Numerical Recipes in C, 1992. * * Reliable and portable, but slow. Benchmarks on wrasse, * using Linux gcc and Linux glibc rand() (see randspeed, in Testsuite): * sre_random(): 0.5 usec/call * rand(): 0.2 usec/call */ double sre_random(void) { static long rnd1; /* random number from LCG1 */ static long rnd2; /* random number from LCG2 */ static long rnd; /* random number we return */ static long tbl[64]; /* table for Bays/Durham shuffle */ long x,y; int i; /* Magic numbers a1,m1, a2,m2 from L'Ecuyer, for 2 LCGs. * q,r derive from them (q=m/a, r=m%a) and are needed for Schrage's algorithm. */ long a1 = 40014; long m1 = 2147483563; long q1 = 53668; long r1 = 12211; long a2 = 40692; long m2 = 2147483399; long q2 = 52774; long r2 = 3791; if (sre_randseed > 0) { rnd1 = sre_randseed; rnd2 = sre_randseed; /* Fill the table for Bays/Durham */ for (i = 0; i < 64; i++) { x = a1*(rnd1%q1); /* LCG1 in action... */ y = r1*(rnd1/q1); rnd1 = x-y; if (rnd1 < 0) rnd1 += m1; x = a2*(rnd2%q2); /* LCG2 in action... */ y = r2*(rnd2/q2); rnd2 = x-y; if (rnd2 < 0) rnd2 += m2; tbl[i] = rnd1-rnd2; if (tbl[i] < 0) tbl[i] += m1; } sre_randseed = 0; /* drop the flag. */ }/* end of initialization*/ x = a1*(rnd1%q1); /* LCG1 in action... */ y = r1*(rnd1/q1); rnd1 = x-y; if (rnd1 < 0) rnd1 += m1; x = a2*(rnd2%q2); /* LCG2 in action... */ y = r2*(rnd2/q2); rnd2 = x-y; if (rnd2 < 0) rnd2 += m2; /* Choose our random number from the table... */ i = (int) (((double) rnd / (double) m1) * 64.); rnd = tbl[i]; /* and replace with a new number by L'Ecuyer. */ tbl[i] = rnd1-rnd2; if (tbl[i] < 0) tbl[i] += m1; return ((double) rnd / (double) m1); } /* Function: sre_srandom() * * Purpose: Initialize with a random seed. Seed must be * >= 0 to work; we silently enforce this. */ void sre_srandom(int seed) { int burnin = 7; if (seed < 0) seed = -1 * seed; if (seed == 0) seed = 42; sre_randseed = seed; /* we observe that the first random number * isn't very random, with closely spaced seeds, like what * we get with using time(). * So, "burn in" the random chain. */ while (burnin--) sre_random(); } /* Function: sre_random_positive() * Date: SRE, Wed Apr 17 13:34:32 2002 [St. Louis] * * Purpose: Assure 0 < x < 1 (positive uniform deviate) */ double sre_random_positive(void) { double x; do { x = sre_random(); } while (x == 0.0); return x; } /* Function: ExponentialRandom() * Date: SRE, Mon Sep 6 21:24:29 1999 [St. Louis] * * Purpose: Pick an exponentially distributed random variable * 0 > x >= infinity * * Args: (void) * * Returns: x */ double ExponentialRandom(void) { return -log(sre_random_positive()); } /* Function: Gaussrandom() * * Pick a Gaussian-distributed random variable * with some mean and standard deviation, and * return it. * * Based on RANLIB.c public domain implementation. * Thanks to the authors, Barry W. Brown and James Lovato, * University of Texas, M.D. Anderson Cancer Center, Houston TX. * Their implementation is from Ahrens and Dieter, "Extensions * of Forsythe's method for random sampling from the normal * distribution", Math. Comput. 27:927-937 (1973). * * Impenetrability of the code is to be blamed on its FORTRAN/f2c lineage. * */ double Gaussrandom(double mean, double stddev) { static double a[32] = { 0.0,3.917609E-2,7.841241E-2,0.11777,0.1573107,0.1970991,0.2372021,0.2776904, 0.3186394,0.36013,0.4022501,0.4450965,0.4887764,0.5334097,0.5791322, 0.626099,0.6744898,0.7245144,0.7764218,0.8305109,0.8871466,0.9467818, 1.00999,1.077516,1.150349,1.229859,1.318011,1.417797,1.534121,1.67594, 1.862732,2.153875 }; static double d[31] = { 0.0,0.0,0.0,0.0,0.0,0.2636843,0.2425085,0.2255674,0.2116342,0.1999243, 0.1899108,0.1812252,0.1736014,0.1668419,0.1607967,0.1553497,0.1504094, 0.1459026,0.14177,0.1379632,0.1344418,0.1311722,0.128126,0.1252791, 0.1226109,0.1201036,0.1177417,0.1155119,0.1134023,0.1114027,0.1095039 }; static double t[31] = { 7.673828E-4,2.30687E-3,3.860618E-3,5.438454E-3,7.0507E-3,8.708396E-3, 1.042357E-2,1.220953E-2,1.408125E-2,1.605579E-2,1.81529E-2,2.039573E-2, 2.281177E-2,2.543407E-2,2.830296E-2,3.146822E-2,3.499233E-2,3.895483E-2, 4.345878E-2,4.864035E-2,5.468334E-2,6.184222E-2,7.047983E-2,8.113195E-2, 9.462444E-2,0.1123001,0.136498,0.1716886,0.2276241,0.330498,0.5847031 }; static double h[31] = { 3.920617E-2,3.932705E-2,3.951E-2,3.975703E-2,4.007093E-2,4.045533E-2, 4.091481E-2,4.145507E-2,4.208311E-2,4.280748E-2,4.363863E-2,4.458932E-2, 4.567523E-2,4.691571E-2,4.833487E-2,4.996298E-2,5.183859E-2,5.401138E-2, 5.654656E-2,5.95313E-2,6.308489E-2,6.737503E-2,7.264544E-2,7.926471E-2, 8.781922E-2,9.930398E-2,0.11556,0.1404344,0.1836142,0.2790016,0.7010474 }; static long i; static double snorm,u,s,ustar,aa,w,y,tt; u = sre_random(); s = 0.0; if(u > 0.5) s = 1.0; u += (u-s); u = 32.0*u; i = (long) (u); if(i == 32) i = 31; if(i == 0) goto S100; /* * START CENTER */ ustar = u-(double)i; aa = *(a+i-1); S40: if(ustar <= *(t+i-1)) goto S60; w = (ustar-*(t+i-1))**(h+i-1); S50: /* * EXIT (BOTH CASES) */ y = aa+w; snorm = y; if(s == 1.0) snorm = -y; return (stddev*snorm + mean); S60: /* * CENTER CONTINUED */ u = sre_random(); w = u*(*(a+i)-aa); tt = (0.5*w+aa)*w; goto S80; S70: tt = u; ustar = sre_random(); S80: if(ustar > tt) goto S50; u = sre_random(); if(ustar >= u) goto S70; ustar = sre_random(); goto S40; S100: /* * START TAIL */ i = 6; aa = *(a+31); goto S120; S110: aa += *(d+i-1); i += 1; S120: u += u; if(u < 1.0) goto S110; u -= 1.0; S140: w = u**(d+i-1); tt = (0.5*w+aa)*w; goto S160; S150: tt = u; S160: ustar = sre_random(); if(ustar > tt) goto S50; u = sre_random(); if(ustar >= u) goto S150; u = sre_random(); goto S140; } /* Functions: DChoose(), FChoose() * * Purpose: Make a random choice from a normalized distribution. * DChoose() is for double-precision vectors; * FChoose() is for single-precision float vectors. * Returns the number of the choice. * * Limitation: * All p's must be >> FLT_EPSILON/DBL_EPSILON. */ int DChoose(double *p, int N) { double roll; /* random fraction */ double sum; /* integrated prob */ int i; /* counter over the probs */ roll = sre_random(); sum = 0.0; for (i = 0; i < N; i++) { sum += p[i]; if (roll < sum) return i; } /* See comment on this next line in FChoose() */ do { i = (int) (sre_random() * N); } while (p[i] == 0.); return i; } int FChoose(float *p, int N) { float roll; /* random fraction */ float sum; /* integrated prob */ int i; /* counter over the probs */ roll = sre_random(); sum = 0.0; for (i = 0; i < N; i++) { sum += p[i]; if (roll < sum) return i; } /* Very rarely, because of machine floating point representation, * our roll is "impossibly" >= total sum, even though any roll of * sre_random() is < 1.0 and the total sum is supposed to be 1.0 by * definition. This can happen when the total_sum is not really 1.0, * but something just less than that in the machine representation, * and the roll happens to also be very very close to 1. I have not * examined this analytically. Empirically, it occurs at a frequency * of about 1/10^8, as measured for bug #sq5. To work around, choose * one of the *nonzero* p[i]'s at random. (If you chooose *any* * p[i] you get bug #sq5; routines like StrMarkov0() fail because * they choose impossible residues.) */ do { i = (int) (sre_random() * N); } while (p[i] == 0.); return i; } /* SampleCountvector(): * Given a probability vector of dimensionality K, sample * ctot counts and store them in the count vector c. * c is K-dimensional and allocated by the caller. */ void SampleCountvector(double *p, int K, int ctot, double *c) { int i; for (i = 0; i < K; i++) c[i] = 0.; for (i = 0; i < ctot; i++) c[DChoose(p,K)] += 1.; } /***************************************************************** * @LICENSE@ *****************************************************************/ squid/sre_stack.c0000644000175000017520000002447310463223377014253 0ustar naolivbiolinux/* sre_stack.c * SRE 1 March 2000 [Seattle] * * Implementations of pushdown stacks. * nstack - integer storage * cstack - character storage * mstack - arbitrary object (pointer) storage. * * Stacks are kept as growable arrays. A stack's memory is * grown when necessary by adding some block size. The * initial allocation and the block size are set to 100 * by default. The block size can be changed by the caller. * ***************************************************************** * * Basic API (using nstack as an example): * * say I want to push the numbers 42, 7, and 3 onto a stack, * then pop them off and print them: * * #include "sre_stack.h" * * Nstack_t *ns; * int x; * * ns = CreateNstack(); * PushNstack(ns, 42); * PushNstack(ns, 7); * PushNstack(ns, 3); * while (PopNstack(ns, &x)) * printf("%d\n", x); * FreeNstack(ns); * * Diagnostics: * CreateNstack() returns NULL on an allocation failure. * PushNstack() returns 0 on an allocation failure, else 1. * PopNstack() returns 0 when the stack is empty, else 1. * * Other functions: * NstackIsEmpty(ns) : returns TRUE if stack is empty, else FALSE. * NstackSetBlocksize(ns) : change the chunk size for reallocation to * something other than the default 100. * * mstack's API is essentially identical, with a void *obj in place * of int x; except that PopMstack returns the pointer to the stored * object, or NULL if the stack is empty. * * cstack has a special function, CstackString(), which converts * the stack into a nul-terminated string, and destroys the stack * (so FreeCstack() is unnecessary). This is useful when using cstack * functions to create a growing string. Caller then frees the * string as normal -- free(s). * * CVS $Id: sre_stack.c,v 1.4 2003/10/27 21:08:13 eddy Exp $ */ #include #include #include #include "sre_stack.h" Nstack_t * CreateNstack(void) { Nstack_t *ns; ns = malloc(sizeof(Nstack_t)); if (ns == NULL) return NULL; ns->memblock = 100; /* optimize if you want; hardcoded for now */ ns->nalloc = ns->memblock; ns->data = malloc(sizeof(int) * ns->nalloc); if (ns->data == NULL) { free(ns); return NULL; } ns->n = 0; return ns; } int PushNstack(Nstack_t *ns, int x) { int *ptr; if (ns->n == ns->nalloc) { ns->nalloc += ns->memblock; ptr = realloc(ns->data, sizeof(int) * ns->nalloc); if (ptr == NULL) return 0; else ns->data = ptr; } ns->data[ns->n] = x; ns->n++; return 1; } int PopNstack(Nstack_t *ns, int *x) { if (ns->n == 0) {*x = 0; return 0;} ns->n--; *x = ns->data[ns->n]; return 1; } void FreeNstack(Nstack_t *ns) { free(ns->data); free(ns); } int NstackIsEmpty(Nstack_t *ns) { if (ns->n == 0) return 1; else return 0; } void NstackSetBlocksize(Nstack_t *ns, int newsize) { if (newsize > 0) ns->memblock = newsize; } Mstack_t * CreateMstack(void) { Mstack_t *ms; ms = malloc(sizeof(Mstack_t)); if (ms == NULL) return NULL; ms->memblock = 100; /* optimize if you want; hardcoded for now */ ms->nalloc = ms->memblock; ms->data = malloc(sizeof(void *) * ms->nalloc); if (ms->data == NULL) { free(ms); return NULL; } ms->n = 0; return ms; } int PushMstack(Mstack_t *ms, void *object) { void **ptr; if (ms->n == ms->nalloc) { ms->nalloc += ms->memblock; ptr = realloc(ms->data, sizeof(void *) * ms->nalloc); if (ptr == NULL) return 0; else ms->data = ptr; } ms->data[ms->n] = object; ms->n++; return 1; } void * PopMstack(Mstack_t *ms) { if (ms->n == 0) return NULL; ms->n--; return ms->data[ms->n]; } void FreeMstack(Mstack_t *ms) { free(ms->data); free(ms); } int MstackIsEmpty(Mstack_t *ms) { if (ms->n == 0) return 1; else return 0; } void MstackSetBlocksize(Mstack_t *ms, int newsize) { if (newsize > 0) ms->memblock = newsize; } /***************************************************************** * cstack - pushdown stack for storing characters *****************************************************************/ Cstack_t * CreateCstack(void) { Cstack_t *cs; cs = malloc(sizeof(Cstack_t)); if (cs == NULL) return NULL; cs->memblock = 100; /* optimize if you want; hardcoded for now */ cs->nalloc = cs->memblock; cs->data = malloc(sizeof(char) * cs->nalloc); if (cs->data == NULL) { free(cs); return NULL; } cs->n = 0; return cs; } int PushCstack(Cstack_t *cs, char c) { char *ptr; if (cs->n == cs->nalloc) { cs->nalloc += cs->memblock; ptr = realloc(cs->data, sizeof(char) * cs->nalloc); if (ptr == NULL) return 0; else cs->data = ptr; } cs->data[cs->n] = c; cs->n++; return 1; } int PopCstack(Cstack_t *cs, char *ret_c) { if (cs->n == 0) {*ret_c = 0; return 0;} cs->n--; *ret_c = cs->data[cs->n]; return 1; } void FreeCstack(Cstack_t *cs) { free(cs->data); free(cs); } int CstackIsEmpty(Cstack_t *cs) { if (cs->n == 0) return 1; else return 0; } void CstackSetBlocksize(Cstack_t *cs, int newsize) { if (newsize > 0) cs->memblock = newsize; } char * CstackString(Cstack_t *cs) { char *s; if (! PushCstack(cs, '\0')) return NULL; /* nul-terminate the data */ s = cs->data; /* data is already just a string - just return ptr to it */ free(cs); /* free the stack */ return s; } #ifdef SRE_STACK_TESTDRIVE /* Test driver for the pushdown stack module. * To compile: * gcc -g -Wall -DSRE_STACK_TESTDRIVE -o test sre_stack.c * To run: * ./test * Returns 0 (success) w/ no output, or returns 1 and says why. */ int main(void) { Mstack_t *ms; Nstack_t *ns; Cstack_t *cs; int *obj; int x; char c; char *s; int n1, n2; int i; /* Exercises of the mstack functions/API. * * Set the blocksize immediately to 50, so it'll allocate once * for 100, then next for 50 more. Putting 200 on the stack * therefore forces two reallocations after the inital 100 alloc. * * Put 200 "objects" on the stack and pop them off; * do this twice, once with a "while pop" loop, and once * with a "while stack not empty" loop. */ if ((ms = CreateMstack()) == NULL) { fprintf(stderr, "memory allocation failed\n"); return EXIT_FAILURE; } MstackSetBlocksize(ms, 50); n1 = 200; for (i = 0; i < n1; i++) { if ((obj = malloc(sizeof(int) * 64)) == NULL) { fprintf(stderr, "memory allocation failed\n"); return EXIT_FAILURE; } if (! PushMstack(ms, obj)) { fprintf(stderr, "memory allocation failed in PushMstack()\n"); return EXIT_FAILURE; } } n2 = 0; while ((obj = PopMstack(ms)) != NULL) { free(obj); n2++; } if (n1 != n2){ fprintf(stderr, "Put %d objects on; got %d off\n", n1, n2); return EXIT_FAILURE; } for (i = 0; i < n1; i++) { if ((obj = malloc(sizeof(int) * 64)) == NULL) return EXIT_FAILURE; if (! PushMstack(ms, obj)) { fprintf(stderr, "memory allocation failed in PushMstack()\n"); return EXIT_FAILURE; } } n2 = 0; while (! MstackIsEmpty(ms)) { if ((obj = PopMstack(ms)) == NULL) { fprintf(stderr, "pop was NULL\n"); return EXIT_FAILURE; } free(obj); n2++; } if (n1 != n2){ fprintf(stderr, "Put %d objects on; got %d off\n", n1, n2); return EXIT_FAILURE; } FreeMstack(ms); /* Exercise of the nstack functions/API for integer stack - * essentially the same as the mstack exercises above. */ if ((ns = CreateNstack()) == NULL) { fprintf(stderr, "memory allocation failed\n"); return EXIT_FAILURE; } NstackSetBlocksize(ns, 50); n1 = 200; for (i = 0; i < n1; i++) { if (! PushNstack(ns, i)) { fprintf(stderr, "memory allocation failed in PushNstack()\n"); return EXIT_FAILURE; } } n2 = 0; while (PopNstack(ns, &x)) n2++; if (n1 != n2){ fprintf(stderr, "Put %d integers on; got %d off\n", n1, n2); return EXIT_FAILURE; } for (i = 0; i < n1; i++) { if (! PushNstack(ns, i)) { fprintf(stderr, "memory allocation failed in PushNstack()\n"); return EXIT_FAILURE; } } n2 = 0; while (! NstackIsEmpty(ns)) { if (! PopNstack(ns, &x)) { fprintf(stderr, "pop was NULL\n"); return EXIT_FAILURE; } n2++; } if (n1 != n2){ fprintf(stderr, "Put %d objects on; got %d off\n", n1, n2); return EXIT_FAILURE; } FreeNstack(ns); /* Exercise of the cstack functions/API for char stack - * essentially the same as the nstack exercises above, but * also including a call to CstackString(). */ if ((cs = CreateCstack()) == NULL) { fprintf(stderr, "memory allocation failed\n"); return EXIT_FAILURE; } CstackSetBlocksize(cs, 50); n1 = 200; for (i = 0; i < n1; i++) { if (! PushCstack(cs, 'X')) { fprintf(stderr, "memory allocation failed in PushCstack()\n"); return EXIT_FAILURE; } } n2 = 0; while (PopCstack(cs, &c)) { if (c != 'X') { fprintf(stderr, "Put X's on; got a %c off\n", c); return EXIT_FAILURE; } n2++; } if (n1 != n2){ fprintf(stderr, "Put %d characters on; got %d off\n", n1, n2); return EXIT_FAILURE; } for (i = 0; i < n1; i++) { if (! PushCstack(cs, i)) { fprintf(stderr, "memory allocation failed in PushCstack()\n"); return EXIT_FAILURE; } } n2 = 0; while (! CstackIsEmpty(cs)) { if (! PopCstack(cs, &c)) { fprintf(stderr, "pop was NULL\n"); return EXIT_FAILURE; } n2++; } if (n1 != n2){ fprintf(stderr, "Put %d characters on; got %d off\n", n1, n2); return EXIT_FAILURE; } FreeCstack(cs); if ((cs = CreateCstack()) == NULL) { fprintf(stderr, "memory allocation failed\n"); return EXIT_FAILURE; } n1 = 200; for (i = 0; i < n1; i++) { if (! PushCstack(cs, 'X')) { fprintf(stderr, "memory allocation failed in PushCstack()\n"); return EXIT_FAILURE; } } s = CstackString(cs); if ((n2 = strlen(s)) != n1) { fprintf(stderr, "thought I'd get %d chars in that string, but got %d\n", n1, n2); return EXIT_FAILURE; } free(s); return EXIT_SUCCESS; } #endif /*SRE_STACK_TESTDRIVE*/ /***************************************************************** * @LICENSE@ *****************************************************************/ squid/sre_string.c0000640000175000017520000003316610463223377014447 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sre_string.c * * my library of extra string functions. Some for portability * across UNIXes * * CVS $Id: sre_string.c,v 1.14 2003/05/26 16:21:50 eddy Exp $ */ #include "squidconf.h" #include "squid.h" #include #include #include #include #include /* Function: Strdup() * * Purpose: Implementation of the common (but non-ANSI) function * strdup(). Robust against being passed a NULL pointer. * */ char * Strdup(char *s) { char *new; if (s == NULL) return NULL; if ((new = (char *) malloc (strlen(s) +1)) == NULL) return NULL; strcpy(new, s); return new; } /* Function: StringChop() * Date: SRE, Wed Oct 29 12:10:02 1997 [TWA 721] * * Purpose: Chop trailing whitespace off of a string. */ void StringChop(char *s) { int i; i = strlen(s) - 1; /* set i at last char in string */ while (i >= 0 && isspace((int) s[i])) i--; /* i now at last non-whitespace char, or -1 */ s[i+1] = '\0'; } int Strinsert(char *s1, /* string to insert a char into */ char c, /* char to insert */ int pos) /* position in s1 to insert c at */ { char oldc; char *s; for (s = s1 + pos; c; s++) { /* swap current char for inserted one */ oldc = *s; /* pick up current */ *s = c; /* put down inserted one */ c = oldc; /* old becomes next to insert */ } *s = '\0'; return 1; } int Strdelete(char *s1, /* string to delete a char from */ int pos) /* position of char to delete 0..n-1 */ { char *s; for (s = s1 + pos; *s; s++) *s = *(s + 1); return 1; } void s2lower(char *s) { for (; *s != '\0'; s++) *s = sre_tolower((int) *s); } void s2upper(char *s) { for (; *s != '\0'; s++) *s = sre_toupper((int) *s); } void * sre_malloc(char *file, int line, size_t size) { void *ptr; SQD_DPRINTF3(("MALLOC: %d bytes (file %s line %d)\n", size, file, line)); if ((ptr = malloc (size)) == NULL) Die("malloc of %ld bytes failed: file %s line %d", size, file, line); return ptr; } void * sre_realloc(char *file, int line, void *p, size_t size) { void *ptr; if ((ptr = realloc(p, size)) == NULL) Die("realloc of %ld bytes failed: file %s line %d", size, file, line); return ptr; } /* Function: Free2DArray(), Free3DArray() * Date: SRE, Tue Jun 1 14:47:14 1999 [St. Louis] * * Purpose: Convenience functions for free'ing 2D * and 3D pointer arrays. Tolerates any of the * pointers being NULL, to allow "sparse" * arrays. * * Args: p - array to be freed * dim1 - n for first dimension * dim2 - n for second dimension * * e.g. a 2d array is indexed p[0..dim1-1][] * a 3D array is indexed p[0..dim1-1][0..dim2-1][] * * Returns: void * * Diagnostics: (void) * "never fails" */ void Free2DArray(void **p, int dim1) { int i; if (p != NULL) { for (i = 0; i < dim1; i++) if (p[i] != NULL) free(p[i]); free(p); } } void Free3DArray(void ***p, int dim1, int dim2) { int i, j; if (p != NULL) { for (i = 0; i < dim1; i++) if (p[i] != NULL) { for (j = 0; j < dim2; j++) if (p[i][j] != NULL) free(p[i][j]); free(p[i]); } free(p); } } /* Function: RandomSequence() * * Purpose: Generate an iid symbol sequence according * to some alphabet, alphabet_size, probability * distribution, and length. Return the * sequence. * * Args: alphabet - e.g. "ACGT" * p - probability distribution [0..n-1] * n - number of symbols in alphabet * len - length of generated sequence * * Return: ptr to random sequence, or NULL on failure. */ char * RandomSequence(char *alphabet, float *p, int n, int len) { char *s; int x; s = (char *) MallocOrDie (sizeof(char) * (len+1)); for (x = 0; x < len; x++) s[x] = alphabet[FChoose(p,n)]; s[x] = '\0'; return s; } /* Function: sre_fgets() * Date: SRE, Thu May 13 10:56:28 1999 [St. Louis] * * Purpose: Dynamic allocation version of fgets(), * capable of reading unlimited line lengths. * * Args: buf - ptr to a string (may be reallocated) * n - ptr to current allocated length of buf, * (may be changed) * fp - open file ptr for reading * * Before the first call to sre_fgets(), * buf should be initialized to NULL and n to 0. * They're a linked pair, so don't muck with the * allocation of buf or the value of n while * you're still doing sre_fgets() calls with them. * * Returns: ptr to the buffer on success. * NULL on EOF (buf isn't to be used in this case) * sre_fgets() *always* results in an allocation * in buf. * * The reason to have it return a ptr to buf * is that it makes wrapper macros easy; see * MSAFileGetLine() for an example. * * Example: char *buf; * int n; * FILE *fp; * * fp = fopen("my_file", "r"); * buf = NULL; * n = 0; * while (sre_fgets(&buf, &n, fp) != NULL) * { * do stuff with buf; * } */ char * sre_fgets(char **buf, int *n, FILE *fp) { char *s; int len; int pos; if (*n == 0) { *buf = MallocOrDie(sizeof(char) * 128); *n = 128; } /* Simple case 1. We're sitting at EOF, or there's an error. * fgets() returns NULL, so we return NULL. */ if (fgets(*buf, *n, fp) == NULL) return NULL; /* Simple case 2. fgets() got a string, and it reached EOF. * return success status, so caller can use * the last line; on the next call we'll * return the 0 for the EOF. */ if (feof(fp)) return *buf; /* Simple case 3. We got a complete string, with \n, * and don't need to extend the buffer. */ len = strlen(*buf); if ((*buf)[len-1] == '\n') return *buf; /* The case we're waiting for. We have an incomplete string, * and we have to extend the buffer one or more times. Make * sure we overwrite the previous fgets's \0 (hence +(n-1) * in first step, rather than 128, and reads of 129, not 128). */ pos = (*n)-1; while (1) { *n += 128; *buf = ReallocOrDie(*buf, sizeof(char) * (*n)); s = *buf + pos; if (fgets(s, 129, fp) == NULL) return *buf; len = strlen(s); if (s[len-1] == '\n') return *buf; pos += 128; } /*NOTREACHED*/ } /* Function: sre_strcat() * Date: SRE, Thu May 13 09:36:32 1999 [St. Louis] * * Purpose: Dynamic memory version of strcat(). * appends src to the string that dest points to, * extending allocation for dest if necessary. * * One timing experiment (100 successive appends of * 1-255 char) shows sre_strcat() has about a 20% * overhead relative to strcat(). However, if optional * length info is passed, sre_strcat() is about 30% * faster than strcat(). * * Args: dest - ptr to string (char **), '\0' terminated * ldest - length of dest, if known; or -1 if length unknown. * src - string to append to dest, '\0' terminated * lsrc - length of src, if known; or -1 if length unknown. * * dest may be NULL, in which case this is * the equivalent of dest = Strdup(src). * * src may also be NULL, in which case * dest is unmodified (but why would you want to pass * a NULL src?) * * if both dest and src are NULL, dest is * unmodified; it stays NULL. * * the length parameters are optional. If a -1 * is passed, sre_strcat() will call strlen() to * determine the length itself. Passing length * info saves the strlen() calls and can speed things * up if lots of successive appends need to be done. * * Returns: new length of dest (>=0 on success); * dest is (probably) reallocated, and modified * to a longer string, '\0' terminated. */ int sre_strcat(char **dest, int ldest, char *src, int lsrc) { int len1, len2; if (ldest < 0) len1 = ((*dest == NULL) ? 0 : strlen(*dest)); else len1 = ldest; if (lsrc < 0) len2 = (( src == NULL) ? 0 : strlen(src)); else len2 = lsrc; if (len2 == 0) return len1; if (*dest == NULL) *dest = MallocOrDie(sizeof(char) * (len2+1)); else *dest = ReallocOrDie(*dest, sizeof(char) * (len1+len2+1)); memcpy((*dest)+len1, src, len2+1); return len1+len2; } /* Function: sre_strtok() * Date: SRE, Wed May 19 16:30:20 1999 [St. Louis] * * Purpose: Thread-safe version of strtok(). * * Returns ptr to next token in a string: skips * until it reaches a character that is not in the delim * string, and sets beginning of token. Skips to * next delim character (or '\0') to set the end; replaces that * character with '\0'. * If there's still more string left, sets s to point to next * character after the '\0' that was written, so successive * calls extract tokens in succession. If there was no string * left, s points at the terminal '\0'. * * If no token is found, returns NULL. * * Also returns the length of the token, which * may save us a strlen() call in some applications. * * Limitations: * *s can't be a constant string, since we write to it. * * Example: * char *tok; * int len; * char *s; * char buf[50] = "This is a sentence."; * * s = buf; * tok = sre_strtok(&s, " ", &len); * tok is "This"; s is "is a sentence."; len is 4. * tok = sre_strtok(&s, " ", &len); * tok is "is"; s is " a sentence."; len is 2. * tok = sre_strtok(&s, " ", &len); * tok is "a"; s is "sentence."; len is 1. * tok = sre_strtok(&s, " ", &len); * tok is "sentence."; s is "\0"; len is 9. * tok = sre_strtok(&s, " ", &len); * tok is NULL; s is "\0", len is undefined. * * Args: s - a tmp, modifiable ptr to string * delim - characters that delimits tokens * len - RETURN: length of token; pass NULL if not wanted * * Returns: ptr to next token, or NULL if there aren't any. */ char * sre_strtok(char **s, char *delim, int *len) { char *begin, *end; int n; begin = *s; begin += strspn(begin, delim); if (! *begin) return NULL; n = strcspn(begin, delim); end = begin + n; if (*end == '\0') { *s = end;} else { *end = '\0'; *s = end+1; } if (len != NULL) *len = n; return begin; } /* Function: sre_strdup() * Date: SRE, Wed May 19 17:57:28 1999 [St. Louis] * * Purpose: A version of the common but non-ANSI strdup() * function. Can pass len, if known, to save a * strlen() call. * * Args: s - string to duplicate * n - length of string, if known; -1 if unknown. * * Returns: allocated copy of string. * NULL on failure. */ char * sre_strdup(char *s, int n) { char *new; if (s == NULL) return NULL; if (n < 0) n = strlen(s); new = MallocOrDie (sizeof(char) * (n+1)); strcpy(new, s); return new; } /* Function: sre_strncpy() * Date: SRE, Tue Jun 22 10:10:46 1999 [Sanger Centre] * * Purpose: a strncpy() that makes sure it adds a trailing \0. * * Args: s1 - string to copy to (allocated n+1 or larger) * s2 - string to copy from * n - number of chars to copy * * Returns: s1. * Done only for consistency with strncpy(). Not clear * why it's useful for a strncpy() to return s1. */ char * sre_strncpy(char *s1, char *s2, int n) { strncpy(s1,s2,n); s1[n] = '\0'; return s1; } /* Function: IsBlankline() * Date: SRE, Fri Jun 18 14:36:08 1999 [St. Louis] * * Purpose: Returns TRUE if string consists solely of whitespace. * * Args: s - string to check */ int IsBlankline(char *s) { for (; *s != '\0'; s++) if (! isspace((int) *s)) return FALSE; return TRUE; } #ifdef CUBS_WIN /* A timing test for sre_strcat() * cc -O2 -g sre_string.c sre_ctype.c sqerror.c sre_math.c hsregex.c -lm * 15.200u - 5.360u = 9.84u if sre_strcat() with no length info passed * 13.660u - 5.360u = 8.30u if strcat(), with a single malloc(). * 11.370u - 5.360u = 6.01u if sre_strcat() with length info passed. */ int main(void) { float p[4] = {0.25, 0.25, 0.25, 0.25}; int buflen; int len; int nappends; int nstrings; char *s1 = NULL; char *s2; int i; nappends = 100; nstrings = 1000; while (nstrings--) { /* s1 = malloc(sizeof(char) * (255*nappends+1)); s1[0] = '\0'; */ s1 = NULL; len = 0; for (i = 0; i < nappends; i++) { buflen = CHOOSE(255) + 1; s2 = RandomSequence("ACGT", p, 4, buflen); /* strcat(s1,s2); */ if ((len = sre_strcat(&s1, len, s2, buflen)) < 0) exit(1); free(s2); } free(s1); } exit(0); } #endif /*CUBS_WIN*/ squid/sreformat_main.c0000640000175000017520000002342410463223377015272 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* sreformat_main.c * Mon Sep 13 13:06:51 1993 * * sreformat - reformat sequence files. * renamed sreformat from reformat, Tue Jun 30 10:53:38 1998 * * CVS $Id: sreformat_main.c,v 1.21 2004/01/20 00:13:08 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" #include "msa.h" static char banner[] = "sreformat - convert between sequence formats"; static char usage[] = "\ Usage: sreformat [-options] \n\ Output format choices: Unaligned Aligned\n\ ----------- -------\n\ fasta stockholm\n\ embl msf\n\ genbank a2m\n\ gcg phylip\n\ gcgdata clustal\n\ pir selex\n\ raw eps\n\n\ Available options are:\n\ -h : help; print brief help on version and usage\n\ -d : force DNA alphabet for nucleic acid sequence\n\ -r : force RNA alphabet for nucleic acid sequence\n\ -l : force lower case\n\ -u : force upper case\n\ -x : convert non-IUPAC chars (i.e. X's) in DNA to N's for IUPAC/BLAST compatibility\n\ -n : remove IUPAC codes; convert all ambiguous chars in DNA/RNA to N's\n\ "; static char experts[] = "\ Expert options:\n\ --informat : input sequence file is in format \n\ --mingap : remove columns containing all gaps (seqfile=alignment)\n\ --nogap : remove columns containing any gaps (seqfile=alignment)\n\ --pfam : modify Stockholm format output to be in PFAM style (1 line/seq)\n\ --sam : try to convert gaps to SAM style (seqfile=alignment)\n\ --samfrac : convert to SAM convention; cols w/ gapfrac > x are inserts\n\ --gapsym : convert all gaps to character ''\n\ \n\ --wussify : convert old format RNA structure markup lines to WUSS\n\ --dewuss : convert WUSS notation RNA structure markup lines to old format\n\ "; static struct opt_s OPTIONS[] = { { "-d", TRUE, sqdARG_NONE }, { "-h", TRUE, sqdARG_NONE }, { "-l", TRUE, sqdARG_NONE }, { "-n", TRUE, sqdARG_NONE }, { "-r", TRUE, sqdARG_NONE }, { "-u", TRUE, sqdARG_NONE }, { "-x", TRUE, sqdARG_NONE }, { "--gapsym", FALSE, sqdARG_CHAR }, { "--informat",FALSE, sqdARG_STRING }, { "--mingap", FALSE, sqdARG_NONE }, { "--nogap", FALSE, sqdARG_NONE }, { "--pfam", FALSE, sqdARG_NONE }, { "--sam", FALSE, sqdARG_NONE }, { "--samfrac", FALSE, sqdARG_FLOAT }, { "--wussify", FALSE, sqdARG_NONE }, { "--dewuss", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *seqfile; /* name of sequence file */ char *format; SQFILE *dbfp; /* open sequence file */ int fmt; /* format of seqfile */ int outfmt; /* output format */ char *seq; /* sequence */ SQINFO sqinfo; int i; int force_rna; /* TRUE to force RNA alphabet */ int force_dna; /* TRUE to force DNA alphabet */ int force_lower; /* TRUE to force lower case */ int force_upper; /* TRUE to force upper case */ int force_iupac_to_n; /* TRUE to convert ambiguities all to N's */ int x_is_bad; /* TRUE to convert X to N */ int do_mingap; /* TRUE to remove columns containing all gaps */ int do_nogap; /* TRUE to remove columns containing any gaps */ int do_pfam; /* TRUE to make SELEX -> PFAM */ int samize; /* TRUE to SAMize an A2M conversion */ float samfrac; /* -1, or gap fraction for a SAM conversion */ char gapsym; /* 0 if unset; else = character to use for gaps */ int wussify; /* TRUE to convert old RNA SS markup to WUSS notation */ int dewuss; /* TRUE to convert WUSS markup back to old notation */ char *optname; /* name of option found by Getopt() */ char *optarg; /* argument found by Getopt() */ int optind; /* index in argv[] */ /*********************************************** * Parse command line ***********************************************/ force_rna = FALSE; force_dna = FALSE; force_upper = FALSE; force_lower = FALSE; force_iupac_to_n = FALSE; x_is_bad = FALSE; do_mingap = FALSE; do_nogap = FALSE; do_pfam = FALSE; samize = FALSE; samfrac = -1.0; fmt = SQFILE_UNKNOWN; gapsym = 0; dewuss = FALSE; wussify = FALSE; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-d") == 0) force_dna = TRUE; else if (strcmp(optname, "-l") == 0) force_lower = TRUE; else if (strcmp(optname, "-n") == 0) force_iupac_to_n = TRUE; else if (strcmp(optname, "-r") == 0) force_rna = TRUE; else if (strcmp(optname, "-u") == 0) force_upper = TRUE; else if (strcmp(optname, "-x") == 0) x_is_bad = TRUE; else if (strcmp(optname, "--gapsym") == 0) gapsym = *optarg; else if (strcmp(optname, "--mingap") == 0) do_mingap = TRUE; else if (strcmp(optname, "--nogap") == 0) do_nogap = TRUE; else if (strcmp(optname, "--pfam") == 0) do_pfam = TRUE; else if (strcmp(optname, "--sam") == 0) samize = TRUE; else if (strcmp(optname, "--samfrac") == 0) samfrac = atof(optarg); else if (strcmp(optname, "--wussify") == 0) wussify = TRUE; else if (strcmp(optname, "--dewuss") == 0) dewuss = TRUE; else if (strcmp(optname, "--informat") == 0) { fmt = String2SeqfileFormat(optarg); if (fmt == SQFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 2) Die("%s\n", usage); if (force_lower && force_upper) Die("Can't force both upper case and lower case. Stop trying to confuse me.\n%s", usage); if (force_rna && force_dna) Die("Can't force both RNA and DNA. Stop trying to find bugs. You'll be sorry.\n%s", usage); format = argv[optind]; optind++; seqfile = argv[optind]; optind++; /* Try to work around inability to autodetect from a pipe or .gz: * assume FASTA format */ if (fmt == SQFILE_UNKNOWN && (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) fmt = SQFILE_FASTA; /*********************************************** * Figure out what format we're supposed to write ***********************************************/ if ((outfmt = String2SeqfileFormat(format)) == SQFILE_UNKNOWN) Die("Unknown output format %s\n%s", format, usage); /*********************************************** * Reformat the file, printing to stdout. ***********************************************/ /* If the output format is an alignment, then the input format * has to be an alignment. */ if (IsAlignmentFormat(outfmt)) { MSAFILE *afp; MSA *msa; if ((afp = MSAFileOpen(seqfile, fmt, NULL)) == NULL) Die("Alignment file %s could not be opened for reading", seqfile); while ((msa = MSAFileRead(afp)) != NULL) { /* If asked, convert upper/lower convention and * gap character conventions now */ if (do_mingap) MSAMingap(msa); if (do_nogap) MSANogap(msa); if (gapsym) AlignmentHomogenousGapsym(msa->aseq, msa->nseq, msa->alen, gapsym); if (samize) SAMizeAlignment(msa->aseq, msa->nseq, msa->alen); if (samfrac >= 0) SAMizeAlignmentByGapFrac(msa->aseq, msa->nseq, msa->alen, samfrac); if (msa->ss_cons != NULL && wussify) KHStoWUSS(msa->ss_cons); if (msa->ss_cons != NULL && dewuss) WUSStoKHS(msa->ss_cons); for (i = 0; i < msa->nseq; i++) { /* Note: Since ToIUPAC() and ToSimplyN() convert to upper case N, * those function calls must precede case conversions. */ if (force_dna) ToDNA(msa->aseq[i]); if (force_rna) ToRNA(msa->aseq[i]); if (x_is_bad) ToIUPAC(msa->aseq[i], TRUE); if (force_iupac_to_n) ToSimplyN(msa->aseq[i], TRUE); if (force_lower) s2lower(msa->aseq[i]); if (force_upper) s2upper(msa->aseq[i]); if (msa->ss != NULL && msa->ss[i] != NULL && wussify) KHStoWUSS(msa->ss[i]); if (msa->ss != NULL && msa->ss[i] != NULL && dewuss) WUSStoKHS(msa->ss[i]); } if (outfmt == MSAFILE_EPS) EPSWriteSmallMSA(stdout, msa); else MSAFileWrite(stdout, msa, outfmt, do_pfam); MSAFree(msa); } MSAFileClose(afp); } else { if ((dbfp = SeqfileOpen(seqfile, fmt, NULL)) == NULL) Die("Failed to open sequence file %s for reading", seqfile); if (wussify || dewuss) Die("--wussify or --dewuss don't make sense; only apply to alignment format markups"); while (ReadSeq(dbfp, fmt, &seq, &sqinfo)) { /* Note: Since ToIUPAC() and ToSimplyN() convert to upper case N, * those function calls must precede case conversions. */ if (force_dna) ToDNA(seq); if (force_rna) ToRNA(seq); if (x_is_bad) ToIUPAC(seq, FALSE); if (force_iupac_to_n) ToSimplyN(seq, FALSE); if (force_lower) s2lower(seq); if (force_upper) s2upper(seq); WriteSeq(stdout, outfmt, seq, &sqinfo); FreeSequence(seq, &sqinfo); } SeqfileClose(dbfp); } return 0; } squid/ssi.c0000640000175000017520000015340610463223377013066 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ #include "squidconf.h" #include #include #include #include #include #include #include "squid.h" #include "ssi.h" static sqd_uint32 v20magic = 0xf3f3e9b1; /* SSI 1.0: "ssi1" + 0x80808080 */ static sqd_uint32 v20swap = 0xb1e9f3f3; /* byteswapped */ static int read_i16(FILE *fp, sqd_uint16 *ret_result); static int read_i32(FILE *fp, sqd_uint32 *ret_result); static int read_i64(FILE *fp, sqd_uint64 *ret_result); static int read_offset(FILE *fp, char mode, SSIOFFSET *ret_offset); static int write_i16(FILE *fp, sqd_uint16 n); static int write_i32(FILE *fp, sqd_uint32 n); static int write_i64(FILE *fp, sqd_uint64 n); static int write_offset(FILE *fp, SSIOFFSET *offset); static int binary_search(SSIFILE *sfp, char *key, int klen, SSIOFFSET *base, sqd_uint32 recsize, sqd_uint32 maxidx); static int indexfile_position(SSIFILE *sfp, SSIOFFSET *base, sqd_uint32 len, sqd_uint32 n); static void clear_ssifile(SSIFILE *sfp); static sqd_uint64 current_index_size(SSIINDEX *g); static int activate_external_sort(SSIINDEX *g); static int load_indexfile(SSIFILE *sfp); static int parse_pkey_info(char *buf, char mode, struct ssipkey_s *pkey); static int parse_skey_info(char *buf, struct ssiskey_s *skey); /* Function: SSIOpen() * Date: SRE, Sun Dec 31 12:40:03 2000 [St. Louis] * * Purpose: Opens the SSI index file {filename} and returns * a SSIFILE * stream thru {ret_sfp}. * The caller must eventually close this stream using * SSIClose(). More than one index file can be open * at once. * * Args: filename - full path to a SSI index file * * Returns: Returns 0 on success, nonzero on failure. */ int SSIOpen(char *filename, SSIFILE **ret_sfp) { SSIFILE *sfp = NULL; int status; if ((sfp = malloc(sizeof(SSIFILE))) == NULL) return SSI_ERR_MALLOC; if ((sfp->fp = fopen(filename, "rb")) == NULL) { free(sfp); return SSI_ERR_NOFILE; } status = load_indexfile(sfp); *ret_sfp = sfp; return status; } /* load_indexfile(): given a SSIFILE structure with an open and positioned * stream (fp) -- but no other data loaded -- read the next SSIFILE * in from disk. We use this routine without its SSIOpen() wrapper * as part of the external mergesort when creating large indices. */ static int load_indexfile(SSIFILE *sfp) { sqd_uint32 magic; sqd_uint16 i; /* counter over files */ int status; /* overall return status if an error is thrown */ status = SSI_ERR_BADFORMAT; /* default: almost every kind of error is a bad format error */ sfp->filename = NULL; sfp->fileformat = NULL; sfp->fileflags = NULL; sfp->bpl = NULL; sfp->rpl = NULL; sfp->nfiles = 0; if (! read_i32(sfp->fp, &magic)) {status = SSI_ERR_BADMAGIC; goto FAILURE; } if (magic != v20magic && magic != v20swap) {status = SSI_ERR_BADMAGIC; goto FAILURE; } if (! read_i32(sfp->fp, &(sfp->flags))) goto FAILURE; /* If we have 64-bit offsets, make sure we can deal with them. */ #ifndef HAS_64BIT_FILE_OFFSETS if ((sfp->flags & SSI_USE64_INDEX) || (sfp->flags & SSI_USE64)) { status = SSI_ERR_NO64BIT; goto FAILURE; } #endif sfp->imode = (sfp->flags & SSI_USE64_INDEX) ? SSI_OFFSET_I64 : SSI_OFFSET_I32; sfp->smode = (sfp->flags & SSI_USE64) ? SSI_OFFSET_I64 : SSI_OFFSET_I32; if (! read_i16(sfp->fp, &(sfp->nfiles))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->nprimary))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->nsecondary))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->flen))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->plen))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->slen))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->frecsize))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->precsize))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->srecsize))) goto FAILURE; if (! read_offset(sfp->fp, sfp->imode, &(sfp->foffset))) goto FAILURE; if (! read_offset(sfp->fp, sfp->imode, &(sfp->poffset))) goto FAILURE; if (! read_offset(sfp->fp, sfp->imode, &(sfp->soffset))) goto FAILURE; /* Read the file information and keep it. * We expect the number of files to be small, so reading it * once should be advantageous overall. If SSI ever had to * deal with large numbers of files, you'd probably want to * read file information on demand. */ if (sfp->nfiles == 0) goto FAILURE; if ((sfp->filename=malloc(sizeof(char *) *sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; } for (i = 0; i < sfp->nfiles; i++) sfp->filename[i] = NULL; if ((sfp->fileformat=malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; } if ((sfp->fileflags =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; } if ((sfp->bpl =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; } if ((sfp->rpl =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; } for (i = 0; i < sfp->nfiles; i++) { /* We have to explicitly position, because header and file * records may expand in the future; frecsize and foffset * give us forwards compatibility. */ if (indexfile_position(sfp, &(sfp->foffset), sfp->frecsize, i) !=0) goto FAILURE; if ((sfp->filename[i] =malloc(sizeof(char)*sfp->flen)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; } if (fread(sfp->filename[i],sizeof(char),sfp->flen, sfp->fp)!=sfp->flen) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->fileformat[i]))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->fileflags[i]))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->bpl[i]))) goto FAILURE; if (! read_i32(sfp->fp, &(sfp->rpl[i]))) goto FAILURE; } /* Success. Return 0. */ return 0; FAILURE: /* Failure: free the damaged structure, return status code. */ SSIClose(sfp); return status; } /* Function: SSIGetOffsetByName() * Date: SRE, Sun Dec 31 13:55:31 2000 [St. Louis] * * Purpose: Looks up the string {key} in the open index {sfp}. * {key} can be either a primary or secondary key. If {key} * is found, {*ret_fh} contains a unique handle on * the file that contains {key} (suitable for an SSIFileInfo() * call, or for comparison to the handle of the last file * that was opened for retrieval), and {offset} is filled * in with the offset in that file. * * Args: sfp - open index file * key - string to search for * ret_fh - RETURN: handle on file that key is in * ret_offset - RETURN: offset of the start of that key's record * * Returns: 0 on success. * non-zero on error. */ int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh, SSIOFFSET *ret_offset) { int status; sqd_uint16 fnum; /* Look in the primary keys. */ status = binary_search(sfp, key, sfp->plen, &(sfp->poffset), sfp->precsize, sfp->nprimary); if (status == 0) { /* We found it as a primary key; get our data & return. */ if (! read_i16(sfp->fp, &fnum)) return SSI_ERR_NODATA; *ret_fh = (int) fnum; if (! read_offset(sfp->fp, sfp->smode, ret_offset)) return SSI_ERR_NODATA; return 0; /* success! (we don't need the other key data) */ } else if (status == SSI_ERR_NO_SUCH_KEY) { /* Not in the primary keys? OK, try the secondary keys. */ if (sfp->nsecondary > 0) { char *pkey; status = binary_search(sfp, key, sfp->slen, &(sfp->soffset), sfp->srecsize, sfp->nsecondary); if (status != 0) return status; if ((pkey = malloc(sizeof(char) * sfp->plen)) == NULL) return SSI_ERR_MALLOC; if (fread(pkey, sizeof(char), sfp->plen, sfp->fp) != sfp->plen) return SSI_ERR_NODATA; status = SSIGetOffsetByName(sfp, pkey, ret_fh, ret_offset); free(pkey); } return status; } else return status; /*NOTREACHED*/ } /* Function: SSIGetOffsetByNumber() * Date: SRE, Mon Jan 1 19:42:42 2001 [St. Louis] * * Purpose: Looks up primary key #{n} in the open index {sfp}. * {n} ranges from 0..nprimary-1. When key #{n} * is found, {*ret_fh} contains a unique * handle on the file that contains {key} (suitable * for an SSIFileInfo() call, or for comparison to * the handle of the last file that was opened for retrieval), * and {offset} is filled in with the offset in that file. * * Args: sfp - open index file * n - primary key number to retrieve. * ret_fh - RETURN: handle on file that key is in * ret_offset - RETURN: offset of the start of that key's record * * Returns: 0 on success. * non-zero on error. */ int SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh, SSIOFFSET *ret_offset) { sqd_uint16 fnum; char *pkey; if (n >= sfp->nprimary) return SSI_ERR_NO_SUCH_KEY; if (indexfile_position(sfp, &(sfp->poffset), sfp->precsize, n) != 0) return SSI_ERR_SEEK_FAILED; if ((pkey = malloc(sizeof(char) * sfp->plen)) == NULL) return SSI_ERR_MALLOC; if (fread(pkey, sizeof(char), sfp->plen, sfp->fp) != sfp->plen) return SSI_ERR_NODATA; if (! read_i16(sfp->fp, &fnum)) return SSI_ERR_NODATA; if (! read_offset(sfp->fp, sfp->smode, ret_offset)) return SSI_ERR_NODATA; *ret_fh = fnum; free(pkey); return 0; } /* Function: SSIGetSubseqOffset() * Date: SRE, Mon Jan 1 19:49:31 2001 [St. Louis] * * Purpose: Implements SSI_FAST_SUBSEQ. * * Looks up a primary or secondary {key} in the open * index {sfp}. Asks for the nearest offset to a * subsequence starting at position {requested_start} * in the sequence (numbering the sequence 1..L). * If {key} is found, on return, {ret_fh} * contains a unique handle on the file that contains * {key} (suitable for an SSIFileInfo() call, or for * comparison to the handle of the last file that was * opened for retrieval); {record_offset} contains the * disk offset to the start of the record; {data_offset} * contains the disk offset either exactly at the requested * residue, or at the start of the line containing the * requested residue; {ret_actual_start} contains the * coordinate (1..L) of the first valid residue at or * after {data_offset}. {ret_actual_start} is <= * {requested_start}. * * Args: sfp - open index file * key - primary or secondary key to find * requested_start - residue we'd like to start at (1..L) * ret_fh - RETURN: handle for file the key is in * record_offset - RETURN: offset of entire record * data_offset - RETURN: offset of subseq (see above) * ret_actual_start- RETURN: coord (1..L) of residue at data_offset * * Returns: 0 on success, non-zero on failure. */ int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start, int *ret_fh, SSIOFFSET *record_offset, SSIOFFSET *data_offset, int *ret_actual_start) { int status; sqd_uint32 len; int r, b, i, l; /* tmp variables for "clarity", to match docs */ /* Look up the key. Rely on the fact that SSIGetOffsetByName() * leaves the index file positioned at the rest of the data for this key. */ status = SSIGetOffsetByName(sfp, key, ret_fh, record_offset); if (status != 0) return status; /* Check that we're allowed to do subseq lookup on that file. */ if (! (sfp->fileflags[*ret_fh] & SSI_FAST_SUBSEQ)) return SSI_ERR_NO_SUBSEQS; /* Read the data we need for subseq lookup */ if (! read_offset(sfp->fp, sfp->smode, data_offset)) return SSI_ERR_NODATA; if (! read_i32(sfp->fp, &len)) return SSI_ERR_NODATA; /* Set up tmp variables for clarity of equations below, * and to make them match documentation (ssi-format.tex). */ r = sfp->rpl[*ret_fh]; /* residues per line */ b = sfp->bpl[*ret_fh]; /* bytes per line */ i = requested_start; /* start position 1..L */ l = (i-1)/r; /* data line # (0..) that the residue is on */ if (r == 0 || b == 0) return SSI_ERR_NO_SUBSEQS; if (i < 0 || i > len) return SSI_ERR_RANGE; /* When b = r+1, there's nothing but sequence on each data line (and the \0), * and we can find each residue precisely. */ if (b == r+1) { if (sfp->smode == SSI_OFFSET_I32) { data_offset->mode = SSI_OFFSET_I32; data_offset->off.i32 = data_offset->off.i32 + l*b + (i-1)%r; } else if (sfp->smode == SSI_OFFSET_I64) { data_offset->mode = SSI_OFFSET_I64; data_offset->off.i64 = data_offset->off.i64 + l*b + (i-1)%r; } *ret_actual_start = requested_start; } else { /* else, there's other stuff on seq lines, so the best * we can do easily is to position at start of relevant line. */ if (sfp->smode == SSI_OFFSET_I32) { data_offset->mode = SSI_OFFSET_I32; data_offset->off.i32 = data_offset->off.i32 + l*b; } else if (sfp->smode == SSI_OFFSET_I64) { data_offset->mode = SSI_OFFSET_I64; data_offset->off.i64 = data_offset->off.i64 + l*b; } /* yes, the eq below is = 1 + (i-1)/r*r but it's not = i. that's an integer /. */ *ret_actual_start = 1 + l*r; } return 0; } /* Function: SSISetFilePosition() * Date: SRE, Tue Jan 2 09:13:46 2001 [St. Louis] * * Purpose: Uses {offset} to sets the file position for {fp}, usually an * open sequence file, relative to the start of the file. * Hides the details of system-dependent shenanigans necessary for * file positioning in large (>2 GB) files. * * Behaves just like fseek(fp, offset, SEEK_SET) for 32 bit * offsets and <2 GB files. * * Warning: if all else fails, in desperation, it will try to * use fsetpos(). This requires making assumptions about fpos_t * that may be unwarranted... assumptions that ANSI C prohibits * me from making... though I believe the ./configure * script robustly tests whether I can play with fpos_t like this. * * Args: fp - file to position. * offset - SSI offset relative to file start. * * Returns: 0 on success, nonzero on error. */ int SSISetFilePosition(FILE *fp, SSIOFFSET *offset) { if (offset->mode == SSI_OFFSET_I32) { if (fseek(fp, offset->off.i32, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED; } #ifndef HAS_64BIT_FILE_OFFSETS else return SSI_ERR_NO64BIT; #elif defined HAVE_FSEEKO && SIZEOF_OFF_T == 8 else if (fseeko(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED; #elif defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8 else if (fseeko64(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED; #elif defined HAVE_FSEEK64 else if (fseek64(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED; #elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8 else if (fsetpos(fp, &(offset->off.i64)) != 0) return SSI_ERR_SEEK_FAILED; #endif return 0; } /* Function: SSIFileInfo() * Date: SRE, Tue Jan 2 10:31:01 2001 [St. Louis] * * Purpose: Given a file number {fh} in an open index file * {sfp}, retrieve file name {ret_filename} and * the file format {ret_format}. * * {ret_filename} is a pointer to a string maintained * internally by {sfp}. It should not be free'd; * SSIClose(sfp) takes care of it. * * Args: sfp - open index file * fh - handle on file to look up * ret_filename - RETURN: name of file n * ret_format - RETURN: format of file n * * Returns: 0 on success, nonzero on failure. */ int SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format) { if (fh < 0 || fh >= sfp->nfiles) return SSI_ERR_BADARG; *ret_filename = sfp->filename[fh]; *ret_format = sfp->fileformat[fh]; return 0; } /* Function: SSIClose() * Date: SRE, Sun Dec 31 14:56:37 2000 [St. Louis] * * Purpose: Close an open {SSIFILE *}. * * Args: sfp - index file to close. * * Returns: (void) */ void SSIClose(SSIFILE *sfp) { if (sfp != NULL) { clear_ssifile(sfp); if (sfp->fp != NULL) fclose(sfp->fp); free(sfp); } } /* clear_ssifile(): free the innards of SSIFILE, without * destroying the structure or closing the stream. */ static void clear_ssifile(SSIFILE *sfp) { int i; if (sfp->filename != NULL) { for (i = 0; i < sfp->nfiles; i++) if (sfp->filename[i] != NULL) free(sfp->filename[i]); free(sfp->filename); } if (sfp->fileformat != NULL) free(sfp->fileformat); if (sfp->fileflags != NULL) free(sfp->fileflags); if (sfp->bpl != NULL) free(sfp->bpl); if (sfp->rpl != NULL) free(sfp->rpl); } /* Function: SSIRecommendMode() * Date: SRE, Fri Feb 16 08:23:47 2001 [St. Louis] * * Purpose: Examines the file and determines whether it should be * indexed with large file support or not; returns * SSI_OFFSET_I32 for most files, SSI_OFFSET_I64 for large * files, or -1 on failure. * * Args: file - name of file to check for size * * Returns: -1 on failure (including case where file is too big) * SSI_OFFSET_I32 for most files (<= 2^31-1 bytes) * SSI_OFFSET_I64 for large files (> 2^31-1 bytes) */ int SSIRecommendMode(char *file) { #if HAVE_STAT64 struct stat64 s1; if (stat64(file, &s1) == 0) { if (s1.st_size <= 2146483647L) return SSI_OFFSET_I32; else return SSI_OFFSET_I64; } #else struct stat s2; if (stat(file, &s2) == 0) { if (s2.st_size <= 2146483647L) return SSI_OFFSET_I32; else return SSI_OFFSET_I64; } #endif return -1; } /* Function: SSICreateIndex() * Date: SRE, Tue Jan 2 11:23:25 2001 [St. Louis] * * Purpose: Creates and initializes a SSI index structure. * Sequence file offset type is specified by {mode}. * * Args: mode - SSI_OFFSET_I32 or SSI_OFFSET_I64, sequence file index mode. * * Returns: ptr to new index structure, or NULL on failure. * Caller is responsible for free'ing the returned * structure with SSIFreeIndex(). */ SSIINDEX * SSICreateIndex(int mode) { SSIINDEX *g; g = NULL; if ((g = malloc(sizeof(SSIINDEX))) == NULL) goto FAILURE; g->smode = mode; g->imode = SSI_OFFSET_I32; /* index always starts as 32-bit; may get upgraded later */ g->external = FALSE; g->max_ram = SSI_MAXRAM; #ifndef HAS_64BIT_FILE_OFFSETS if (mode == SSI_OFFSET_I64) Die("\ Can't create a 64-bit SSI index on this system, sorry;\n\ I don't have 64-bit file offset functions available.\n"); #endif g->filenames = NULL; g->fileformat = NULL; g->bpl = NULL; g->rpl = NULL; g->flen = 0; g->nfiles = 0; g->pkeys = NULL; g->plen = 0; g->nprimary = 0; g->ptmpfile = "tmp.ssi.1"; /* hardcoded, for now. */ g->ptmp = NULL; g->skeys = NULL; g->slen = 0; g->nsecondary = 0; g->stmpfile = "tmp.ssi.2"; /* hardcoded, for now. */ g->stmp = NULL; /* All mallocs must go after NULL initializations, because of the cleanup strategy; * we'll try to free anything non-NULL if a malloc fails. */ if ((g->filenames = malloc(sizeof(char *) * SSI_FILE_BLOCK)) == NULL) goto FAILURE; if ((g->fileformat= malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE; if ((g->bpl = malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE; if ((g->rpl = malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE; if ((g->pkeys = malloc(sizeof(struct ssipkey_s)* SSI_KEY_BLOCK))== NULL) goto FAILURE; if ((g->skeys = malloc(sizeof(struct ssipkey_s)* SSI_KEY_BLOCK))== NULL) goto FAILURE; return g; FAILURE: SSIFreeIndex(g); /* free the damaged structure */ return NULL; } /* Function: SSIGetFilePosition() * Date: SRE, Tue Jan 2 09:59:26 2001 [St. Louis] * * Purpose: Fills {ret_offset} with the current disk * offset of {fp}, relative to the start of the file. * {mode} is set to either SSI_OFFSET_I32 or * SSI_OFFSET_I64. If {mode} is _I32 (32 bit), just wraps * a call to ftell(); otherwise deals with system-dependent * details of 64-bit file offsets. * * Args: fp - open stream * mode - SSI_OFFSET_I32 or SSI_OFFSET_I64 * ret_offset - RETURN: file position * * Returns: 0 on success. nonzero on error. */ int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset) { if (mode == SSI_OFFSET_I32) { ret_offset->mode = SSI_OFFSET_I32; ret_offset->off.i32 = ftell(fp); if (ret_offset->off.i32 == -1) return SSI_ERR_TELL_FAILED; } else if (mode != SSI_OFFSET_I64) abort(); /* only happens on a coding error */ else { ret_offset->mode = SSI_OFFSET_I64; #ifndef HAS_64BIT_FILE_OFFSETS return SSI_ERR_NO64BIT; #elif defined HAVE_FTELLO && SIZEOF_OFF_T == 8 if ((ret_offset->off.i64 = ftello(fp)) == -1) return SSI_ERR_TELL_FAILED; #elif defined HAVE_FTELLO64 && SIZEOF_OFF64_T == 8 if ((ret_offset->off.i64 = ftello64(fp)) == -1) return SSI_ERR_TELL_FAILED; #elif defined HAVE_FTELL64 if ((ret_offset->off.i64 = ftell64(fp)) == -1) return SSI_ERR_TELL_FAILED; #elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8 if (fgetpos(fp, &(ret_offset->off.i64)) != 0) return SSI_ERR_TELL_FAILED; #endif } return 0; } /* Function: SSIAddFileToIndex() * Date: SRE, Tue Jan 2 12:54:36 2001 [St. Louis] * * Purpose: Adds the sequence file {filename}, which is known to * be in format {fmt}, to the index {g}. Creates and returns * a unique filehandle {fh} for then associating primary keys * with this file using SSIAddPrimaryKeyToIndex(). * * Args: g - active index * filename - file to add * fmt - format code for this file (e.g. SQFILE_FASTA) * ret_fh - RETURN: unique handle for this file * * Returns: 0 on success; nonzero on error. */ int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh) { int n; if (g->nfiles >= SSI_MAXFILES) return SSI_ERR_TOOMANY_FILES; n = strlen(filename); if ((n+1) > g->flen) g->flen = n+1; g->filenames[g->nfiles] = FileTail(filename, FALSE); g->fileformat[g->nfiles] = fmt; g->bpl[g->nfiles] = 0; g->rpl[g->nfiles] = 0; *ret_fh = g->nfiles; /* handle is simply = file number */ g->nfiles++; if (g->nfiles % SSI_FILE_BLOCK == 0) { g->filenames = realloc(g->filenames, sizeof(char *) * (g->nfiles+SSI_FILE_BLOCK)); if (g->filenames == NULL) return SSI_ERR_MALLOC; g->fileformat= realloc(g->fileformat, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK)); if (g->fileformat == NULL) return SSI_ERR_MALLOC; g->bpl = realloc(g->bpl, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK)); if (g->bpl == NULL) return SSI_ERR_MALLOC; g->rpl = realloc(g->rpl, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK)); if (g->rpl == NULL) return SSI_ERR_MALLOC; } return 0; } /* Function: SSISetFileForSubseq() * Date: SRE, Tue Jan 9 10:02:05 2001 [St. Louis] * * Purpose: Set SSI_FAST_SUBSEQ for the file indicated by * filehandle {fh} in the index {g}, setting * parameters {bpl} and {rpl} to the values given. * {bpl} is the number of bytes per sequence data line. * {rpl} is the number of residues per sequence data line. * Caller must be sure that {bpl} and {rpl} do not change * on any line of any sequence record in the file * (except for the last data line of each record). If * this is not the case in this file, SSI_FAST_SUBSEQ * will not work, and this routine should not be * called. * * Args: g - the active index * fh - handle for file to set SSI_FAST_SUBSEQ on * bpl - bytes per data line * rpl - residues per data line * * Returns: 0 on success; 1 on error. */ int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl) { if (fh < 0 || fh >= g->nfiles) return SSI_ERR_BADARG; if (bpl <= 0 || rpl <= 0) return SSI_ERR_BADARG; g->bpl[fh] = bpl; g->rpl[fh] = rpl; return 0; } /* Function: SSIAddPrimaryKeyToIndex() * Date: SRE, Tue Jan 2 11:50:54 2001 [St. Louis] * * Purpose: Put primary key {key} in the index {g}, while telling * the index this primary key is in the file associated * with filehandle {fh} (returned by a previous call * to SSIAddFileToIndex()), and its record starts at * position {r_off} in the file. * * {d_off} and {L} are optional; they may be left unset * by passing NULL and 0, respectively. (If one is * provided, both must be provided.) If they are provided, * {d_off} gives the position of the first line of sequence * data in the record, and {L} gives the length of * the sequence in residues. They are used when * SSI_FAST_SUBSEQ is set for this file. If SSI_FAST_SUBSEQ * is not set for the file, {d_off} and {L} will be * ignored by the index reading API even if they are stored * by the index writing API, so it doesn't hurt for the * indexing program to provide them; typically they * won't know whether it's safe to set SSI_FAST_SUBSEQ * for the whole file until the whole file has been * read and every key has already been added to the index. * * Args: g - active index * key - primary key to add * fh - handle on file that this key's in * r_off - offset to start of record * d_off - offset to start of sequence data * L - length of sequence, or 0 * * Returns: 0 on success, nonzero on error. */ int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh, SSIOFFSET *r_off, SSIOFFSET *d_off, int L) { int n; /* a string length */ if (fh >= SSI_MAXFILES) return SSI_ERR_TOOMANY_FILES; if (g->nprimary >= SSI_MAXKEYS) return SSI_ERR_TOOMANY_KEYS; if (L > 0 && d_off == NULL) abort(); /* need both. */ /* Before adding the key: check how big our index is. * If it's getting too large, switch to external mode. */ if (!g->external && current_index_size(g) >= g->max_ram) if (activate_external_sort(g) != 0) return SSI_ERR_NOFILE; /* Update maximum pkey length, if needed. */ n = strlen(key); if ((n+1) > g->plen) g->plen = n+1; /* External mode? Simply append to disk... */ if (g->external) { if (g->smode == SSI_OFFSET_I32) { fprintf(g->ptmp, "%s\t%d\t%lu\t%lu\t%lu\n", key, fh, (unsigned long) r_off->off.i32, (unsigned long) (d_off == NULL? 0 : d_off->off.i32), (unsigned long) L); } else { fprintf(g->ptmp, "%s\t%d\t%llu\t%llu\t%lu\n", key, fh, (unsigned long long) r_off->off.i64, (unsigned long long) (d_off == NULL? 0 : d_off->off.i64), (unsigned long) L); } g->nprimary++; return 0; } /* Else: internal mode, keep keys in memory... */ if ((g->pkeys[g->nprimary].key = sre_strdup(key, n)) == NULL) return SSI_ERR_MALLOC; g->pkeys[g->nprimary].fnum = (sqd_uint16) fh; g->pkeys[g->nprimary].r_off = *r_off; if (d_off != NULL && L > 0) { g->pkeys[g->nprimary].d_off = *d_off; g->pkeys[g->nprimary].len = L; } else { /* yeah, this looks stupid, but look: we have to give a valid looking, non-NULL d_off of some sort, or writes will fail. It's going to be unused anyway. */ g->pkeys[g->nprimary].d_off = *r_off; g->pkeys[g->nprimary].len = 0; } g->nprimary++; if (g->nprimary % SSI_KEY_BLOCK == 0) { g->pkeys = realloc(g->pkeys, sizeof(struct ssipkey_s) * (g->nprimary+SSI_KEY_BLOCK)); if (g->pkeys == NULL) return SSI_ERR_MALLOC; } return 0; } /* Function: SSIAddSecondaryKeyToIndex() * Date: SRE, Tue Jan 2 12:44:40 2001 [St. Louis] * * Purpose: Puts secondary key {key} in the index {g}, associating * it with primary key {pkey} that was previously * registered by SSIAddPrimaryKeyToIndex(). * * Args: g - active index * key - secondary key to add * pkey - primary key to associate this key with * * Returns: 0 on success, nonzero on failure. */ int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey) { int n; /* a string length */ if (g->nsecondary >= SSI_MAXKEYS) return SSI_ERR_TOOMANY_KEYS; /* Before adding the key: check how big our index is. * If it's getting too large, switch to external mode. */ if (!g->external && current_index_size(g) >= g->max_ram) if (activate_external_sort(g) != 0) return SSI_ERR_NOFILE; /* Update maximum secondary key length, if necessary. */ n = strlen(key); if ((n+1) > g->slen) g->slen = n+1; /* if external mode: write info to disk. */ if (g->external) { fprintf(g->stmp, "%s\t%s\n", key, pkey); g->nsecondary++; return 0; } /* else, internal mode... store info in memory. */ if ((g->skeys[g->nsecondary].key = sre_strdup(key, n)) == NULL) return SSI_ERR_MALLOC; if ((g->skeys[g->nsecondary].pkey = sre_strdup(pkey, -1)) == NULL) return SSI_ERR_MALLOC; g->nsecondary++; if (g->nsecondary % SSI_KEY_BLOCK == 0) { g->skeys = realloc(g->skeys, sizeof(struct ssiskey_s) * (g->nsecondary+SSI_KEY_BLOCK)); if (g->skeys == NULL) return SSI_ERR_MALLOC; } return 0; } /* Function: SSIWriteIndex() * Date: SRE, Tue Jan 2 13:55:56 2001 [St. Louis] * * Purpose: Writes complete index {g} in SSI format to a * binary file {file}. Does all * the overhead of sorting the primary and secondary keys, * and maintaining the association of secondary keys * with primary keys during and after the sort. * * Args: file - file to write to * g - index to sort & write out. * * Returns: 0 on success, nonzero on error. */ /* needed for qsort() */ static int pkeysort(const void *k1, const void *k2) { struct ssipkey_s *key1; struct ssipkey_s *key2; key1 = (struct ssipkey_s *) k1; key2 = (struct ssipkey_s *) k2; return strcmp(key1->key, key2->key); } static int skeysort(const void *k1, const void *k2) { struct ssiskey_s *key1; struct ssiskey_s *key2; key1 = (struct ssiskey_s *) k1; key2 = (struct ssiskey_s *) k2; return strcmp(key1->key, key2->key); } int SSIWriteIndex(char *file, SSIINDEX *g) { FILE *fp; int status; int i; sqd_uint32 header_flags, file_flags; sqd_uint32 frecsize, precsize, srecsize; sqd_uint64 foffset, poffset, soffset; char *s, *s2; if ((fp = fopen(file,"wb")) == NULL) return SSI_ERR_NOFILE; status = 0; /* How big is the index? If it's going to be > 2GB, we need * to flip to 64-bit index mode. 2047 (instead of 2048) gives us * some slop room. * die'ing here is pretty brutal - if we flip to 64-bit index * mode, we hve 100's of millions of keys, so we've processed * a long time before reaching this point. Ah well. */ if (current_index_size(g) >= 2047) { g->imode = SSI_OFFSET_I64; #ifndef HAS_64BIT_FILE_OFFSETS Die("\ Can't switch to 64-bit SSI index mode on this system, sorry;\n\ I don't have 64-bit file offset functions available.\n"); #endif } /* Magic-looking numbers come from adding up sizes * of things in bytes */ frecsize = 16 + g->flen; precsize = (g->smode == SSI_OFFSET_I64) ? 22+g->plen : 14+g->plen; srecsize = g->slen + g->plen; header_flags = 0; if (g->smode == SSI_OFFSET_I64) header_flags |= SSI_USE64; if (g->imode == SSI_OFFSET_I64) header_flags |= SSI_USE64_INDEX; /* Magic-looking numbers again come from adding up sizes * of things in bytes */ foffset = (header_flags & SSI_USE64_INDEX) ? 66 : 54; poffset = foffset + frecsize*g->nfiles; soffset = poffset + precsize*g->nprimary; /* Sort the keys * If external mode, make system calls to UNIX/POSIX "sort" in place, then * open new sorted files for reading thru ptmp and stmp handles. * If internal mode, call qsort. * * Note that you'd better force a POSIX locale for the sort; else, * some silly distro (e.g. Mandrake Linux >=8.1) may have specified * LC_COLLATE=en_US, and this'll give a sort "bug" in which it doesn't * sort by byte order. */ if (g->external) { char cmd[1024]; fclose(g->ptmp); g->ptmp = NULL; sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", g->ptmpfile, g->ptmpfile); if ((status = system(cmd)) != 0) return SSI_ERR_EXTERNAL_SORT; if ((g->ptmp = fopen(g->ptmpfile, "r")) == NULL) return SSI_ERR_EXTERNAL_SORT; fclose(g->stmp); g->stmp = NULL; sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", g->stmpfile, g->stmpfile); if ((status = system(cmd)) != 0) return SSI_ERR_EXTERNAL_SORT; if ((g->stmp = fopen(g->stmpfile, "r")) == NULL) return SSI_ERR_EXTERNAL_SORT; } else { qsort((void *) g->pkeys, g->nprimary, sizeof(struct ssipkey_s), pkeysort); qsort((void *) g->skeys, g->nsecondary, sizeof(struct ssiskey_s), skeysort); } /* Write the header */ if (! write_i32(fp, v20magic)) return SSI_ERR_FWRITE; if (! write_i32(fp, header_flags)) return SSI_ERR_FWRITE; if (! write_i16(fp, g->nfiles)) return SSI_ERR_FWRITE; if (! write_i32(fp, g->nprimary)) return SSI_ERR_FWRITE; if (! write_i32(fp, g->nsecondary)) return SSI_ERR_FWRITE; if (! write_i32(fp, g->flen)) return SSI_ERR_FWRITE; if (! write_i32(fp, g->plen)) return SSI_ERR_FWRITE; if (! write_i32(fp, g->slen)) return SSI_ERR_FWRITE; if (! write_i32(fp, frecsize)) return SSI_ERR_FWRITE; if (! write_i32(fp, precsize)) return SSI_ERR_FWRITE; if (! write_i32(fp, srecsize)) return SSI_ERR_FWRITE; if (g->imode == SSI_OFFSET_I32) { if (! write_i32(fp, foffset)) return SSI_ERR_FWRITE; if (! write_i32(fp, poffset)) return SSI_ERR_FWRITE; if (! write_i32(fp, soffset)) return SSI_ERR_FWRITE; } else { if (! write_i64(fp, foffset)) return SSI_ERR_FWRITE; if (! write_i64(fp, poffset)) return SSI_ERR_FWRITE; if (! write_i64(fp, soffset)) return SSI_ERR_FWRITE; } /* The file section */ if ((s = malloc(sizeof(char) * g->flen)) == NULL) return SSI_ERR_MALLOC; for (i = 0; i < g->nfiles; i++) { file_flags = 0; if (g->bpl[i] > 0 && g->rpl[i] > 0) file_flags |= SSI_FAST_SUBSEQ; strcpy(s, g->filenames[i]); if (fwrite(s, sizeof(char), g->flen, fp) != g->flen) return SSI_ERR_FWRITE; if (! write_i32(fp, g->fileformat[i])) return SSI_ERR_FWRITE; if (! write_i32(fp, file_flags)) return SSI_ERR_FWRITE; if (! write_i32(fp, g->bpl[i])) return SSI_ERR_FWRITE; if (! write_i32(fp, g->rpl[i])) return SSI_ERR_FWRITE; } free(s); /* The primary key section */ if ((s = malloc(sizeof(char) * g->plen)) == NULL) return SSI_ERR_MALLOC; if (g->external) { char *buf = NULL; int buflen = 0; struct ssipkey_s pkey; for (i = 0; i < g->nprimary; i++) { if (sre_fgets(&buf, &buflen, g->ptmp) == NULL) return SSI_ERR_NODATA; if (parse_pkey_info(buf, g->smode, &pkey) != 0) return SSI_ERR_BADFORMAT; strcpy(s, pkey.key); if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE; if (! write_i16( fp, pkey.fnum)) return SSI_ERR_FWRITE; if (! write_offset(fp, &(pkey.r_off))) return SSI_ERR_FWRITE; if (! write_offset(fp, &(pkey.d_off))) return SSI_ERR_FWRITE; if (! write_i32( fp, pkey.len)) return SSI_ERR_FWRITE; } free(buf); } else { for (i = 0; i < g->nprimary; i++) { strcpy(s, g->pkeys[i].key); if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE; if (! write_i16( fp, g->pkeys[i].fnum)) return SSI_ERR_FWRITE; if (! write_offset(fp, &(g->pkeys[i].r_off))) return SSI_ERR_FWRITE; if (! write_offset(fp, &(g->pkeys[i].d_off))) return SSI_ERR_FWRITE; if (! write_i32( fp, g->pkeys[i].len)) return SSI_ERR_FWRITE; } } /* The secondary key section */ if (g->nsecondary > 0) { if ((s2 = malloc(sizeof(char) * g->slen)) == NULL) return SSI_ERR_MALLOC; if (g->external) { struct ssiskey_s skey; char *buf = NULL; int n = 0; for (i = 0; i < g->nsecondary; i++) { if (sre_fgets(&buf, &n, g->stmp) == NULL) return SSI_ERR_NODATA; if (parse_skey_info(buf, &skey) != 0) return SSI_ERR_BADFORMAT; strcpy(s2, skey.key); strcpy(s, skey.pkey); if (fwrite(s2, sizeof(char), g->slen, fp) != g->slen) return SSI_ERR_FWRITE; if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE; } free(buf); } else { for (i = 0; i < g->nsecondary; i++) { strcpy(s2, g->skeys[i].key); strcpy(s, g->skeys[i].pkey); if (fwrite(s2, sizeof(char), g->slen, fp) != g->slen) return SSI_ERR_FWRITE; if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE; } } free(s2); } free(s); fclose(fp); return status; } /* Function: SSIFreeIndex() * Date: SRE, Tue Jan 2 11:44:08 2001 [St. Louis] * * Purpose: Free an index structure {g}. * * Args: g - ptr to an open index. * * Returns: (void) */ void SSIFreeIndex(SSIINDEX *g) { int i; if (g != NULL) { if (g->external == FALSE) { for (i = 0; i < g->nprimary; i++) free(g->pkeys[i].key); for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].key); for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].pkey); if (g->pkeys != NULL) free(g->pkeys); if (g->skeys != NULL) free(g->skeys); } else { if (g->ptmp != NULL) fclose(g->ptmp); if (g->stmp != NULL) fclose(g->stmp); #if DEBUGLEVEL == 0 remove(g->ptmpfile); remove(g->stmpfile); #endif } for (i = 0; i < g->nfiles; i++) free(g->filenames[i]); if (g->filenames != NULL) free(g->filenames); if (g->fileformat != NULL) free(g->fileformat); if (g->bpl != NULL) free(g->bpl); if (g->rpl != NULL) free(g->rpl); free(g); } } /* Function: SSIErrorString() * Date: SRE, Tue Jan 2 10:38:10 2001 [St. Louis] * * Purpose: Returns a ptr to an internal string corresponding * to error {n}, a code returned from any of the * functions in the API that return non-zero on error. * * Args: n - error code * * Returns: ptr to an internal string. */ char * SSIErrorString(int n) { switch (n) { case SSI_ERR_OK: return "ok (no error)"; case SSI_ERR_NODATA: return "no data, fread() failed"; case SSI_ERR_NO_SUCH_KEY: return "no such key"; case SSI_ERR_MALLOC: return "out of memory, malloc() failed"; case SSI_ERR_NOFILE: return "file not found, fopen() failed"; case SSI_ERR_BADMAGIC: return "not a SSI file? (bad magic)"; case SSI_ERR_BADFORMAT: return "corrupt format? unexpected data"; case SSI_ERR_NO64BIT: return "no large file support for this system"; case SSI_ERR_SEEK_FAILED: return "failed to reposition on disk"; case SSI_ERR_TELL_FAILED: return "failed to get file position on disk"; case SSI_ERR_NO_SUBSEQS: return "no fast subseq support for this seqfile"; case SSI_ERR_RANGE: return "subseq start is out of range"; case SSI_ERR_BADARG: return "an argument is out of range"; case SSI_ERR_TOOMANY_FILES: return "number of files exceeds limit"; case SSI_ERR_TOOMANY_KEYS: return "number of keys exceeds limit"; case SSI_ERR_FWRITE: return "an fwrite() failed"; case SSI_ERR_EXTERNAL_SORT: return "some problem with external sorting"; default: return "unrecognized code"; } /*NOTREACHED*/ } static int read_i16(FILE *fp, sqd_uint16 *ret_result) { sqd_uint16 result; if (fread(&result, sizeof(sqd_uint16), 1, fp) != 1) return 0; *ret_result = sre_ntoh16(result); return 1; } static int write_i16(FILE *fp, sqd_uint16 n) { n = sre_hton16(n); if (fwrite(&n, sizeof(sqd_uint16), 1, fp) != 1) return 0; return 1; } static int read_i32(FILE *fp, sqd_uint32 *ret_result) { sqd_uint32 result; if (fread(&result, sizeof(sqd_uint32), 1, fp) != 1) return 0; *ret_result = sre_ntoh32(result); return 1; } static int write_i32(FILE *fp, sqd_uint32 n) { n = sre_hton32(n); if (fwrite(&n, sizeof(sqd_uint32), 1, fp) != 1) return 0; return 1; } static int read_i64(FILE *fp, sqd_uint64 *ret_result) { sqd_uint64 result; if (fread(&result, sizeof(sqd_uint64), 1, fp) != 1) return 0; *ret_result = sre_ntoh64(result); return 1; } static int write_i64(FILE *fp, sqd_uint64 n) { n = sre_hton64(n); if (fwrite(&n, sizeof(sqd_uint64), 1, fp) != 1) return 0; return 1; } static int read_offset(FILE *fp, char mode, SSIOFFSET *ret_offset) { if (mode == SSI_OFFSET_I32) { ret_offset->mode = SSI_OFFSET_I32; if (! read_i32(fp, &(ret_offset->off.i32))) return 0; } else if (mode == SSI_OFFSET_I64) { ret_offset->mode = SSI_OFFSET_I64; if (! read_i64(fp, &(ret_offset->off.i64))) return 0; } else return 0; return 1; } static int write_offset(FILE *fp, SSIOFFSET *offset) { if (offset->mode == SSI_OFFSET_I32) return write_i32(fp, offset->off.i32); else if (offset->mode == SSI_OFFSET_I64) return write_i64(fp, offset->off.i64); else abort(); /*UNREACHED*/ return 1; /* silence bitchy compilers */ } static int parse_pkey_info(char *buf, char mode, struct ssipkey_s *pkey) { char *s, *tok; int n; s = buf; if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->key = tok; if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->fnum = (sqd_uint16) atoi(tok); if (mode == SSI_OFFSET_I32) { if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->r_off.mode = mode; pkey->r_off.off.i32 = (sqd_uint32) strtoul(tok, NULL, 10); if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->d_off.mode = mode; pkey->d_off.off.i32 = (sqd_uint32) strtoul(tok, NULL, 10); } #ifdef HAS_64BIT_FILE_OFFSETS else { if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->r_off.mode = mode; pkey->r_off.off.i64 = (sqd_uint64) strtoull(tok, NULL, 10); if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->d_off.mode = mode; pkey->d_off.off.i64 = (sqd_uint64) strtoull(tok, NULL, 10); } #else else { return SSI_ERR_NO64BIT; } #endif if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; pkey->len = (sqd_uint32) strtoul(tok, NULL, 10); return 0; } static int parse_skey_info(char *buf, struct ssiskey_s *skey) { char *s, *tok; int n; s = buf; if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; skey->key = tok; if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT; skey->pkey = tok; return 0; } /* Function: binary_search() * Date: SRE, Sun Dec 31 16:05:03 2000 [St. Louis] * * Purpose: Find a key in a SSI index, by a binary search * in an alphabetically sorted list of keys. If successful, * return 0, and the index file is positioned to read * the rest of the data for that key. Else returns nonzero. * * Args: sfp - an open SSIFILE * key - key to find * klen - key length to allocate (plen or slen from sfp) * base - base offset (poffset or soffset) * recsize - size of each key record in bytes (precsize or srecsize) * maxidx - # of keys (nprimary or nsecondary) * * Returns: 0 on success, and leaves file positioned for reading remaining * data for the key. * Nonzero on failure: * SSI_ERR_NO_SUCH_KEY - that key's not in the index * SSI_ERR_MALLOC - a memory allocation failure * SSI_ERR_NODATA - an fread() failed */ static int binary_search(SSIFILE *sfp, char *key, int klen, SSIOFFSET *base, sqd_uint32 recsize, sqd_uint32 maxidx) { char *name; sqd_uint32 left, right, mid; int cmp; int status; if (maxidx == 0) return SSI_ERR_NO_SUCH_KEY; /* special case: empty index */ if ((name = malloc (sizeof(char)*klen)) == NULL) return SSI_ERR_MALLOC; left = 0; right = maxidx-1; while (1) { /* A binary search: */ mid = (left+right) / 2; /* careful here. only works because we limit unsigned vars to signed ranges. */ if ((status = indexfile_position(sfp, base, recsize, mid)) != 0) { free(name); return status; } if (fread(name, sizeof(char), klen, sfp->fp) != klen) { free(name); return SSI_ERR_NODATA; } cmp = strcmp(name, key); if (cmp == 0) break; /* found it! */ else if (left >= right) /* oops, missed it; fail */ { free(name); return SSI_ERR_NO_SUCH_KEY; } else if (cmp < 0) left = mid+1; /* it's right of mid */ else if (cmp > 0) { if (mid == 0) { free(name); return SSI_ERR_NO_SUCH_KEY; } /* special case, beware */ else right = mid-1; /* it's left of mid */ } } free(name); return 0; /* and sfp->fp is positioned... */ } /* Function: indexfile_position() * Date: SRE, Mon Jan 1 19:32:49 2001 [St. Louis] * * Purpose: Position the open index file {sfp} at the start * of record {n} in a list of records that starts at * base offset {base}, where each record takes up {l} * bytes. (e.g. the position is byte (base + n*l)). * * Args: sfp - open SSIFILE * base - offset of record 0 (e.g. sfp->foffset) * len - size of each record in bytes (e.g. sfp->frecsize) * n - which record to get (e.g. 0..sfp->nfiles) * * Returns: 0 on success, non-zero on failure. */ static int indexfile_position(SSIFILE *sfp, SSIOFFSET *base, sqd_uint32 len, sqd_uint32 n) { SSIOFFSET pos; int status; if (base->mode == SSI_OFFSET_I32) { pos.mode = SSI_OFFSET_I32; pos.off.i32 = base->off.i32 + n*len; } else if (base->mode == SSI_OFFSET_I64) { pos.mode = SSI_OFFSET_I64; pos.off.i64 = base->off.i64 + n*len; } else return 0; if ((status = SSISetFilePosition(sfp->fp, &pos)) != 0) return status; return 0; } /* Function: current_index_size() * Date: SRE, Tue Feb 20 18:23:30 2001 [St. Louis] * * Purpose: Calculates the size of the current index, * in megabytes. */ static sqd_uint64 current_index_size(SSIINDEX *g) { sqd_uint64 frecsize, precsize, srecsize; sqd_uint64 total; /* Magic-looking numbers come from adding up sizes * of things in bytes */ frecsize = 16 + g->flen; precsize = (g->smode == SSI_OFFSET_I64) ? 22+g->plen : 14+g->plen; srecsize = g->plen+g->slen; total = (66L + /* header size, if 64bit index offsets */ frecsize * g->nfiles + /* file section size */ precsize * g->nprimary + /* primary key section size */ srecsize * g->nsecondary) / /* secondary key section size */ 1048576L; return total; } /* Function: activate_external_sort() * Date: SRE, Mon Feb 4 09:08:08 2002 [St. Louis] * * Purpose: Switch to external sort mode. * Open file handles for external index files (ptmp, stmp). * Flush current index information to these files. * Free current memory, turn over control to the tmpfiles. * * Return: 0 on success; non-zero on failure. */ static int activate_external_sort(SSIINDEX *g) { int i; /* it's a bit late to be checking this, but... */ if (g->external) return 0; /* we already are external, fool */ if (FileExists(g->ptmpfile)) return 1; if (FileExists(g->stmpfile)) return 1; if ((g->ptmp = fopen(g->ptmpfile, "w")) == NULL) return 1; if ((g->stmp = fopen(g->stmpfile, "w")) == NULL) return 1; /* Flush the current indices. */ SQD_DPRINTF1(("Switching to external sort - flushing ssiindex to disk...\n")); for (i = 0; i < g->nprimary; i++) { if (g->smode == SSI_OFFSET_I32) { fprintf(g->ptmp, "%s\t%u\t%lu\t%lu\t%lu\n", g->pkeys[i].key, g->pkeys[i].fnum, (unsigned long) g->pkeys[i].r_off.off.i32, (unsigned long) g->pkeys[i].d_off.off.i32, (unsigned long) g->pkeys[i].len); } else { fprintf(g->ptmp, "%s\t%u\t%llu\t%llu\t%lu\n", g->pkeys[i].key, g->pkeys[i].fnum, (unsigned long long) g->pkeys[i].r_off.off.i64, (unsigned long long) g->pkeys[i].d_off.off.i64, (unsigned long) g->pkeys[i].len); } } for (i = 0; i < g->nsecondary; i++) fprintf(g->stmp, "%s\t%s\n", g->skeys[i].key, g->skeys[i].pkey); /* Free the memory now that we've flushed our lists to disk */ for (i = 0; i < g->nprimary; i++) free(g->pkeys[i].key); for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].key); for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].pkey); if (g->pkeys != NULL) free(g->pkeys); if (g->skeys != NULL) free(g->skeys); g->pkeys = NULL; g->skeys = NULL; /* Turn control over to external accumulation mode. */ g->external = TRUE; return 0; } /***************************************************************** * Debugging API *****************************************************************/ void SSIForceExternalSort(SSIINDEX *g) { if (activate_external_sort(g) != 0) Die("failed to turn external sorting on."); } /***************************************************************** * Test driving mode *****************************************************************/ #ifdef MUGGINS_LETS_ME_SLEEP /* Minimally: cc -g -Wall -o shiva -DDEBUGLEVEL=1 -DMUGGINS_LETS_ME_SLEEP ssi.c sqerror.c sre_string.c types.c sre_ctype.c sre_math.c file.c -lm */ int main(int argc, char **argv) { char name[32], accession[32]; SSIINDEX *ssi; int mode; SSIOFFSET r_off, d_off; FILE *ofp; int i; int fh; /* a file handle */ int status; /* return status from a SSI call */ mode = SSI_OFFSET_I32; if ((ssi = SSICreateIndex(mode)) == NULL) Die("Failed to allocate SSI index"); /* Generate two FASTA files, tmp.0 and tmp.1, and index them. */ if ((ofp = fopen("tmp.0", "w")) == NULL) Die("failed to open tmp.0"); if ((status = SSIAddFileToIndex(ssi, "tmp.0", SQFILE_FASTA, &fh)) != 0) Die("SSIAddFileToIndex() failed: %s", SSIErrorString(status)); for (i = 0; i < 10; i++) { if ((status = SSIGetFilePosition(ofp, mode, &r_off)) != 0) Die("SSIGetFilePosition() failed: %s", SSIErrorString(status)); sprintf(name, "seq%d", i); sprintf(accession, "ac%d", i); fprintf(ofp, ">%s [%s] Description? we don't need no steenking description.\n", name, accession); if ((status = SSIGetFilePosition(ofp, mode, &d_off)) != 0) Die("SSIGetFilePosition() failed: %s", SSIErrorString(status)); fprintf(ofp, "AAAAAAAAAA\n"); fprintf(ofp, "CCCCCCCCCC\n"); fprintf(ofp, "GGGGGGGGGG\n"); fprintf(ofp, "TTTTTTTTTT\n"); if ((status = SSIAddPrimaryKeyToIndex(ssi, name, fh, &r_off, &d_off, 40)) != 0) Die("SSIAddPrimaryKeyToIndex() failed: %s", SSIErrorString(status)); if ((status = SSIAddSecondaryKeyToIndex(ssi, accession, name)) != 0) Die("SSIAddSecondaryKeyToIndex() failed: %s", SSIErrorString(status)); } SSISetFileForSubseq(ssi, fh, 11, 10); fclose(ofp); if ((ofp = fopen("tmp.1", "w")) == NULL) Die("failed to open tmp.1"); if ((status = SSIAddFileToIndex(ssi, "tmp.1", SQFILE_FASTA, &fh)) != 0) Die("SSIAddFileToIndex() failed: %s", SSIErrorString(status)); for (i = 10; i < 20; i++) { if ((status = SSIGetFilePosition(ofp, mode, &r_off)) != 0) Die("SSIGetFilePosition() failed: %s", SSIErrorString(status)); sprintf(name, "seq%d", i); sprintf(accession, "ac%d", i); fprintf(ofp, ">%s [%s] i/o, i/o, it's off to disk we go.\n", name, accession); if ((status = SSIGetFilePosition(ofp, mode, &d_off)) != 0) Die("SSIGetFilePosition() failed: %s", SSIErrorString(status)); fprintf(ofp, "AAAAAAAAAA 10\n"); fprintf(ofp, "CCCCCCCCCC 20\n"); fprintf(ofp, "GGGGGGGGGG 30\n"); fprintf(ofp, "TTTTTTTTTT 40\n"); if ((status = SSIAddPrimaryKeyToIndex(ssi, name, fh, &r_off, &d_off, 40)) != 0) Die("SSIAddPrimaryKeyToIndex() failed: %s", SSIErrorString(status)); if ((status = SSIAddSecondaryKeyToIndex(ssi, accession, name)) != 0) Die("SSIAddSecondaryKeyToIndex() failed: %s", SSIErrorString(status)); } SSISetFileForSubseq(ssi, fh, 14, 10); fclose(ofp); /* Write the index to tmp.ssi */ if ((status = SSIWriteIndex("tmp.ssi", ssi)) != 0) Die("SSIWriteIndex() failed: %s", SSIErrorString(status)); SSIFreeIndex(ssi); /* Now reopen the index and run some tests. */ exit(0); } #endif /* test driving code */ squid/stockholm.c0000640000175000017520000004501110463223377014263 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* stockholm.c * SRE, Fri May 28 15:46:41 1999 * * Reading/writing of Stockholm format multiple sequence alignments. * * example of API: * * MSA *msa; * FILE *fp; -- opened for write with fopen() * MSAFILE *afp; -- opened for read with MSAFileOpen() * * while ((msa = ReadStockholm(afp)) != NULL) * { * WriteStockholm(fp, msa); * MSAFree(msa); * } * * RCS $Id: stockholm.c,v 1.8 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "msa.h" static int parse_gf(MSA *msa, char *buf); static int parse_gs(MSA *msa, char *buf); static int parse_gc(MSA *msa, char *buf); static int parse_gr(MSA *msa, char *buf); static int parse_comment(MSA *msa, char *buf); static int parse_sequence(MSA *msa, char *buf); static void actually_write_stockholm(FILE *fp, MSA *msa, int cpl); #ifdef TESTDRIVE_STOCKHOLM /***************************************************************** * stockholm.c test driver: * cc -DTESTDRIVE_STOCKHOLM -g -O2 -Wall -o test stockholm.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm * */ int main(int argc, char **argv) { MSAFILE *afp; MSA *msa; char *file; file = argv[1]; if ((afp = MSAFileOpen(file, MSAFILE_STOCKHOLM, NULL)) == NULL) Die("Couldn't open %s\n", file); while ((msa = ReadStockholm(afp)) != NULL) { WriteStockholm(stdout, msa); MSAFree(msa); } MSAFileClose(afp); exit(0); } /******************************************************************/ #endif /* testdriver */ /* Function: ReadStockholm() * Date: SRE, Fri May 21 17:33:10 1999 [St. Louis] * * Purpose: Parse the next alignment from an open Stockholm * format alignment file. Return the alignment, or * NULL if there are no more alignments in the file. * * Args: afp - open alignment file * * Returns: MSA * - an alignment object. * caller responsible for an MSAFree() * NULL if no more alignments * * Diagnostics: * Will Die() here with a (potentially) useful message * if a parsing error occurs */ MSA * ReadStockholm(MSAFILE *afp) { MSA *msa; char *s; int status; if (feof(afp->f)) return NULL; /* Initialize allocation of the MSA. */ msa = MSAAlloc(10, 0); /* Check the magic Stockholm header line. * We have to skip blank lines here, else we perceive * trailing blank lines in a file as a format error when * reading in multi-record mode. */ do { if ((s = MSAFileGetLine(afp)) == NULL) { MSAFree(msa); return NULL; } } while (IsBlankline(s)); if (strncmp(s, "# STOCKHOLM 1.", 14) != 0) Die("\ File %s doesn't appear to be in Stockholm format.\n\ Assuming there isn't some other problem with your file (it is an\n\ alignment file, right?), please either:\n\ a) use the Babelfish format autotranslator option (-B, usually);\n\ b) specify the file's format with the --informat option; or\n\ a) reformat the alignment to Stockholm format.\n", afp->fname); /* Read the alignment file one line at a time. */ while ((s = MSAFileGetLine(afp)) != NULL) { while (*s == ' ' || *s == '\t') s++; /* skip leading whitespace */ if (*s == '#') { if (strncmp(s, "#=GF", 4) == 0) status = parse_gf(msa, s); else if (strncmp(s, "#=GS", 4) == 0) status = parse_gs(msa, s); else if (strncmp(s, "#=GC", 4) == 0) status = parse_gc(msa, s); else if (strncmp(s, "#=GR", 4) == 0) status = parse_gr(msa, s); else status = parse_comment(msa, s); } else if (strncmp(s, "//", 2) == 0) break; else if (*s == '\n') continue; else status = parse_sequence(msa, s); if (status == 0) Die("Stockholm format parse error: line %d of file %s while reading alignment %s", afp->linenumber, afp->fname, msa->name == NULL? "" : msa->name); } if (s == NULL && msa->nseq != 0) Die ("Didn't find // at end of alignment %s", msa->name == NULL ? "" : msa->name); if (s == NULL && msa->nseq == 0) { /* probably just some junk at end of file */ MSAFree(msa); return NULL; } MSAVerifyParse(msa); return msa; } /* Function: WriteStockholm() * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis] * * Purpose: Write an alignment in standard multi-block * Stockholm format to an open file. A wrapper * for actually_write_stockholm(). * * Args: fp - file that's open for writing * msa - alignment to write * * Returns: (void) */ void WriteStockholm(FILE *fp, MSA *msa) { actually_write_stockholm(fp, msa, 50); /* 50 char per block */ } /* Function: WriteStockholmOneBlock() * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis] * * Purpose: Write an alignment in Pfam's single-block * Stockholm format to an open file. A wrapper * for actually_write_stockholm(). * * Args: fp - file that's open for writing * msa - alignment to write * * Returns: (void) */ void WriteStockholmOneBlock(FILE *fp, MSA *msa) { actually_write_stockholm(fp, msa, msa->alen); /* one big block */ } /* Function: actually_write_stockholm() * Date: SRE, Fri May 21 17:39:22 1999 [St. Louis] * * Purpose: Write an alignment in Stockholm format to * an open file. This is the function that actually * does the work. The API's WriteStockholm() * and WriteStockholmOneBlock() are wrappers. * * Args: fp - file that's open for writing * msa - alignment to write * cpl - characters to write per line in alignment block * * Returns: (void) */ static void actually_write_stockholm(FILE *fp, MSA *msa, int cpl) { int i, j; int len = 0; int namewidth; int typewidth = 0; /* markup tags are up to 5 chars long */ int markupwidth = 0; /* #=GR, #=GC are four char wide + 1 space */ char *buf; int currpos; char *s, *tok; /* Figure out how much space we need for name + markup * to keep the alignment in register. Required by Stockholm * spec, even though our Stockholm parser doesn't care (Erik's does). */ namewidth = 0; for (i = 0; i < msa->nseq; i++) if ((len = strlen(msa->sqname[i])) > namewidth) namewidth = len; /* Figure out how much space we need for markup tags * markupwidth = always 4 if we're doing markup: strlen("#=GR") * typewidth = longest markup tag */ if (msa->ss != NULL) { markupwidth = 4; typewidth = 2; } if (msa->sa != NULL) { markupwidth = 4; typewidth = 2; } for (i = 0; i < msa->ngr; i++) if ((len = strlen(msa->gr_tag[i])) > typewidth) typewidth = len; if (msa->rf != NULL) { markupwidth = 4; if (typewidth < 2) typewidth = 2; } if (msa->ss_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; } if (msa->sa_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; } for (i = 0; i < msa->ngc; i++) if ((len = strlen(msa->gc_tag[i])) > typewidth) typewidth = len; buf = MallocOrDie(sizeof(char) * (cpl+namewidth+typewidth+markupwidth+61)); /* Magic Stockholm header */ fprintf(fp, "# STOCKHOLM 1.0\n"); /* Free text comments */ for (i = 0; i < msa->ncomment; i++) fprintf(fp, "# %s\n", msa->comment[i]); if (msa->ncomment > 0) fprintf(fp, "\n"); /* GF section: per-file annotation */ if (msa->name != NULL) fprintf(fp, "#=GF ID %s\n", msa->name); if (msa->acc != NULL) fprintf(fp, "#=GF AC %s\n", msa->acc); if (msa->desc != NULL) fprintf(fp, "#=GF DE %s\n", msa->desc); if (msa->au != NULL) fprintf(fp, "#=GF AU %s\n", msa->au); /* Thresholds are hacky. Pfam has two. Rfam has one. */ if (msa->cutoff_is_set[MSA_CUTOFF_GA1] && msa->cutoff_is_set[MSA_CUTOFF_GA2]) fprintf(fp, "#=GF GA %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_GA1], msa->cutoff[MSA_CUTOFF_GA2]); else if (msa->cutoff_is_set[MSA_CUTOFF_GA1]) fprintf(fp, "#=GF GA %.1f\n", msa->cutoff[MSA_CUTOFF_GA1]); if (msa->cutoff_is_set[MSA_CUTOFF_NC1] && msa->cutoff_is_set[MSA_CUTOFF_NC2]) fprintf(fp, "#=GF NC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_NC1], msa->cutoff[MSA_CUTOFF_NC2]); else if (msa->cutoff_is_set[MSA_CUTOFF_NC1]) fprintf(fp, "#=GF NC %.1f\n", msa->cutoff[MSA_CUTOFF_NC1]); if (msa->cutoff_is_set[MSA_CUTOFF_TC1] && msa->cutoff_is_set[MSA_CUTOFF_TC2]) fprintf(fp, "#=GF TC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_TC1], msa->cutoff[MSA_CUTOFF_TC2]); else if (msa->cutoff_is_set[MSA_CUTOFF_TC1]) fprintf(fp, "#=GF TC %.1f\n", msa->cutoff[MSA_CUTOFF_TC1]); for (i = 0; i < msa->ngf; i++) fprintf(fp, "#=GF %-5s %s\n", msa->gf_tag[i], msa->gf[i]); fprintf(fp, "\n"); /* GS section: per-sequence annotation */ if (msa->flags & MSA_SET_WGT) { for (i = 0; i < msa->nseq; i++) fprintf(fp, "#=GS %-*.*s WT %.2f\n", namewidth, namewidth, msa->sqname[i], msa->wgt[i]); fprintf(fp, "\n"); } if (msa->sqacc != NULL) { for (i = 0; i < msa->nseq; i++) if (msa->sqacc[i] != NULL) fprintf(fp, "#=GS %-*.*s AC %s\n", namewidth, namewidth, msa->sqname[i], msa->sqacc[i]); fprintf(fp, "\n"); } if (msa->sqdesc != NULL) { for (i = 0; i < msa->nseq; i++) if (msa->sqdesc[i] != NULL) fprintf(fp, "#=GS %*.*s DE %s\n", namewidth, namewidth, msa->sqname[i], msa->sqdesc[i]); fprintf(fp, "\n"); } for (i = 0; i < msa->ngs; i++) { /* Multiannotated GS tags are possible; for example, * #=GS foo DR PDB; 1xxx; * #=GS foo DR PDB; 2yyy; * These are stored, for example, as: * msa->gs[0][0] = "PDB; 1xxx;\nPDB; 2yyy;" * and must be decomposed. */ for (j = 0; j < msa->nseq; j++) if (msa->gs[i][j] != NULL) { s = msa->gs[i][j]; while ((tok = sre_strtok(&s, "\n", NULL)) != NULL) fprintf(fp, "#=GS %*.*s %5s %s\n", namewidth, namewidth, msa->sqname[j], msa->gs_tag[i], tok); } fprintf(fp, "\n"); } /* Alignment section: * contains aligned sequence, #=GR annotation, and #=GC annotation */ for (currpos = 0; currpos < msa->alen; currpos += cpl) { if (currpos > 0) fprintf(fp, "\n"); for (i = 0; i < msa->nseq; i++) { strncpy(buf, msa->aseq[i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "%-*.*s %s\n", namewidth+typewidth+markupwidth, namewidth+typewidth+markupwidth, msa->sqname[i], buf); if (msa->ss != NULL && msa->ss[i] != NULL) { strncpy(buf, msa->ss[i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GR %-*.*s SS %s\n", namewidth, namewidth, msa->sqname[i], buf); } if (msa->sa != NULL && msa->sa[i] != NULL) { strncpy(buf, msa->sa[i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GR %-*.*s SA %s\n", namewidth, namewidth, msa->sqname[i], buf); } for (j = 0; j < msa->ngr; j++) if (msa->gr[j][i] != NULL) { strncpy(buf, msa->gr[j][i] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GR %-*.*s %5s %s\n", namewidth, namewidth, msa->sqname[i], msa->gr_tag[j], buf); } } if (msa->ss_cons != NULL) { strncpy(buf, msa->ss_cons + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "SS_cons", buf); } if (msa->sa_cons != NULL) { strncpy(buf, msa->sa_cons + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "SA_cons", buf); } if (msa->rf != NULL) { strncpy(buf, msa->rf + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "RF", buf); } for (j = 0; j < msa->ngc; j++) { strncpy(buf, msa->gc[j] + currpos, cpl); buf[cpl] = '\0'; fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, msa->gc_tag[j], buf); } } fprintf(fp, "//\n"); free(buf); } /* Format of a GF line: * #=GF */ static int parse_gf(MSA *msa, char *buf) { char *gf; char *featurename; char *text; char *s; s = buf; if ((gf = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0; while (*text && (*text == ' ' || *text == '\t')) text++; if (strcmp(featurename, "ID") == 0) msa->name = sre_strdup(text, -1); else if (strcmp(featurename, "AC") == 0) msa->acc = sre_strdup(text, -1); else if (strcmp(featurename, "DE") == 0) msa->desc = sre_strdup(text, -1); else if (strcmp(featurename, "AU") == 0) msa->au = sre_strdup(text, -1); else if (strcmp(featurename, "GA") == 0) { /* Pfam has GA1, GA2. Rfam just has GA1. */ s = text; if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; msa->cutoff[MSA_CUTOFF_GA1] = atof(text); msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE; if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) { msa->cutoff[MSA_CUTOFF_GA2] = atof(text); msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE; } } else if (strcmp(featurename, "NC") == 0) { s = text; if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; msa->cutoff[MSA_CUTOFF_NC1] = atof(text); msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE; if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) { msa->cutoff[MSA_CUTOFF_NC2] = atof(text); msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE; } } else if (strcmp(featurename, "TC") == 0) { s = text; if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; msa->cutoff[MSA_CUTOFF_TC1] = atof(text); msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE; if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) { msa->cutoff[MSA_CUTOFF_TC2] = atof(text); msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE; } } else MSAAddGF(msa, featurename, text); return 1; } /* Format of a GS line: * #=GS */ static int parse_gs(MSA *msa, char *buf) { char *gs; char *seqname; char *featurename; char *text; int seqidx; char *s; s = buf; if ((gs = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0; while (*text && (*text == ' ' || *text == '\t')) text++; /* GS usually follows another GS; guess lastidx+1 */ seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1); msa->lastidx = seqidx; if (strcmp(featurename, "WT") == 0) { msa->wgt[seqidx] = atof(text); msa->flags |= MSA_SET_WGT; } else if (strcmp(featurename, "AC") == 0) MSASetSeqAccession(msa, seqidx, text); else if (strcmp(featurename, "DE") == 0) MSASetSeqDescription(msa, seqidx, text); else MSAAddGS(msa, featurename, seqidx, text); return 1; } /* Format of a GC line: * #=GC */ static int parse_gc(MSA *msa, char *buf) { char *gc; char *featurename; char *text; char *s; int len; s = buf; if ((gc = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0; if (strcmp(featurename, "SS_cons") == 0) sre_strcat(&(msa->ss_cons), -1, text, len); else if (strcmp(featurename, "SA_cons") == 0) sre_strcat(&(msa->sa_cons), -1, text, len); else if (strcmp(featurename, "RF") == 0) sre_strcat(&(msa->rf), -1, text, len); else MSAAppendGC(msa, featurename, text); return 1; } /* Format of a GR line: * #=GR */ static int parse_gr(MSA *msa, char *buf) { char *gr; char *seqname; char *featurename; char *text; int seqidx; int len; int j; char *s; s = buf; if ((gr = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0; /* GR usually follows sequence it refers to; guess msa->lastidx */ seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx); msa->lastidx = seqidx; if (strcmp(featurename, "SS") == 0) { if (msa->ss == NULL) { msa->ss = MallocOrDie(sizeof(char *) * msa->nseqalloc); msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc); for (j = 0; j < msa->nseqalloc; j++) { msa->ss[j] = NULL; msa->sslen[j] = 0; } } msa->sslen[seqidx] = sre_strcat(&(msa->ss[seqidx]), msa->sslen[seqidx], text, len); } else if (strcmp(featurename, "SA") == 0) { if (msa->sa == NULL) { msa->sa = MallocOrDie(sizeof(char *) * msa->nseqalloc); msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc); for (j = 0; j < msa->nseqalloc; j++) { msa->sa[j] = NULL; msa->salen[j] = 0; } } msa->salen[seqidx] = sre_strcat(&(msa->sa[seqidx]), msa->salen[seqidx], text, len); } else MSAAppendGR(msa, featurename, seqidx, text); return 1; } /* comments are simply stored verbatim, not parsed */ static int parse_comment(MSA *msa, char *buf) { char *s; char *comment; s = buf + 1; /* skip leading '#' */ if (*s == '\n') { *s = '\0'; comment = s; } /* deal with blank comment */ else if ((comment = sre_strtok(&s, "\n", NULL)) == NULL) return 0; MSAAddComment(msa, comment); return 1; } static int parse_sequence(MSA *msa, char *buf) { char *s; char *seqname; char *text; int seqidx; int len; s = buf; if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0; /* seq usually follows another seq; guess msa->lastidx +1 */ seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1); msa->lastidx = seqidx; msa->sqlen[seqidx] = sre_strcat(&(msa->aseq[seqidx]), msa->sqlen[seqidx], text, len); return 1; } squid/stopwatch.c0000640000175000017520000001773210463223377014305 0ustar naolivbiolinux/************************************************************ * @LICENSE@ ************************************************************/ /* stopwatch.c * SRE, Fri Nov 26 14:54:21 1999 [St. Louis] [HMMER] * SRE, Thu Aug 3 08:11:52 2000 [St. Louis] [moved to SQUID] * * Reporting of cpu/system/elapsed time used by a process. * thanks to Warren Gish for assistance. * * Basic API: * * Stopwatch_t *w; * w = StopwatchCreate(); * * StopwatchStart(w); * do_lots_of_stuff; * StopwatchStop(w); * StopwatchDisplay(stdout, "CPU time: ", w); * * StopwatchFree(w); * * Some behavior can be controlled at compile time by #define's: * * SRE_STRICT_ANSI: By default, stopwatch module assumes that a * machine is POSIX-compliant (e.g. has struct tms, sys/times.h, * and times()). If compiled with -DSRE_STRICT_ANSI, reverts to * pure ANSI C conformant implementation. This simpler system * won't report system times, only user and elapsed times. * * SRE_ENABLE_PVM: If compiled with -DSRE_ENABLE_PVM, the * functions StopwatchPVMPack() and StopwatchPVMUnpack() * are compiled, providing PVM communications ability. * * One additional compile-time configuration note: * PTHREAD_TIMES_HACK: Linux pthreads, as of RH6.0/glibc-devel-2.1.1-6, * appears to interact poorly with times() -- usage times in all * but the master thread are lost. A workaround for this bug is * to run stopwatches in each worker thread, and accumulate those * times back into the master stopwatch using StopwatchInclude(). * (Just like a PVM implementation has to do.) In HMMER, this * behavior is compiled in with -DPTHREAD_TIMES_HACK. No * changes are made in stopwatch functions themselves, though; * all the extra code is HMMER code. See hmmcalibrate.c for * an example. * * See hmmcalibrate.c for examples of more complex usage * in dealing with pthreads and PVM. */ #include "squidconf.h" #include #include #include #ifdef SRE_ENABLE_PVM #include #endif #include "stopwatch.h" /* Function: format_time_string() * Date: SRE, Fri Nov 26 15:06:28 1999 [St. Louis] * * Purpose: Given a number of seconds, format into * hh:mm:ss.xx in a provided buffer. * * Args: buf - allocated space (128 is plenty!) * sec - number of seconds * do_frac - TRUE (1) to include hundredths of a sec */ static void format_time_string(char *buf, double sec, int do_frac) { int h, m, s, hs; h = (int) (sec / 3600.); m = (int) (sec / 60.) - h * 60; s = (int) (sec) - h * 3600 - m * 60; if (do_frac) { hs = (int) (sec * 100.) - h * 360000 - m * 6000 - s * 100; sprintf(buf, "%02d:%02d:%02d.%02d", h,m,s,hs); } else { sprintf(buf, "%02d:%02d:%02d", h,m,s); } } /* Function: StopwatchStart() * Date: SRE, Fri Nov 26 15:07:48 1999 [St. Louis] * * Purpose: Start a stopwatch. * * Args: w - the watch */ void StopwatchStart(Stopwatch_t *w) { w->t0 = time(NULL); #ifdef SRE_STRICT_ANSI w->cpu0 = clock(); #else (void) times(&(w->cpu0)); #endif w->elapsed = 0.; w->user = 0.; w->sys = 0.; } /* Function: StopwatchStop() * Date: SRE, Fri Nov 26 15:08:16 1999 [St. Louis] * * Purpose: Stop a stopwatch. * * The implementation allows "split times": * you can stop a watch multiple times, reporting * times at multiple points during program * execution. * * Args: w - the watch */ void StopwatchStop(Stopwatch_t *w) { time_t t1; #ifdef SRE_STRICT_ANSI clock_t cpu1; #else struct tms cpu1; long clk_tck; #endif t1 = time(NULL); w->elapsed = difftime(t1, w->t0); #ifdef SRE_STRICT_ANSI cpu1 = clock(); w->user = (double) (cpu1- w->cpu0) / (double) CLOCKS_PER_SEC; w->sys = 0.; /* no way to portably get system time in ANSI C */ #else /* assume we're on a POSIX system by default */ (void) times(&cpu1); clk_tck = sysconf(_SC_CLK_TCK); w->user = (double) (cpu1.tms_utime + cpu1.tms_cutime - w->cpu0.tms_utime - w->cpu0.tms_cutime) / (double) clk_tck; w->sys = (double) (cpu1.tms_stime + cpu1.tms_cstime - w->cpu0.tms_stime - w->cpu0.tms_cstime) / (double) clk_tck; #endif } /* Function: StopwatchInclude() * Date: SRE, Fri Nov 26 15:09:34 1999 [St. Louis] * * Purpose: Merge the cpu and system times from a slave into * a master stopwatch. Both watches must be * stopped, and should not be stopped again unless * You Know What You're Doing. * * Elapsed time is *not* merged; master is assumed * to be keeping track of the wall clock time, * and the slave/worker watch is ignored. * * Used in two cases: * 1) PVM; merge in the stopwatch(es) from separate * process(es) in a cluster. * 2) Threads, for broken pthreads/times() implementations * that lose track of cpu times used by spawned * threads. * * Args: w1 - the master stopwatch * w2 - the slave/worker watch * */ void StopwatchInclude(Stopwatch_t *w1, Stopwatch_t *w2) { w1->user += w2->user; w1->sys += w2->sys; } /* Function: StopwatchAlloc(), StopwatchZero(), StopwatchCopy(), * StopwatchFree() * Date: SRE, Fri Nov 26 15:13:14 1999 [St. Louis] * * Purpose: The usual creation/manipulation/destruction routines * for a stopwatch object. */ Stopwatch_t * StopwatchCreate(void) { Stopwatch_t *w; w = malloc(sizeof(Stopwatch_t)); return w; } void StopwatchZero(Stopwatch_t *w) { w->elapsed = 0.; w->user = 0.; w->sys = 0.; } void StopwatchCopy(Stopwatch_t *w1, Stopwatch_t *w2) { w1->t0 = w2->t0; #ifdef SRE_STRICT_ANSI w1->cpu0 = w2->cpu0; #else w1->cpu0.tms_utime = w2->cpu0.tms_utime; w1->cpu0.tms_stime = w2->cpu0.tms_stime; w1->cpu0.tms_cutime = w2->cpu0.tms_cutime; w1->cpu0.tms_cstime = w2->cpu0.tms_cstime; #endif w1->elapsed = w2->elapsed; w1->user = w2->user; w1->sys = w2->sys; } void StopwatchFree(Stopwatch_t *w) { free(w); } /* Function: StopwatchDisplay() * Date: SRE, Fri Nov 26 15:14:12 1999 [St. Louis] * * Purpose: Output a usage summary line from a *stopped* * stopwatch (the times will reflect the last * time StopwatchStop() was called.) * * For s = "CPU Time: " an example output line is: * CPU Time: 142.55u 7.17s 149.72 Elapsed: 00:02:35.00 * * Args: fp - open file for writing (stdout, possibly) * s - prefix for the report line * w - a (recently stopped) stopwatch * */ void StopwatchDisplay(FILE *fp, char *s, Stopwatch_t *w) { char buf[128]; /* (safely holds up to 10^14 years) */ if (s == NULL) fputs("CPU Time: ", fp); else fputs(s, fp); format_time_string(buf, w->user+w->sys, 1); #ifdef SRE_STRICT_ANSI fprintf(fp, "%.2fu %s ", w->user, buf); #else fprintf(fp, "%.2fu %.2fs %s ", w->user, w->sys, buf); #endif format_time_string(buf, w->elapsed, 0); fprintf(fp, "Elapsed: %s\n", buf); } #ifdef SRE_ENABLE_PVM /* Function: StopwatchPVMPack(), StopwatchPVMUnpack() * Date: SRE, Fri Nov 26 15:22:04 1999 [St. Louis] * * Purpose: Transmission of stopwatch data in a PVM * cluster. */ void StopwatchPVMPack(Stopwatch_t *w) { pvm_pkdouble(&(w->elapsed), 1, 1); pvm_pkdouble(&(w->user), 1, 1); pvm_pkdouble(&(w->sys), 1, 1); } void StopwatchPVMUnpack(Stopwatch_t *w) { pvm_upkdouble(&(w->elapsed), 1, 1); pvm_upkdouble(&(w->user), 1, 1); pvm_upkdouble(&(w->sys), 1, 1); } #endif /*SRE_ENABLE_PVM*/ #ifdef TESTDRIVER int main(int argc, char **argv) { Stopwatch_t stopwatch; StopwatchStart(&stopwatch); sleep(5); StopwatchStop(&stopwatch); StopwatchDisplay(stdout, "CPU Time: ", &stopwatch); } #endif squid/test_main.c0000640000175000017520000000070010463223377014237 0ustar naolivbiolinux/* Test of the file.c functions * cp to ../test_main.c and "make test". * Usage: ./test */ #include "squidconf.h" #include #include #include "squid.h" int main(int argc, char **argv) { char *env; char *file; FILE *fp; env = argv[1]; file = argv[2]; fp = EnvFileOpen(file, env); if (fp != NULL) printf("File open succeeded\n"); else printf("File open FAILED\n"); return 0; } squid/translate.c0000640000175000017520000000423010463223377014253 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* * translate.c - functions for translating nucleic acid sequence * created Tue Jan 12 11:27:29 1993, SRE * * RCS $Id: translate.c,v 1.3 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" /* Function: Translate(char *seq, char **code) * * Given a ptr to the start of a nucleic acid sequence, * and a genetic code, translate the sequence into * amino acid sequence. * * code is an array of 65 strings, representing * the translations of the 64 codons, arranged * in order AAA, AAC, AAG, AAU, ..., UUA, UUC, UUG, UUU. * '*' or '***' is used to represent termination * codons, usually. The final string, code[64], * is the code for an ambiguous amino acid. * * Because of the way space is allocated for the amino * acid sequence, the amino acid strings cannot be * longer than 3 letters each. (I don't foresee using * anything but the single- and triple- letter codes.) * * Returns a ptr to the translation string on success, * or NULL on failure. */ char * Translate(char *seq, char **code) { int codon; /* index for codon */ char *aaseq; /* RETURN: the translation */ char *aaptr; /* ptr into aaseq */ int i; if (seq == NULL) { squid_errno = SQERR_NODATA; return NULL; } if ((aaseq = (char *) calloc (strlen(seq) + 1, sizeof(char))) == NULL) Die("calloc failed"); aaptr = aaseq; for (; *seq != '\0' && *(seq+1) != '\0' && *(seq+2) != '\0'; seq += 3) { /* calculate the lookup value for this codon */ codon = 0; for (i = 0; i < 3; i++) { codon *= 4; switch (*(seq + i)) { case 'A': case 'a': break; case 'C': case 'c': codon += 1; break; case 'G': case 'g': codon += 2; break; case 'T': case 't': codon += 3; break; case 'U': case 'u': codon += 3; break; default: codon = 64; break; } if (codon == 64) break; } strcpy(aaptr, code[codon]); aaptr += strlen(code[codon]); } return aaseq; } squid/translate_main.c0000640000175000017520000002115010463223377015257 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* translate_main.c * * translate - create a file of all possible protein ORFs, given * an input nucleic acid sequence * * 1.02 Thu Apr 20 16:12:41 1995 * + incorporated into squid * + -a, -s options added * * CVS $Id: translate_main.c,v 1.10 2004/09/12 22:48:26 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "squid.h" static char banner[] = "translate - Translate a nucleic acid sequence to protein ORFs"; static char usage[] = "\ Usage: translate [-options] \n\ Translate a nucleic acid sequence into protein ORFs.\n\ Available options are:\n\ -a : translate in full, with stops; no individual ORFs\n\ -h : help; show brief usage and version info\n\ -l : report only ORFs greater than minlen (default 20)\n\ -m : require ORFs to start with AUG/Met\n\ -o : save results in output file\n\ -q : quiet; silence banner, for piping or redirection\n\ -s : with -a, set stop character to \n\ "; static char experts[] = "\ --tetrahymena : use the Tetrahymena/Oxytricha genetic code\n\ --watson : only do the top strand (frames 0/1/2)\n\ --crick : only do the bottom strand (frames 3/4/5)\n\ "; static struct opt_s OPTIONS[] = { { "-a", TRUE, sqdARG_NONE }, { "-h", TRUE, sqdARG_NONE }, { "-l", TRUE, sqdARG_INT }, { "-m", TRUE, sqdARG_NONE }, { "-o", TRUE, sqdARG_STRING }, { "-q", TRUE, sqdARG_NONE }, { "-c", TRUE, sqdARG_STRING }, { "--tetrahymena", FALSE, sqdARG_NONE }, { "--watson", FALSE, sqdARG_NONE }, { "--crick", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *seqfile; /* name of seq file to read */ SQFILE *seqfp; /* ptr to opened seq file */ int format; /* format of sequence file */ char *seq; /* ptr to current sequence */ SQINFO sqinfo; /* sequence information */ char *revseq; /* reverse complement of seq */ int start, end; /* coords of ORF in current seq */ int orfnumber; /* counter for ORFs in current seq */ char *aaseq[6]; /* full translations in all 6 frames */ int do_frame[6]; /* TRUE/FALSE for which frames to do */ char *orf; /* ptr to translated ORF sequence */ char *sptr; /* ptr into orf */ int len; /* length of an ORF */ int frame; /* counter for frames (3..5 are reverse)*/ int minimum_len; /* minimum length of ORFs to print out */ char *outfile; /* file to save output in */ FILE *ofp; /* where to direct output */ char stopchar; /* what to use as a stop character */ int keepstops; /* TRUE to do six big ORFs */ int quiet; /* TRUE to silence banner */ int require_met; /* TRUE to start orfs with M */ int do_tetrahymena; /* TRUE to use the tetrahymena code */ char *optname; /* option character */ char *optarg; /* for Getopt() */ int optind; /* for Getopt() */ /*********************************************** * Parse the command line ***********************************************/ format = SQFILE_UNKNOWN; /* autodetect by default */ minimum_len = 20; outfile = NULL; stopchar = '*'; keepstops = FALSE; quiet = FALSE; require_met = FALSE; do_tetrahymena = FALSE; for (frame = 0; frame < 6; frame++) do_frame[frame] = TRUE; while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-a") == 0) keepstops = TRUE; else if (strcmp(optname, "-l") == 0) minimum_len = atoi(optarg); else if (strcmp(optname, "-m") == 0) require_met = TRUE; else if (strcmp(optname, "-o") == 0) outfile = optarg; else if (strcmp(optname, "-q") == 0) quiet = TRUE; else if (strcmp(optname, "-s") == 0) stopchar = *optarg; else if (strcmp(optname, "--tetrahymena") == 0) do_tetrahymena = TRUE; else if (strcmp(optname, "--crick") == 0) { for (frame = 0; frame < 3; frame++) do_frame[frame] = FALSE; } else if (strcmp(optname, "--watson") == 0) { for (frame = 3; frame < 6; frame++) do_frame[frame] = FALSE; } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc - optind != 1) Die("Incorrect number of command line arguments\n%s\n", usage); seqfile = argv[optind]; /*********************************************** * Open sequence file and output file ***********************************************/ seqfp = SeqfileOpen(seqfile, format, NULL); if (seqfp == NULL) Die("Failed to open sequence file %s\n%s\n", seqfile, usage); if (outfile != NULL) { if ((ofp = fopen(outfile, "w")) == NULL) Die("Failed to open output file %s\n", outfile); } else ofp = stdout; /*********************************************** * Set up alternative genetic codes; overwrite stdcode1 * UAA = 48 in this coding A=0 C=1 G=2 T=3 * UAG = 50 XYZ = 16*X + 4*Y + Z * UGA = 56 * * http://prowl.rockefeller.edu/aainfo/gencode.html is * a quick reference for alternative codes. ***********************************************/ if (do_tetrahymena) { stdcode1[48] = "Q"; stdcode3[48] = "Gln"; /* UAA */ stdcode1[50] = "Q"; stdcode3[50] = "Gln"; /* UAG */ } /*********************************************** * Main routine ***********************************************/ if (! quiet) printf("translate %s, %s\n", SQUID_VERSION, SQUID_DATE); while (ReadSeq(seqfp, seqfp->format, &seq, &sqinfo)) { s2upper(seq); revseq = (char *) malloc (sqinfo.len + 1); revcomp(revseq, seq); orfnumber = 1; /* Translate seq in all six frames */ aaseq[0] = Translate(seq, stdcode1); aaseq[1] = Translate(seq + 1, stdcode1); aaseq[2] = Translate(seq + 2, stdcode1); aaseq[3] = Translate(revseq, stdcode1); aaseq[4] = Translate(revseq + 1, stdcode1); aaseq[5] = Translate(revseq + 2, stdcode1); if (keepstops) { /* full translation including stops */ for (frame = 0; frame < 6; frame++) { if (! do_frame[frame]) continue; fprintf(ofp, ">%s:%d", sqinfo.name, frame); for (sptr = aaseq[frame]; *sptr; sptr++) { if (*sptr == '*') *sptr = stopchar; if (! ((sptr - aaseq[frame]) % 50)) putc('\n', ofp); putc((int) *sptr, ofp); } putc('\n', ofp); } } else { /* Print all decent ORF's in FASTA format */ for (frame = 0; frame < 6; frame++) { if (! do_frame[frame]) continue; /* initialize strtok on the first ORF; termination codons are '*' symbols */ orf = strtok(aaseq[frame], "*"); while (orf != NULL && *orf != '\0') { if (require_met) { while (*orf != 'M' && *orf != '\0') orf++; } if (*orf != '\0') { len = strlen(orf); if (len > minimum_len) { /* calculate coords */ start = (orf - aaseq[frame]) * 3 + 1; if (frame < 3) start += frame; /* frame corrections */ else start += frame-3; if (frame < 3) end = start + len * 3 - 1; else { start = -1 * (start - sqinfo.len - 1); end = start - len * 3 + 1; } fprintf(ofp, ">%s.%d length %d, nt %d..%d", sqinfo.name, orfnumber, len, start, end); for (sptr = orf; *sptr; sptr++) { if (! ((sptr - orf) % 50)) putc('\n', ofp); putc((int) *sptr, ofp); } putc('\n', ofp); orfnumber++; } } /* pick off next orf */ orf = strtok(NULL, "*"); } } } for (frame = 0; frame < 6; frame++) free(aaseq[frame]); FreeSequence(seq, &sqinfo); free(revseq); } SeqfileClose(seqfp); /************************************************** * Successful return to invocation environment **************************************************/ return 0; } squid/types.c0000640000175000017520000001145010463223377013424 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* file: types.c * * Finicky type checkers for strings. Return 1 (TRUE) if ok, 0 elsewise. * Also, finicky type converters (sre_ntoh32() and friends) * * CVS $Id: types.c,v 1.6 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" /* Function: IsInt() * * Returns TRUE if s points to something that atoi() will parse * completely and convert to an integer. */ int IsInt(char *s) { int hex = 0; if (s == NULL) {squid_errno = SQERR_PARAMETER; return 0; } /* skip whitespace */ while (isspace((int) (*s))) s++; /* skip leading sign */ if (*s == '-' || *s == '+') s++; /* skip leading conversion signals */ if ((strncmp(s, "0x", 2) == 0 && (int) strlen(s) > 2) || (strncmp(s, "0X", 2) == 0 && (int) strlen(s) > 2)) { s += 2; hex = 1; } else if (*s == '0' && (int) strlen(s) > 1) s++; /* examine remainder for garbage chars */ if (!hex) while (*s != '\0') { if (!isdigit((int) (*s))) return 0; s++; } else while (*s != '\0') { if (!isxdigit((int) (*s))) return 0; s++; } return 1; } /* Function: IsReal() * * Purpose: Returns TRUE if s is a string representation * of a valid floating point number. */ int IsReal(char *s) { int gotdecimal = 0; int gotexp = 0; int gotreal = 0; if (s == NULL) return 0; while (isspace((int) (*s))) s++; /* skip leading whitespace */ if (*s == '-' || *s == '+') s++; /* skip leading sign */ /* Examine remainder for garbage. Allowed one '.' and * one 'e' or 'E'; if both '.' and e/E occur, '.' * must be first. */ while (*s != '\0') { if (isdigit((int) (*s))) gotreal++; else if (*s == '.') { if (gotdecimal) return 0; /* can't have two */ if (gotexp) return 0; /* e/E preceded . */ else gotdecimal++; } else if (*s == 'e' || *s == 'E') { if (gotexp) return 0; /* can't have two */ else gotexp++; } else if (isspace((int) (*s))) break; s++; } while (isspace((int) (*s))) s++; /* skip trailing whitespace */ if (*s == '\0' && gotreal) return 1; else return 0; } /* Function: Byteswap() * * Purpose: Swap between big-endian and little-endian. * For example: * int foo = 0x12345678; * byteswap((char *) &foo, sizeof(int)); * printf("%x\n", foo) * gives 78563412. * * I don't fully understand byte-swapping issues. * However, I have tested this on chars through floats, * on various machines: * SGI IRIX 4.0.5, SunOS 4.1.3, DEC Alpha OSF/1, Alliant * * Date: Sun Feb 12 10:26:22 1995 */ void Byteswap(char *swap, int nbytes) { int x; char byte; for (x = 0; x < nbytes / 2; x++) { byte = swap[nbytes - x - 1]; swap[nbytes - x - 1] = swap[x]; swap[x] = byte; } } /* Functions: sre_ntoh16(), etc. * Date: SRE, Sun Dec 31 11:26:53 2000 [St. Louis] * * Purpose: Provide functionality of ntohs(), etc; extended * to 64-bit unsigned ints, and explicitly provided * in case a machine doesn't have the ntohs() * family. * * If we're using the host functions, * USE_HOST_BYTESWAP_FUNCTIONS was set to 1 in * squidconf.h, and we #define'd sre_hton16(x)=hton(x), etc. * in squid.h. In doing this, we assumed that the * host functions work on 16- and 32-bit unsigned quantities. * If for some reason that's not true, set * USE_HOST_BYTESWAP_FUNCTIONS to 0. */ #ifndef USE_HOST_BYTESWAP_FUNCTIONS sqd_uint16 sre_ntoh16(sqd_uint16 netshort) { #ifdef WORDS_BIGENDIAN return netshort; #else Byteswap((char *) &netshort, 2); return netshort; #endif } sqd_uint32 sre_ntoh32(sqd_uint32 netlong) { #ifdef WORDS_BIGENDIAN return netlong; #else Byteswap((char *) &netlong, 4); return netlong; #endif } sqd_uint16 sre_hton16(sqd_uint16 hostshort) { #ifdef WORDS_BIGENDIAN return hostshort; #else Byteswap((char *) &hostshort, 2); return hostshort; #endif } sqd_uint32 sre_hton32(sqd_uint32 hostlong) { #ifdef WORDS_BIGENDIAN return hostlong; #else Byteswap((char *) &hostlong, 4); return hostlong; #endif } #endif /*USE_HOST_BYTESWAP_FUNCTIONS*/ sqd_uint64 sre_ntoh64(sqd_uint64 net_int64) { #ifdef WORDS_BIGENDIAN return net_int64; #else Byteswap((char *) &net_int64, 8); return net_int64; #endif } sqd_uint64 sre_hton64(sqd_uint64 host_int64) { #ifdef WORDS_BIGENDIAN return host_int64; #else Byteswap((char *) &host_int64, 8); return host_int64; #endif } squid/vectorops.c0000644000175000017520000001307210463223377014312 0ustar naolivbiolinux/* vectorops.c * Operations on vectors of floats or doubles. * * DSet(), FSet() - set all items in vector to value. * DScale(), FScale() - multiply all items in vector by scale * DSum(), FSum() - return sum of values in vector * DAdd(), FAdd() - add vec2 to vec1. * DCopy(), FCopy() - set vec1 to be same as vec2. * DDot(), FDot() - return dot product of two vectors. * DMax(), FMax() - return value of maximum element in vector * DMin(), FMin() - return value of minimum element in vector * DArgMax(), FArgMax() - return index of maximum element in vector * DArgMin(), FArgMin() - return index of minimum element in vector * * DNorm(), FNorm() - normalize a probability vector of length n. * DLog(), FLog() - convert to log probabilities * DExp(), FExp() - convert log p's back to probabilities * DLogSum(), FLogSum() - given vector of log p's; return log of summed p's. * DEntropy(), FEntropy() - return Shannon entropy of probability vector, in bits * * SRE, Tue Oct 1 15:23:25 2002 [St. Louis] * CVS $Id: vectorops.c,v 1.5 2004/05/24 15:49:07 eddy Exp $ */ #include "squidconf.h" #include #include #include #include "vectorops.h" void DSet(double *vec, int n, double value) { int x; for (x = 0; x < n; x++) vec[x] = value; } void FSet(float *vec, int n, float value) { int x; for (x = 0; x < n; x++) vec[x] = value; } void DScale(double *vec, int n, double scale) { int x; for (x = 0; x < n; x++) vec[x] *= scale; } void FScale(float *vec, int n, float scale) { int x; for (x = 0; x < n; x++) vec[x] *= scale; } double DSum(double *vec, int n) { double sum = 0.; int x; for (x = 0; x < n; x++) sum += vec[x]; return sum; } float FSum(float *vec, int n) { float sum = 0.; int x; for (x = 0; x < n; x++) sum += vec[x]; return sum; } void DAdd(double *vec1, double *vec2, int n) { int x; for (x = 0; x < n; x++) vec1[x] += vec2[x]; } void FAdd(float *vec1, float *vec2, int n) { int x; for (x = 0; x < n; x++) vec1[x] += vec2[x]; } void DCopy(double *vec1, double *vec2, int n) { int x; for (x = 0; x < n; x++) vec1[x] = vec2[x]; } void FCopy(float *vec1, float *vec2, int n) { int x; for (x = 0; x < n; x++) vec1[x] = vec2[x]; } double DDot(double *vec1, double *vec2, int n) { double result = 0.; int x; for (x = 0; x < n; x++) result += vec1[x] * vec2[x]; return result; } float FDot(float *vec1, float *vec2, int n) { float result = 0.; int x; for (x = 0; x < n; x++) result += vec1[x] * vec2[x]; return result; } double DMax(double *vec, int n) { int i; double best; best = vec[0]; for (i = 1; i < n; i++) if (vec[i] > best) best = vec[i]; return best; } float FMax(float *vec, int n) { int i; float best; best = vec[0]; for (i = 1; i < n; i++) if (vec[i] > best) best = vec[i]; return best; } double DMin(double *vec, int n) { int i; double best; best = vec[0]; for (i = 1; i < n; i++) if (vec[i] < best) best = vec[i]; return best; } float FMin(float *vec, int n) { int i; float best; best = vec[0]; for (i = 1; i < n; i++) if (vec[i] < best) best = vec[i]; return best; } int DArgMax(double *vec, int n) { int i; int best = 0; for (i = 1; i < n; i++) if (vec[i] > vec[best]) best = i; return best; } int FArgMax(float *vec, int n) { int i; int best = 0; for (i = 1; i < n; i++) if (vec[i] > vec[best]) best = i; return best; } int DArgMin(double *vec, int n) { int i; int best = 0; for (i = 1; i < n; i++) if (vec[i] < vec[best]) best = i; return best; } int FArgMin(float *vec, int n) { int i; int best = 0; for (i = 1; i < n; i++) if (vec[i] < vec[best]) best = i; return best; } void DNorm(double *vec, int n) { int x; double sum; sum = DSum(vec, n); if (sum != 0.0) for (x = 0; x < n; x++) vec[x] /= sum; else for (x = 0; x < n; x++) vec[x] = 1. / (double) n; } void FNorm(float *vec, int n) { int x; float sum; sum = FSum(vec, n); if (sum != 0.0) for (x = 0; x < n; x++) vec[x] /= sum; else for (x = 0; x < n; x++) vec[x] = 1. / (float) n; } void DLog(double *vec, int n) { int x; for (x = 0; x < n; x++) if (vec[x] > 0.) vec[x] = log(vec[x]); else vec[x] = -DBL_MAX; } void FLog(float *vec, int n) { int x; for (x = 0; x < n; x++) if (vec[x] > 0.) vec[x] = log(vec[x]); else vec[x] = -FLT_MAX; } void DExp(double *vec, int n) { int x; for (x = 0; x < n; x++) vec[x] = exp(vec[x]); } void FExp(float *vec, int n) { int x; for (x = 0; x < n; x++) vec[x] = exp(vec[x]); } double DLogSum(double *vec, int n) { int x; double max, sum; max = DMax(vec, n); sum = 0.0; for (x = 0; x < n; x++) if (vec[x] > max - 50.) sum += exp(vec[x] - max); sum = log(sum) + max; return sum; } float FLogSum(float *vec, int n) { int x; float max, sum; max = FMax(vec, n); sum = 0.0; for (x = 0; x < n; x++) if (vec[x] > max - 50.) sum += exp(vec[x] - max); sum = log(sum) + max; return sum; } double DEntropy(double *p, int n) { int i; double entropy; entropy = 0.; for(i = 0; i < n; i++) if (p[i] > 0.) entropy += p[i] * log(p[i]); return(-1.44269504 * entropy); /* converts to bits */ } float FEntropy(float *p, int n) { int i; float entropy; entropy = 0.; for(i = 0; i < n; i++) if (p[i] > 0.) entropy += p[i] * log(p[i]); return(-1.44269504 * entropy); /* converts to bits */ } squid/weight.c0000640000175000017520000005775410463223377013570 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* weight.c * SRE, Thu Mar 3 07:56:01 1994 * * Calculate weights for sequences in an alignment. * RCS $Id: weight.c,v 1.11 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include "squid.h" #include "sre_random.h" static void upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node); static void downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, float *fwt, int node); static float simple_distance(char *s1, char *s2); static int simple_diffmx(char **aseqs,int num, float ***ret_dmx); /* Function: GSCWeights() * * Purpose: Use Erik's tree-based algorithm to set weights for * sequences in an alignment. upweight() and downweight() * are derived from Graeme Mitchison's code. * * Args: aseq - array of (0..nseq-1) aligned sequences * nseq - number of seqs in alignment * alen - length of alignment * wgt - allocated [0..nseq-1] array of weights to be returned * * Return: (void) * wgt is filled in. */ void GSCWeights(char **aseq, int nseq, int alen, float *wgt) { float **dmx; /* distance (difference) matrix */ struct phylo_s *tree; float *lwt, *rwt; /* weight on left, right of this tree node */ float *fwt; /* final weight assigned to this node */ int i; /* Sanity check first */ if (nseq == 1) { wgt[0] = 1.0; return; } /* I use a simple fractional difference matrix derived by * pairwise identity. Perhaps I should include a Poisson * distance correction. */ MakeDiffMx(aseq, nseq, &dmx); if (! Cluster(dmx, nseq, CLUSTER_MIN, &tree)) Die("Cluster() failed"); /* Allocations */ lwt = MallocOrDie (sizeof(float) * (2 * nseq - 1)); rwt = MallocOrDie (sizeof(float) * (2 * nseq - 1)); fwt = MallocOrDie (sizeof(float) * (2 * nseq - 1)); /* lwt and rwt are the total branch weight to the left and * right of a node or sequence. They are 0..2N-2. 0..N-1 are * the sequences; these have weight 0. N..2N-2 are the actual * tree nodes. */ for (i = 0; i < nseq; i++) lwt[i] = rwt[i] = 0.0; /* recursively calculate rwt, lwt, starting at node nseq (the root) */ upweight(tree, nseq, lwt, rwt, nseq); /* recursively distribute weight across the tree */ fwt[nseq] = nseq; downweight(tree, nseq, lwt, rwt, fwt, nseq); /* collect the weights */ for (i = 0; i < nseq; i++) wgt[i] = fwt[i]; FMX2Free(dmx); FreePhylo(tree, nseq); free(lwt); free(rwt); free(fwt); } static void upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node) { int ld,rd; ld = tree[node-nseq].left; if (ld >= nseq) upweight(tree, nseq, lwt, rwt, ld); rd = tree[node-nseq].right; if (rd >= nseq) upweight(tree, nseq, lwt, rwt, rd); lwt[node] = lwt[ld] + rwt[ld] + tree[node-nseq].lblen; rwt[node] = lwt[rd] + rwt[rd] + tree[node-nseq].rblen; } static void downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, float *fwt, int node) { int ld,rd; float lnum, rnum; ld = tree[node-nseq].left; rd = tree[node-nseq].right; if (lwt[node] + rwt[node] > 0.0) { fwt[ld] = fwt[node] * (lwt[node] / (lwt[node] + rwt[node])); fwt[rd] = fwt[node] * (rwt[node] / (lwt[node] + rwt[node])); } else { lnum = (ld >= nseq) ? tree[ld-nseq].incnum : 1.0; rnum = (rd >= nseq) ? tree[rd-nseq].incnum : 1.0; fwt[ld] = fwt[node] * lnum / (lnum + rnum); fwt[rd] = fwt[node] * rnum / (lnum + rnum); } if (ld >= nseq) downweight(tree, nseq, lwt, rwt, fwt, ld); if (rd >= nseq) downweight(tree, nseq, lwt, rwt, fwt, rd); } /* Function: VoronoiWeights() * * Purpose: Calculate weights using the scheme of Sibbald & * Argos (JMB 216:813-818 1990). The scheme is * slightly modified because the original algorithm * actually doesn't work on gapped alignments. * The sequences are assumed to be protein. * * Args: aseq - array of (0..nseq-1) aligned sequences * nseq - number of sequences * alen - length of alignment * wgt - allocated [0..nseq-1] array of weights to be returned * * Return: void * wgt is filled in. */ void VoronoiWeights(char **aseq, int nseq, int alen, float *wgt) { float **dmx; /* distance (difference) matrix */ float *halfmin; /* 1/2 minimum distance to other seqs */ char **psym; /* symbols seen in each column */ int *nsym; /* # syms seen in each column */ int symseen[27]; /* flags for observed syms */ char *randseq; /* randomly generated sequence */ int acol; /* pos in aligned columns */ int idx; /* index in sequences */ int symidx; /* 0..25 index for symbol */ int i; /* generic counter */ float min; /* minimum distance */ float dist; /* distance between random and real */ float challenge, champion; /* for resolving ties */ int itscale; /* how many iterations per seq */ int iteration; int best; /* index of nearest real sequence */ /* Sanity check first */ if (nseq == 1) { wgt[0] = 1.0; return; } itscale = 50; /* Precalculate 1/2 minimum distance to other * sequences for each sequence */ if (! simple_diffmx(aseq, nseq, &dmx)) Die("simple_diffmx() failed"); halfmin = MallocOrDie (sizeof(float) * nseq); for (idx = 0; idx < nseq; idx++) { for (min = 1.0, i = 0; i < nseq; i++) { if (i == idx) continue; if (dmx[idx][i] < min) min = dmx[idx][i]; } halfmin[idx] = min / 2.0; } Free2DArray((void **) dmx, nseq); /* Set up the random sequence generating model. */ psym = MallocOrDie (alen * sizeof(char *)); nsym = MallocOrDie (alen * sizeof(int)); for (acol = 0; acol < alen; acol++) psym[acol] = MallocOrDie (27 * sizeof(char)); /* #ifdef ORIGINAL_SIBBALD_ALGORITHM_IS_BROKEN */ for (acol = 0; acol < alen; acol++) { memset(symseen, 0, sizeof(int) * 27); for (idx = 0; idx < nseq; idx++) if (! isgap(aseq[idx][acol])) { if (isupper((int) aseq[idx][acol])) symidx = aseq[idx][acol] - 'A'; else symidx = aseq[idx][acol] - 'a'; if (symidx >= 0 && symidx < 26) symseen[symidx] = 1; } else symseen[26] = 1; /* a gap */ for (nsym[acol] = 0, i = 0; i < 26; i++) if (symseen[i]) { psym[acol][nsym[acol]] = 'A'+i; nsym[acol]++; } if (symseen[26]) { psym[acol][nsym[acol]] = ' '; nsym[acol]++; } } /* #endif ORIGINAL_SIBBALD_ALGORITHM_IS_BROKEN */ /* Note: the original Sibbald&Argos algorithm calls for * bounding the sampled space using a template-like random * sequence generator. However, this leads to one minor * and one major problem. The minor problem is that * exceptional amino acids in a column can have a * significant effect by altering the amount of sampled * sequence space; the larger the data set, the worse * this problem becomes. The major problem is that * there is no reasonable way to deal with gaps. * Gapped sequences simply inhabit a different dimensionality * and it's pretty painful to imagine calculating Voronoi * volumes when the N in your N-space is varying. * Note that all the examples shown by Sibbald and Argos * are *ungapped* examples. * * The best way I've found to circumvent this problem is * just not to bound the sampled space; count gaps as * symbols and generate completely random sequences. */ #ifdef ALL_SEQUENCE_SPACE for (acol = 0; acol < alen; acol++) { strcpy(psym[acol], "ACDEFGHIKLMNPQRSTVWY "); nsym[acol] = 21; } #endif /* Sibbald and Argos algorithm: * 1) assign all seqs weight 0. * 2) generate a "random" sequence * 3) calculate distance to every other sequence * (if we get a distance < 1/2 minimum distance * to other real seqs, we can stop) * 4) if unique closest sequence, increment its weight 1. * if multiple closest seq, choose one randomly * 5) repeat 2-4 for lots of iterations * 6) normalize all weights to sum to nseq. */ randseq = MallocOrDie ((alen+1) * sizeof(char)); best = 42.; /* solely to silence GCC uninit warnings. */ FSet(wgt, nseq, 0.0); for (iteration = 0; iteration < itscale * nseq; iteration++) { for (acol = 0; acol < alen; acol++) randseq[acol] = (nsym[acol] == 0) ? ' ' : psym[acol][CHOOSE(nsym[acol])]; randseq[acol] = '\0'; champion = sre_random(); for (min = 1.0, idx = 0; idx < nseq; idx++) { dist = simple_distance(aseq[idx], randseq); if (dist < halfmin[idx]) { best = idx; break; } if (dist < min) { champion = sre_random(); best = idx; min = dist; } else if (dist == min) { challenge = sre_random(); if (challenge > champion) { champion = challenge; best = idx; min = dist; } } } wgt[best] += 1.0; } for (idx = 0; idx < nseq; idx++) wgt[idx] = wgt[idx] / (float) itscale; free(randseq); free(nsym); free(halfmin); Free2DArray((void **) psym, alen); } /* Function: simple_distance() * * Purpose: For two identical-length null-terminated strings, return * the fractional difference between them. (0..1) * (Gaps don't count toward anything.) */ static float simple_distance(char *s1, char *s2) { int diff = 0; int valid = 0; for (; *s1 != '\0'; s1++, s2++) { if (isgap(*s1) || isgap(*s2)) continue; if (*s1 != *s2) diff++; valid++; } return (valid > 0 ? ((float) diff / (float) valid) : 0.0); } /* Function: simple_diffmx() * * Purpose: Given a set of flushed, aligned sequences, construct * an NxN fractional difference matrix using the * simple_distance rule. * * Args: aseqs - flushed, aligned sequences * num - number of aseqs * ret_dmx - RETURN: difference matrix (caller must free) * * Return: 1 on success, 0 on failure. */ static int simple_diffmx(char **aseqs, int num, float ***ret_dmx) { float **dmx; /* RETURN: distance matrix */ int i,j; /* counters over sequences */ /* Allocate */ if ((dmx = (float **) malloc (sizeof(float *) * num)) == NULL) Die("malloc failed"); for (i = 0; i < num; i++) if ((dmx[i] = (float *) malloc (sizeof(float) * num)) == NULL) Die("malloc failed"); /* Calculate distances, symmetric matrix */ for (i = 0; i < num; i++) for (j = i; j < num; j++) dmx[i][j] = dmx[j][i] = simple_distance(aseqs[i], aseqs[j]); /* Return */ *ret_dmx = dmx; return 1; } /* Function: BlosumWeights() * Date: SRE, Fri Jul 16 17:33:59 1999 (St. Louis) * * Purpose: Assign weights to a set of aligned sequences * using the BLOSUM rule: * - do single linkage clustering at some pairwise identity * - in each cluster, give each sequence 1/clustsize * total weight. * * The clusters have no pairwise link >= maxid. * * O(N) in memory. Probably ~O(NlogN) in time; O(N^2) * in worst case, which is no links between sequences * (e.g., values of maxid near 1.0). * * Args: aseqs - alignment * nseq - number of seqs in alignment * alen - # of columns in alignment * maxid - fractional identity (e.g. 0.62 for BLOSUM62) * wgt - [0..nseq-1] array of weights to be returned */ void BlosumWeights(char **aseqs, int nseq, int alen, float maxid, float *wgt) { int *c, nc; int *nmem; /* number of seqs in each cluster */ int i; /* loop counter */ SingleLinkCluster(aseqs, nseq, alen, maxid, &c, &nc); FSet(wgt, nseq, 1.0); nmem = MallocOrDie(sizeof(int) * nc); for (i = 0; i < nc; i++) nmem[i] = 0; for (i = 0; i < nseq; i++) nmem[c[i]]++; for (i = 0; i < nseq; i++) wgt[i] = 1. / (float) nmem[c[i]]; free(nmem); free(c); return; } /* Function: PositionBasedWeights() * Date: SRE, Fri Jul 16 17:47:22 1999 [St. Louis] * * Purpose: Implementation of Henikoff and Henikoff position-based * weights (JMB 243:574-578, 1994) [Henikoff94b]. * * A significant advantage of this approach that Steve and Jorja * don't point out is that it is O(N) in memory, unlike * many other approaches like GSC weights or Voronoi. * * A potential disadvantage that they don't point out * is that in the theoretical limit of infinite sequences * in the alignment, weights go flat: eventually every * column has at least one representative of each of 20 aa (or 4 nt) * in it. * * They also don't give a rule for how to handle gaps. * The rule used here seems the obvious and sensible one * (ignore them). This means that longer sequences * initially get more weight; hence a "double * normalization" in which the weights are first divided * by sequence length (to compensate for that effect), * then normalized to sum to nseq. * * Limitations: * Implemented in a way that's alphabet-independent: * it uses the 26 upper case letters as "residues". * Any alphabetic character in aseq is interpreted as * a unique "residue" (case insensitively; lower case * mapped to upper case). All other characters are * interpreted as gaps. * * This way, we don't have to pass around any alphabet * type info (DNA vs. RNA vs. protein) and don't have * to deal with remapping IUPAC degenerate codes * probabilistically. However, on the down side, * a sequence with a lot of degenerate IUPAC characters * will get an artifactually high PB weight. * * Args: aseq - sequence alignment to weight * nseq - number of sequences in alignment * alen - length of alignment * wgt - RETURN: weights filled in (pre-allocated 0..nseq-1) * * Returns: (void) * wgt is allocated (0..nseq-1) by caller, and filled in here. */ void PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt) { int rescount[26]; /* count of A-Z residues in a column */ int nres; /* number of different residues in col */ int idx, pos; /* indices into aseq */ int x; float norm; FSet(wgt, nseq, 0.0); for (pos = 0; pos < alen; pos++) { for (x = 0; x < 26; x++) rescount[x] = 0; for (idx = 0; idx < nseq; idx++) if (isalpha((int) aseq[idx][pos])) rescount[toupper((int) aseq[idx][pos]) - 'A'] ++; nres = 0; for (x = 0; x < 26; x++) if (rescount[x] > 0) nres++; for (idx = 0; idx < nseq; idx++) if (isalpha((int) aseq[idx][pos])) wgt[idx] += 1. / (float) (nres * rescount[toupper((int) aseq[idx][pos]) - 'A']); } for (idx = 0; idx < nseq; idx++) wgt[idx] /= (float) DealignedLength(aseq[idx]); norm = (float) nseq / FSum(wgt, nseq); FScale(wgt, nseq, norm); return; } /* Function: FilterAlignment() * Date: SRE, Wed Jun 30 09:19:30 1999 [St. Louis] * * Purpose: Constructs a new alignment by removing near-identical * sequences from a given alignment (where identity is * calculated *based on the alignment*). * Does not affect the given alignment. * Keeps earlier sequence, discards later one. * * Usually called as an ad hoc sequence "weighting" mechanism. * * Limitations: * Unparsed Stockholm markup is not propagated into the * new alignment. * * Args: msa -- original alignment * cutoff -- fraction identity cutoff. 0.8 removes sequences > 80% id. * ret_new -- RETURN: new MSA, usually w/ fewer sequences * * Return: (void) * ret_new must be free'd by caller: MSAFree(). */ void FilterAlignment(MSA *msa, float cutoff, MSA **ret_new) { int nnew; /* number of seqs in new alignment */ int *list; int *useme; float ident; int i,j; int remove; /* find which seqs to keep (list) */ /* diff matrix; allow ragged ends */ list = MallocOrDie (sizeof(int) * msa->nseq); useme = MallocOrDie (sizeof(int) * msa->nseq); for (i = 0; i < msa->nseq; i++) useme[i] = FALSE; nnew = 0; for (i = 0; i < msa->nseq; i++) { remove = FALSE; for (j = 0; j < nnew; j++) { ident = PairwiseIdentity(msa->aseq[i], msa->aseq[list[j]]); if (ident > cutoff) { remove = TRUE; printf("removing %12s -- fractional identity %.2f to %s\n", msa->sqname[i], ident, msa->sqname[list[j]]); break; } } if (remove == FALSE) { list[nnew++] = i; useme[i] = TRUE; } } MSASmallerAlignment(msa, useme, ret_new); free(list); free(useme); return; } /* Function: SampleAlignment() * Date: SRE, Wed Jun 30 10:13:56 1999 [St. Louis] * * Purpose: Constructs a new, smaller alignment by sampling a given * number of sequences at random. Does not change the * alignment nor the order of the sequences. * * If you ask for a sample that is larger than nseqs, * it silently returns the original alignment. * * Not really a weighting method, but this is as good * a place as any to keep it, since it's similar in * construction to FilterAlignment(). * * Args: msa -- original alignment * sample -- number of sequences in new alignment (0 < sample <= nseq) * ret_new -- RETURN: new MSA * * Return: (void) * ret_new must be free'd by caller: MSAFree(). */ void SampleAlignment(MSA *msa, int sample, MSA **ret_new) { int *list; /* array for random selection w/o replace */ int *useme; /* array of flags 0..nseq-1: TRUE to use */ int i, idx; int len; /* Allocations */ list = (int *) MallocOrDie (sizeof(int) * msa->nseq); useme = (int *) MallocOrDie (sizeof(int) * msa->nseq); for (i = 0; i < msa->nseq; i++) { list[i] = i; useme[i] = FALSE; } /* Sanity check. */ if (sample >= msa->nseq) sample = msa->nseq; /* random selection w/o replacement */ for (len = msa->nseq, i = 0; i < sample; i++) { idx = CHOOSE(len); printf("chose %d: %s\n", list[idx], msa->sqname[list[idx]]); useme[list[idx]] = TRUE; list[idx] = list[--len]; } MSASmallerAlignment(msa, useme, ret_new); free(list); free(useme); return; } /* Function: SingleLinkCluster() * Date: SRE, Fri Jul 16 15:02:57 1999 [St. Louis] * * Purpose: Perform simple single link clustering of seqs in a * sequence alignment. A pairwise identity threshold * defines whether two sequences are linked or not. * * Important: runs in O(N) memory, unlike standard * graph decomposition algorithms that use O(N^2) * adjacency matrices or adjacency lists. Requires * O(N^2) time in worst case (which is when you have * no links at all), O(NlogN) in "average" * case, and O(N) in best case (when there is just * one cluster in a completely connected graph. * * (Developed because hmmbuild could no longer deal * with GP120, a 16,013 sequence alignment.) * * Limitations: * CASE-SENSITIVE. Assumes aseq have been put into * either all lower or all upper case; or at least, * within a column, there's no mixed case. * * Algorithm: * I don't know if this algorithm is published. I * haven't seen it in graph theory books, but that might * be because it's so obvious that nobody's bothered. * * In brief, we're going to do a breadth-first search * of the graph, and we're going to calculate links * on the fly rather than precalculating them into * some sort of standard adjacency structure. * * While working, we keep two stacks of maximum length N: * a : list of vertices that are still unconnected. * b : list of vertices that we've connected to * in our current breadth level, but we haven't * yet tested for other connections to a. * The current length (number of elements in) a and b are * kept in na, nb. * * We store our results in an array of length N: * c : assigns each vertex to a component. for example * c[4] = 1 means that vertex 4 is in component 1. * nc is the number of components. Components * are numbered from 0 to nc-1. We return c and nc * to our caller. * * The algorithm is: * * Initialisation: * a <-- all the vertices * na <-- N * b <-- empty set * nb <-- 0 * nc <-- 0 * * Then: * while (a is not empty) * pop a vertex off a, push onto b * while (b is not empty) * pop vertex v off b * assign c[v] = nc * for each vertex w in a: * compare v,w. If w is linked to v, remove w * from a, push onto b. * nc++ * q.e.d. :) * * Args: aseq - aligned sequences * nseq - number of sequences in aseq * alen - alignment length * maxid - fractional identity threshold 0..1. if id >= maxid, seqs linked * ret_c - RETURN: 0..nseq-1 assignments of seqs to components (clusters) * ret_nc - RETURN: number of components * * Returns: void. * ret_c is allocated here. Caller free's with free(*ret_c) */ void SingleLinkCluster(char **aseq, int nseq, int alen, float maxid, int **ret_c, int *ret_nc) { int *a, na; /* stack of available vertices */ int *b, nb; /* stack of working vertices */ int *c; /* array of results */ int nc; /* total number of components */ int v,w; /* index of a working vertices */ int i; /* loop counter */ /* allocations and initializations */ a = MallocOrDie (sizeof(int) * nseq); b = MallocOrDie (sizeof(int) * nseq); c = MallocOrDie (sizeof(int) * nseq); for (i = 0; i < nseq; i++) a[i] = i; na = nseq; nb = 0; nc = 0; /* Main algorithm */ while (na > 0) { v = a[na-1]; na--; /* pop a vertex off a, */ b[nb] = v; nb++; /* and push onto b */ while (nb > 0) { v = b[nb-1]; nb--; /* pop vertex off b */ c[v] = nc; /* assign it to component nc */ for (i = na-1; i >= 0; i--)/* backwards, becase of deletion/swapping we do*/ if (simple_distance(aseq[v], aseq[a[i]]) <= 1. - maxid) /* linked? */ { w = a[i]; a[i] = a[na-1]; na--; /* delete w from a (note swap) */ b[nb] = w; nb++; /* push w onto b */ } } nc++; } /* Cleanup and return */ free(a); free(b); *ret_c = c; *ret_nc = nc; return; } squid/weight_main.c0000640000175000017520000001366510463223377014565 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* weight_main.c * SRE, Thu Mar 3 13:43:39 1994 * * Calculate weights for a sequence alignment. * CVS $Id: weight_main.c,v 1.6 2003/04/14 16:00:16 eddy Exp $ */ #include "squidconf.h" #include #include #include #include #include "squid.h" #include "msa.h" static char banner[] = "weight - calculate sequence weights for an alignment"; static char usage[] = "\ Usage: weight [-options] \n\ Available options:\n\ -b : use BLOSUM weighting scheme at fractional identity\n\ -f : filter out seqs w/ fractional ident > [0-1]\n\ -h : help; print version and usage info\n\ -o : save weight-annotated alignment in \n\ -p : use position based weight scheme (Henikoff & Henikoff)\n\ -s : sample sequences at random into a new alignment\n\ -v : use Voronoi weight scheme (Sibbald & Argos) \n\ "; static char experts[] = "\ Expert options:\n\ --informat : specify alignment file format \n\ allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP\n\ --quiet : suppress verbose banner\n\ "; static struct opt_s OPTIONS[] = { { "-b", TRUE, sqdARG_FLOAT }, { "-f", TRUE, sqdARG_FLOAT }, { "-h", TRUE, sqdARG_NONE }, { "-o", TRUE, sqdARG_STRING }, { "-p", TRUE, sqdARG_NONE }, { "-s", TRUE, sqdARG_INT }, { "-v", TRUE, sqdARG_NONE }, { "--informat", FALSE, sqdARG_STRING }, { "--quiet", FALSE, sqdARG_NONE }, }; #define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s)) int main(int argc, char **argv) { char *seqfile; /* file containing aligned seqs */ MSAFILE *afp; /* pointer to open alignment file */ MSA *msa; /* multiple sequence alignment */ int fmt; /* expected format of alignment file */ int idx; char *outfile; /* output file for weighted alignment */ FILE *ofp; /* open outfile */ int do_voronoi; /* use Sibbald/Argos Voronoi scheme */ int do_blosum; /* use BLOSUM weighting scheme */ int do_pbased; /* use position-based weights */ int do_filter; /* use filtering scheme */ float idlevel; /* identity level to filter at, [0-1] */ int samplesize; /* if >0, don't weight, random sample */ int be_quiet; /* TRUE to suppress banner */ char *optname; /* name of option found by Getopt() */ char *optarg; /* argument found by Getopt() */ int optind; /* index in argv[] */ /*********************************************** * Parse command line ***********************************************/ fmt = MSAFILE_UNKNOWN; /* autodetect file format by default */ outfile = NULL; do_blosum = FALSE; do_voronoi = FALSE; do_pbased = FALSE; do_filter = FALSE; samplesize = 0; be_quiet = FALSE; idlevel = 0.; /* just to suppress gcc uninit warnings */ while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage, &optind, &optname, &optarg)) { if (strcmp(optname, "-b") == 0) { do_blosum = TRUE; idlevel = atof(optarg); } else if (strcmp(optname, "-f") == 0) { do_filter = TRUE; idlevel = atof(optarg); } else if (strcmp(optname, "-o") == 0) outfile = optarg; else if (strcmp(optname, "-p") == 0) do_pbased = TRUE; else if (strcmp(optname, "-s") == 0) samplesize = atoi(optarg); else if (strcmp(optname, "-v") == 0) do_voronoi = TRUE; else if (strcmp(optname, "--quiet") == 0) be_quiet = TRUE; else if (strcmp(optname, "--informat") == 0) { fmt = String2SeqfileFormat(optarg); if (fmt == MSAFILE_UNKNOWN) Die("unrecognized sequence file format \"%s\"", optarg); if (! IsAlignmentFormat(fmt)) Die("%s is an unaligned format, can't read as an alignment", optarg); } else if (strcmp(optname, "-h") == 0) { SqdBanner(stdout, banner); puts(usage); puts(experts); exit(EXIT_SUCCESS); } } if (argc -optind != 1) Die("Wrong number of arguments specified on command line\n%s\n", usage); seqfile = argv[optind]; if (outfile == NULL) ofp = stdout; else if ((ofp = fopen(outfile, "w")) == NULL) Die("Failed to open alignment output file %s", outfile); if (do_voronoi + do_pbased + do_blosum + do_filter + samplesize > 1) Die("Choose only one weighting scheme, please.\n%s\n", usage); if (do_voronoi || samplesize > 0) sre_srandom(time(0)); if (! be_quiet) SqdBanner(stdout, banner); /*********************************************** * Open the input alignment file and start... * be prepared to deal with multiple entries in Stockholm files ***********************************************/ if ((afp = MSAFileOpen(seqfile, fmt, NULL)) == NULL) Die("Alignment file %s could not be opened for reading", seqfile); while ((msa = MSAFileRead(afp)) != NULL) { for (idx = 0; idx < msa->nseq; idx++) s2upper(msa->aseq[idx]); if (do_filter || samplesize > 0) { MSA *new; if (do_filter) FilterAlignment(msa, idlevel, &new); else if (samplesize > 0) SampleAlignment(msa, samplesize, &new); if (new != NULL) { WriteStockholm(ofp, new); MSAFree(msa); MSAFree(new); } } else { if (do_voronoi) VoronoiWeights(msa->aseq, msa->nseq, msa->alen, msa->wgt); else if (do_blosum) BlosumWeights(msa->aseq, msa->nseq, msa->alen, idlevel, msa->wgt); else if (do_pbased) PositionBasedWeights(msa->aseq, msa->nseq, msa->alen, msa->wgt); else GSCWeights (msa->aseq, msa->nseq, msa->alen, msa->wgt); msa->flags |= MSA_SET_WGT; WriteStockholm(ofp, msa); MSAFree(msa); } } MSAFileClose(afp); fclose(ofp); return EXIT_SUCCESS; } squid/wuss.c0000644000175000017520000001505310463223377013270 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ /* wuss.c * SRE, Fri Jul 28 09:37:18 2000 [St. Louis] * CVS $Id: wuss.c,v 1.1 2004/01/19 14:45:04 eddy Exp $ * * Common functions for manipulating RNA secondary structure markup * (WUSS notation). * */ #include #include #include #include "squid.h" #include "sre_stack.h" /* Function: WUSS2ct() * Incept: SRE 29 Feb 2000 [Seattle]; from COVE 1.0 code * * Purpose: Convert a secondary structure string (0..len-1) to an array of integers * representing what position each position is base-paired * to (1..len), or 0 if none. This 1..len representation is * the same as the Zuker .ct file representation, but differs * from my previous 0..len-1 implementations of ct operations. * * The structure string is in WUSS notation; "<>", etc. * for base pairs and gap symbols (usually '.') for unpaired bases. * * The .ct representation can accomodate pseudoknots. * WUSS notation in a secondary structure string cannot capture * all possible pseudoknots, but it can contain "Aa", "Bb", etc. pairs as * a representation of up to a 26th order pseudoknot. * (The highest order biological pseudoknot I know of is the * S1 pseudoknot, which is 3rd order: order in the Rivas and * Eddy, JMB 1998 sense, referring to the depth of nesting.) * Other symbols are ignored. If allow_pseudoknots is FALSE, * the pseudoknot symbols will also be ignored and these positions * will be treated as single stranded. * * Return: ret_ct is allocated here and must be free'd by caller. * Returns 1 on success; 0 if ss is somehow inconsistent. */ int WUSS2ct(char *ss, int len, int allow_pseudoknots, int **ret_ct) { Nstack_t *pda[27]; /* 1 secondary structure + up to 26 levels of pk's */ int *ct; int i; int pos, pair; int status = 1; /* success or failure return status */ /* Initialization: always initialize the main pda (0), * and also the 26 pk pda's if we're allowing pseudoknots. */ pda[0] = CreateNstack(); if (allow_pseudoknots) for (i = 1; i < 27; i++) pda[i] = CreateNstack(); ct = MallocOrDie ((len+1) * sizeof(int)); for (pos = 0; pos <= len; pos++) ct[pos] = 0; for (pos = 1; pos <= len; pos++) { if (!isprint((int) ss[pos-1])) status = 0; /* armor against garbage strings */ /* left side of a pair: push position onto stack 0 (pos = 1..L) */ else if (ss[pos-1] == '<' || ss[pos-1] == '(' || ss[pos-1] == '[' || ss[pos-1] == '{') PushNstack(pda[0], pos); /* right side of a pair; resolve pair; check for agreement */ else if (ss[pos-1] == '>' || ss[pos-1] == ')' || ss[pos-1] == ']' || ss[pos-1] == '}') { if (! PopNstack(pda[0], &pair)) { status = 0; } /* a failure code */ else if ((ss[pair-1] == '<' && ss[pos-1] != '>') || (ss[pair-1] == '(' && ss[pos-1] != ')') || (ss[pair-1] == '[' && ss[pos-1] != ']') || (ss[pair-1] == '{' && ss[pos-1] != '}')) { status = 0; } /* a failure code */ else { ct[pos] = pair; ct[pair] = pos; } } /* same stuff for pseudoknots */ else if (isupper((int) ss[pos-1])) { if (allow_pseudoknots) PushNstack(pda[ss[pos-1] - 'A' + 1], pos); } else if (islower((int) ss[pos-1])) { if (allow_pseudoknots) { if (! PopNstack(pda[ss[pos-1] - 'a' + 1], &pair)) { status = 0; } else { ct[pos] = pair; ct[pair] = pos; } } } else if (strchr(":,_-.~", ss[pos-1]) == NULL) status = 0; /* bogus character */ } /* nothing should be left on stacks */ if (! NstackIsEmpty(pda[0])) status = 0; FreeNstack(pda[0]); if (allow_pseudoknots) { for (i = 1; i < 27; i++) { if (! NstackIsEmpty(pda[i])) status = 0; FreeNstack(pda[i]); } } *ret_ct = ct; return status; } /* Function: WUSStoKHS() * Incept: SRE, Fri Jan 16 12:49:28 2004 [St. Louis] * * Purpose: Converts a secondary structure string in WUSS notation * back to old KHS format. The conversion is done in * place: the secondary structure string is modified. * * Characters <([{ are converted to > (left base of base pairs) * Characters >)]} are converted to < (right base of base pairs) * Characters _-,:~ are converted to . (unpaired bases) * Character . is untouched (unpaired) * Everything else is untouched, including any pseudoknot notation. * * Args: ss - the string to convert * * Returns: (void) */ void WUSStoKHS(char *ss) { char *s; for (s = ss; *s != '\0'; s++) { if (*s == '<') *s = '>'; else if (*s == '(') *s = '>'; else if (*s == '[') *s = '>'; else if (*s == '{') *s = '>'; else if (*s == '>') *s = '<'; else if (*s == ')') *s = '<'; else if (*s == ']') *s = '<'; else if (*s == '}') *s = '<'; else if (*s == '_') *s = '.'; else if (*s == '-') *s = '.'; else if (*s == ',') *s = '.'; else if (*s == ':') *s = '.'; else if (*s == '~') *s = '.'; } return; } /* Function: KHStoWUSS() * Incept: SRE, Fri Jan 16 12:57:16 2004 [St. Louis] * * Purpose: Converts an old format secondary structure string to * shorthand WUSS format. * * String is converted in place - i.e. it is modified by * this function. * * Character > is converted to < (left base of base pairs) * Character < is converted to > (right base of base pairs) * A space is converted to . (just in case) * Any other character is untouched, including pseudoknots. * * Args: ss - the secondary structure markup string to convert * * Returns: (void) */ void KHStoWUSS(char *ss) { char *s; for (s = ss; *s != '\0'; s++) { if (*s == '>') *s = '<'; else if (*s == '<') *s = '>'; else if (*s == ' ') *s = '.'; } return; } squid/dirichlet.h0000644000175000017520000000260310463223377014240 0ustar naolivbiolinux/* dirichlet.h * * Dirichlets, mixture Dirichlets, gamma functions, and beta functions; * evaluation and sampling routines. * * SRE, Sat Oct 25 09:47:09 2003 * CVS $Id: dirichlet.h,v 1.1 2003/10/27 21:08:13 eddy Exp $ */ #ifndef DIRICHLETH_INCLUDED #define DIRICHLETH_INCLUDED typedef struct mixdchlet_s { double *q; /* mixture coefficients q[0..N-1] */ double **alpha; /* Dirichlet params alpha[0..N-1][0..K-1] */ int N; /* number of mixtures, e.g. 9 for Sjolander */ int K; /* alphabet size, e.g. 20 */ char *alphabet; /* alphabet, e.g. "ACDEFGHIKLMNPQRSTVWY" */ } MIXDCHLET; extern MIXDCHLET *AllocDirichlet(int N, char *alphabet); extern void FreeDirichlet(MIXDCHLET *d); extern MIXDCHLET *ReadDirichletFile(char *file); extern double Gammln(double x); extern double IncompleteGamma(double a, double x); extern double SampleGamma(double alpha); extern double SampleBeta(double theta1, double theta2); extern double Dchlet_logp_counts(double *c, double *alpha, int K); extern double Dchlet_logp_probs(double *p, double *alpha, int K); extern void SampleDirichlet(double *alpha, int K, double *p); #endif /* DIRICHLETH_INCLUDED */ /***************************************************************** * @LICENSE@ *****************************************************************/ squid/gki.h0000640000175000017520000000200710463223377013035 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SQUID_GKI_INCLUDED #define SQUID_GKI_INCLUDED /* gki.h * SRE, Sat May 1 15:07:22 1999 * * Declarations of structures, functions for generic key index * module: emulation of Perl hashes. See gki.c. * * RCS $Id: gki.h,v 1.2 1999/07/15 22:30:45 eddy Exp $ */ /* gki_elem: * key, array index pairs are kept in linked list structures. */ struct gki_elem { char *key; int idx; struct gki_elem *nxt; }; /* gki: * a dynamically resized hash structure; * contains a hash table and associated data */ typedef struct { struct gki_elem **table; int primelevel; int nhash; int nkeys; } GKI; GKI *GKIInit(void); void GKIFree(GKI *hash); int GKIHashValue(GKI *hash, char *key); int GKIStoreKey(GKI *hash, char *key); int GKIKeyIndex(GKI *hash, char *key); void GKIStatus(GKI *hash); #endif /* SQUID_GKI_INCLUDED */ squid/msa.h0000640000175000017520000002777410463223377013065 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SQUID_MSA_INCLUDED #define SQUID_MSA_INCLUDED /* msa.h * SRE, Mon May 17 10:24:30 1999 * * Header file for SQUID's multiple sequence alignment * manipulation code. * * RCS $Id: msa.h,v 1.14 2004/02/04 14:44:03 eddy Exp $ */ #include "squidconf.h" #include /* FILE support */ #include "gki.h" /* hash table support */ #include "ssi.h" /* sequence file index support */ #include "squid.h" /* need SQINFO */ /**************************************************** * Obsolete alignment information, AINFO * Superceded by MSA structure further below; but we * need AINFO for the near future for backwards * compatibility. ****************************************************/ /* Structure: aliinfo_s * * Purpose: Optional information returned from an alignment file. * * flags: always used. Flags for which info is valid/alloced. * * alen: mandatory. Alignments are always flushed right * with gaps so that all aseqs are the same length, alen. * Available for all alignment formats. * * nseq: mandatory. Aligned seqs are indexed 0..nseq-1. * * wgt: 0..nseq-1 vector of sequence weights. Mandatory. * If not explicitly set, weights are initialized to 1.0. * * cs: 0..alen-1, just like the alignment. Contains single-letter * secondary structure codes for consensus structure; "<>^+" * for RNA, "EHL." for protein. May be NULL if unavailable * from seqfile. Only available for SELEX format files. * * rf: 0..alen-1, just like the alignment. rf is an arbitrary string * of characters, used for annotating columns. Blanks are * interpreted as non-canonical columns and anything else is * considered canonical. Only available from SELEX files. * * sqinfo: mandatory. Array of 0..nseq-1 * per-sequence information structures, carrying * name, id, accession, coords. * */ struct aliinfo_s { int flags; /* flags for what info is valid */ int alen; /* length of alignment (columns) */ int nseq; /* number of seqs in alignment */ float *wgt; /* sequence weights [0..nseq-1] */ char *cs; /* consensus secondary structure string */ char *rf; /* reference coordinate system */ struct seqinfo_s *sqinfo; /* name, id, coord info for each sequence */ /* Pfam/HMMER pick-ups */ char *name; /* name of alignment */ char *desc; /* description of alignment */ char *acc; /* accession of alignment */ char *au; /* "author" information */ float tc1, tc2; /* trusted score cutoffs (per-seq, per-domain) */ float nc1, nc2; /* noise score cutoffs (per-seq, per-domain) */ float ga1, ga2; /* gathering cutoffs */ }; typedef struct aliinfo_s AINFO; #define AINFO_TC (1 << 0) #define AINFO_NC (1 << 1) #define AINFO_GA (1 << 2) /***************************************************************** * MSA * SRE, Sun Jun 27 15:03:35 1999 [TW 723 over Greenland] * * Defines the new data structure and API for multiple * sequence alignment i/o. *****************************************************************/ /* The following constants define the Pfam/Rfam cutoff set we'll propagate * from msa's into HMMER and Infernal models. */ #define MSA_CUTOFF_TC1 0 #define MSA_CUTOFF_TC2 1 #define MSA_CUTOFF_GA1 2 #define MSA_CUTOFF_GA2 3 #define MSA_CUTOFF_NC1 4 #define MSA_CUTOFF_NC2 5 #define MSA_MAXCUTOFFS 6 /* Structure: MSA * SRE, Tue May 18 11:33:08 1999 * * Our object for a multiple sequence alignment. */ typedef struct msa_struct { /* Mandatory information associated with the alignment. */ char **aseq; /* the alignment itself, [0..nseq-1][0..alen-1] */ char **sqname; /* names of sequences, [0..nseq-1][] */ float *wgt; /* sequence weights [0..nseq-1] */ int alen; /* length of alignment (columns) */ int nseq; /* number of seqs in alignment */ /* Optional information that we understand, and might have. */ int flags; /* flags for what optional info is valid */ int type; /* kOtherSeq, kRNA/hmmNUCLEIC, or kAmino/hmmAMINO */ char *name; /* name of alignment, or NULL */ char *desc; /* description of alignment, or NULL */ char *acc; /* accession of alignment, or NULL */ char *au; /* "author" information, or NULL */ char *ss_cons; /* consensus secondary structure string, or NULL */ char *sa_cons; /* consensus surface accessibility string, or NULL */ char *rf; /* reference coordinate system, or NULL */ char **sqacc; /* accession numbers for individual sequences */ char **sqdesc; /* description lines for individual sequences */ char **ss; /* per-seq secondary structure annotation, or NULL */ char **sa; /* per-seq surface accessibility annotation, or NULL */ float cutoff[MSA_MAXCUTOFFS]; /* NC, TC, GA cutoffs propagated to Pfam/Rfam */ int cutoff_is_set[MSA_MAXCUTOFFS];/* TRUE if a cutoff is set; else FALSE */ /* Optional information that we don't understand. * That is, we know what type of information it is, but it's * either (interpreted as) free-text comment, or it's Stockholm * markup with unfamiliar tags. */ char **comment; /* free text comments, or NULL */ int ncomment; /* number of comment lines */ int alloc_ncomment; /* number of comment lines alloc'ed */ char **gf_tag; /* markup tags for unparsed #=GF lines */ char **gf; /* annotations for unparsed #=GF lines */ int ngf; /* number of unparsed #=GF lines */ int alloc_ngf; /* number of gf lines alloc'ed */ char **gs_tag; /* markup tags for unparsed #=GS lines */ char ***gs; /* [0..ngs-1][0..nseq-1][free text] markup */ GKI *gs_idx; /* hash of #=GS tag types */ int ngs; /* number of #=GS tag types */ char **gc_tag; /* markup tags for unparsed #=GC lines */ char **gc; /* [0..ngc-1][0..alen-1] markup */ GKI *gc_idx; /* hash of #=GC tag types */ int ngc; /* number of #=GC tag types */ char **gr_tag; /* markup tags for unparsed #=GR lines */ char ***gr; /* [0..ngr][0..nseq-1][0..alen-1] markup */ GKI *gr_idx; /* hash of #=GR tag types */ int ngr; /* number of #=GR tag types */ /* Stuff we need for our own maintenance of the data structure */ GKI *index; /* name ->seqidx hash table */ int nseqalloc; /* number of seqs currently allocated for */ int nseqlump; /* lump size for dynamic expansions of nseq */ int *sqlen; /* individual sequence lengths during parsing */ int *sslen; /* individual ss lengths during parsing */ int *salen; /* individual sa lengths during parsing */ int lastidx; /* last index we saw; use for guessing next */ } MSA; #define MSA_SET_WGT (1 << 0) /* track whether wgts were set, or left at default 1.0 */ /* Structure: MSAFILE * SRE, Tue May 18 11:36:54 1999 * * Defines an alignment file that's open for reading. */ typedef struct msafile_struct { FILE *f; /* open file pointer */ char *fname; /* name of file. used for diagnostic output */ int linenumber; /* what line are we on in the file */ char *buf; /* buffer for line input w/ sre_fgets() */ int buflen; /* current allocated length for buf */ SSIFILE *ssi; /* open SSI index file; or NULL, if none. */ int do_gzip; /* TRUE if f is a pipe from gzip -dc (need pclose(f)) */ int do_stdin; /* TRUE if f is stdin (don't close f, not our problem) */ int format; /* format of alignment file we're reading */ } MSAFILE; /* Alignment file formats. * Must coexist with sqio.c/squid.h unaligned file format codes. * Rules: * - 0 is an unknown/unassigned format * - <100 reserved for unaligned formats * - >100 reserved for aligned formats */ #define MSAFILE_UNKNOWN 0 /* unknown format */ #define MSAFILE_STOCKHOLM 101 /* Pfam/HMMER's Stockholm format */ #define MSAFILE_SELEX 102 /* Obsolete(!): old HMMER/SELEX format */ #define MSAFILE_MSF 103 /* GCG MSF format */ #define MSAFILE_CLUSTAL 104 /* Clustal V/W format */ #define MSAFILE_A2M 105 /* aligned FASTA (A2M is UCSC terminology) */ #define MSAFILE_PHYLIP 106 /* Felsenstein's PHYLIP format */ #define MSAFILE_EPS 107 /* Encapsulated PostScript (output only) */ #define IsAlignmentFormat(fmt) ((fmt) > 100) /* from msa.c */ extern MSAFILE *MSAFileOpen(char *filename, int format, char *env); extern MSA *MSAFileRead(MSAFILE *afp); extern void MSAFileClose(MSAFILE *afp); extern void MSAFree(MSA *msa); extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline); extern int MSAFileRewind(MSAFILE *afp); extern int MSAFilePositionByKey(MSAFILE *afp, char *key); extern int MSAFilePositionByIndex(MSAFILE *afp, int idx); extern int MSAFileFormat(MSAFILE *afp); extern MSA *MSAAlloc(int nseq, int alen); extern void MSAExpand(MSA *msa); extern char *MSAFileGetLine(MSAFILE *afp); extern void MSASetSeqAccession(MSA *msa, int seqidx, char *acc); extern void MSASetSeqDescription(MSA *msa, int seqidx, char *desc); extern void MSAAddComment(MSA *msa, char *s); extern void MSAAddGF(MSA *msa, char *tag, char *value); extern void MSAAddGS(MSA *msa, char *tag, int seqidx, char *value); extern void MSAAppendGC(MSA *msa, char *tag, char *value); extern char *MSAGetGC(MSA *msa, char *tag); extern void MSAAppendGR(MSA *msa, char *tag, int seqidx, char *value); extern void MSAVerifyParse(MSA *msa); extern int MSAGetSeqidx(MSA *msa, char *name, int guess); extern MSA *MSAFromAINFO(char **aseq, AINFO *ainfo); extern void MSAMingap(MSA *msa); extern void MSANogap(MSA *msa); extern void MSAShorterAlignment(MSA *msa, int *useme); extern void MSASmallerAlignment(MSA *msa, int *useme, MSA **ret_new); extern char *MSAGetSeqAccession(MSA *msa, int idx); extern char *MSAGetSeqDescription(MSA *msa, int idx); extern char *MSAGetSeqSS(MSA *msa, int idx); extern char *MSAGetSeqSA(MSA *msa, int idx); extern float MSAAverageSequenceLength(MSA *msa); /* from a2m.c */ extern MSA *ReadA2M(MSAFILE *afp); extern void WriteA2M(FILE *fp, MSA *msa); /* from clustal.c */ extern MSA *ReadClustal(MSAFILE *afp); extern void WriteClustal(FILE *fp, MSA *msa); /* from eps.c */ extern void EPSWriteSmallMSA(FILE *fp, MSA *msa); /* from msf.c */ extern MSA *ReadMSF(MSAFILE *afp); extern void WriteMSF(FILE *fp, MSA *msa); /* from phylip.c */ extern MSA *ReadPhylip(MSAFILE *afp); extern void WritePhylip(FILE *fp, MSA *msa); /* from selex.c */ extern MSA *ReadSELEX(MSAFILE *afp); extern void WriteSELEX(FILE *fp, MSA *msa); extern void WriteSELEXOneBlock(FILE *fp, MSA *msa); /* from stockholm.c */ extern MSA *ReadStockholm(MSAFILE *afp); extern void WriteStockholm(FILE *fp, MSA *msa); extern void WriteStockholmOneBlock(FILE *fp, MSA *msa); #endif /*SQUID_MSA_INCLUDED*/ squid/rk.h0000640000175000017520000000162310463223377012702 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SQRKH_INCLUDED #define SQRKH_INCLUDED /* rk.h * * Header file for Rabin-Karp pattern searching on encoded * sequence strings. * * Sean Eddy, Thu Oct 1 11:45:42 1992 * RCS $Id: rk.h,v 1.2 1998/10/09 18:07:16 eddy Exp $ */ /* expect 32 bits for 8 nt */ typedef unsigned long Hashseq; /* but we count to be sure... RK_HASHSIZE is the number of nt that fit in one probe */ #define RK_HASHSIZE (sizeof(Hashseq)*2) /* empirically, how many nt minimum we require in a pattern before we abandon rk and go with something else */ #define RK_REQUIRE 4 extern int rkseq(Hashseq hashprobe, char *sequence); extern Hashseq rkcomp(char *probe); /* compile a Hashseq from a pattern */ #endif /* SQRKH_INCLUDED */ squid/sqfuncs.h0000640000175000017520000002406210463223377013752 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SQFUNCSH_INCLUDED #define SQFUNCSH_INCLUDED /* sqfuncs.h * * Prototypes for squid library functions; * also makes a good reference list for what the package contains. * * Warning: squid is a slowly evolving beast. Some functions are * obsolete. Some functions are probably just wrong, dating to * a primordial era before I knew anything about what I was doing. * Some functions are both obsolete and wrong but still necessary * to get legacy code to compile. * * CVS $Id: sqfuncs.h,v 1.34 2004/05/24 15:49:07 eddy Exp $ */ /* * from aligneval.c */ extern float ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2); extern float CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2); extern float CompareMultAlignments(char **kseqs, char **tseqs, int N); extern float CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N); extern float PairwiseIdentity(char *s1, char *s2); extern float AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample); extern char *MajorityRuleConsensus(char **aseq, int nseq, int alen); /* * from alignio.c */ extern void AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo); extern void InitAinfo(AINFO *ainfo); extern void FreeAlignment(char **aseqs, AINFO *ainfo); extern void SAMizeAlignment(char **aseq, int nseq, int alen); extern void SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap); extern int MakeAlignedString(char *aseq, int alen, char *ss, char **ret_s); extern int MakeDealignedString(char *aseq, int alen, char *ss, char **ret_s); extern int DealignedLength(char *aseq); extern int WritePairwiseAlignment(FILE *ofp, char *aseq1, char *name1, int spos1, char *aseq2, char *name2, int spos2, int **pam, int indent); extern int MingapAlignment(char **aseqs, AINFO *ainfo); extern int RandomAlignment(char **rseqs, SQINFO *sqinfo, int nseq, float pop, float pex, char ***ret_aseqs, AINFO *ainfo); extern void AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym); /* from cluster.c */ extern int Cluster(float **mx, int N, enum clust_strategy mode, struct phylo_s **ret_tree); extern struct phylo_s *AllocPhylo(int N); extern void FreePhylo(struct phylo_s *tree, int N); extern void MakeDiffMx(char **aseqs, int num, float ***ret_dmx); extern void MakeIdentityMx(char **aseqs, int num, float ***ret_imx); extern void PrintNewHampshireTree(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N); extern void PrintPhylo(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N); /* * from dayhoff.c */ extern int ParsePAMFile(FILE *fp, int ***ret_pam, float *ret_scale); extern void ScalePAM(int **pam, int scale); /* from file.c */ extern char *FileDirname(char *filename); extern char *FileTail(char *file, int noextension); extern char *FileSameDirectory(char *full, char *file); extern char *FileConcat(char *dir, char *file); extern char *FileAddSuffix(char *filename, char *sfx); extern FILE *EnvFileOpen(char *fname, char *env, char **ret_dir); extern int FileExists(char *filename); /* from getopt.c */ extern int Getopt(int argc, char **argv, struct opt_s *opt, int nopts, char *usage, int *ret_optind, char **ret_optname, char **ret_optarg); /* from hsregex.c * Henry Spencer's regex() code */ extern int Strparse(char *rexp, char *s, int ntok); extern void SqdClean(void); extern sqd_regexp *sqd_regcomp(const char *re); extern int sqd_regexec(sqd_regexp *rp, const char *s); extern void sqd_regsub(const sqd_regexp *rp, const char *src, char *dst); extern void sqd_regerror(char *message); /* from interleaved.c */ extern int IsInterleavedFormat(int format); extern int ReadInterleaved(char *seqfile, int (*skip_header)(FILE *), int (*parse_header)(FILE *, AINFO *), int (*is_dataline)(char *, char *), char ***ret_aseqs, AINFO *ainfo); extern int ReadAlignment(char *seqfile, int format, char ***ret_aseqs, AINFO *ainfo); /* from revcomp.c */ extern char *revcomp(char *comp, char *seq); /* * from selex.c */ extern int DealignAseqs(char **aseqs, int num, char ***ret_rseqs); extern int IsSELEXFormat(char *filename); extern int TruncateNames(char **names, int N); /* OBSOLETE? */ /* * from seqencode.c */ extern int seqcmp(char *s1, char *s2, int allow); extern int seqncmp(char *s1, char *s2, int n, int allow); extern int seqencode(char *codeseq,char *str); extern int coded_revcomp(char *comp, char *seq); extern int seqdecode(char *str, char *codeseq); extern int seqndecode(char *str, char *codeseq, int n); /* * from shuffle.c */ extern int StrShuffle(char *s1, char *s2); extern int StrDPShuffle(char *s1, char *s2); extern int StrMarkov0(char *s1, char *s2); extern int StrMarkov1(char *s1, char *s2); extern int StrReverse(char *s1, char *s2); extern int StrRegionalShuffle(char *s1, char *s2, int w); extern int AlignmentShuffle(char **ali1, char **ali2, int nseq, int alen); extern int AlignmentBootstrap(char **ali1, char **ali2, int nseq, int alen); extern int QRNAShuffle(char *xs, char *ys, char *x, char *y); /* * from sqerror.c */ extern void Die(char *format, ...); extern void Warn(char *format, ...); extern void Panic(char *file, int line); /* * from sqio.c */ extern void FreeSequence(char *seq, SQINFO *sqinfo); extern int SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag); extern void SeqinfoCopy(SQINFO *sq1, SQINFO *sq2); extern void ToDNA(char *seq); extern void ToRNA(char *seq); extern void ToIUPAC(char *seq, int is_aseq); extern void ToSimplyN(char *seq, int is_aseq); extern int ReadMultipleRseqs(char *seqfile, int fformat, char ***ret_rseqs, SQINFO **ret_sqinfo, int *ret_num); extern SQFILE *SeqfileOpen(char *filename, int format, char *env); extern SQFILE *SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode); extern int SeqfileFormat(FILE *fp); extern void SeqfilePosition(SQFILE *sfp, SSIOFFSET *offset); extern void SeqfileRewind(SQFILE *sfp); extern void SeqfileClose(SQFILE *sfp); extern int ReadSeq(SQFILE *fp, int format, char **ret_seq, SQINFO *sqinfo); extern int GCGBinaryToSequence(char *seq, int len); extern int GCGchecksum(char *seq, int seqlen); extern int GCGMultchecksum(char **seqs, int nseq); extern void WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc); extern int WriteSeq(FILE *outf, int outfmt, char *seq, SQINFO *sqinfo); extern int Seqtype(char *seq); extern int GuessAlignmentSeqtype(char **aseq, int nseq); extern int String2SeqfileFormat(char *s); extern char *SeqfileFormat2String(int code); extern SQINFO *MSAToSqinfo(MSA *msa); /* from squidcore.c */ extern void SqdBanner(FILE *fp, char *banner); /* from sre_ctype.c */ extern int sre_tolower(int c); extern int sre_toupper(int c); /* from sre_math.c */ extern int Linefit(float *x, float *y, int N, float *ret_a, float *ret_b, float *ret_r); extern void WeightedLinefit(float *x, float *y, float *var, int N, float *ret_m, float *ret_b); extern float **FMX2Alloc(int rows, int cols); extern void FMX2Free(float **mx); extern double **DMX2Alloc(int rows, int cols); extern void DMX2Free(double **mx); extern void FMX2Multiply(float **A, float **B, float **C, int m, int p, int n); extern void FMX2Copy(float **mx_dest, float **mx_src, int m, int n); /* from sre_string.c */ #ifdef NOSTR extern char *strstr(char *s, char *subs); #endif extern char *Strdup(char *s); extern void StringChop(char *s); extern int Strinsert(char *s1, char c, int pos); extern int Strdelete(char *s1, int pos); extern void s2lower(char *s); extern void s2upper(char *s); extern void *sre_malloc(char *file, int line, size_t size); extern void *sre_realloc(char *file, int line, void *p, size_t size); extern void Free2DArray(void **p, int dim1); extern void Free3DArray(void ***p, int dim1, int dim2); extern char *RandomSequence(char *alphabet, float *p, int n, int len); extern char *sre_fgets(char **buf, int *n, FILE *fp); extern int sre_strcat(char **dest, int ldest, char *src, int lsrc); extern char *sre_strtok(char **s, char *delim, int *len); extern char *sre_strdup(char *s, int n); extern char *sre_strncat(char *s1, char *s2, int n); extern char *sre_strncpy(char *s1, char *s2, int n); extern int IsBlankline(char *s); /* from stack.c */ extern struct intstack_s *InitIntStack(void); extern void PushIntStack(struct intstack_s *stack, int data); extern int PopIntStack(struct intstack_s *stack, int *ret_data); extern void ReverseIntStack(struct intstack_s *stack); extern int FreeIntStack( struct intstack_s *stack ); /* * from translate.c */ extern char *Translate(char *seq, char **code); /* * from types.c */ extern int IsInt(char *s); extern int IsReal(char *s); extern void Byteswap(char *swap, int nbytes); #ifndef USE_HOST_BYTESWAP_FUNCTIONS extern sqd_uint16 sre_ntoh16(sqd_uint16 netshort); extern sqd_uint32 sre_ntoh32(sqd_uint32 netlong); extern sqd_uint16 sre_hton16(sqd_uint16 hostshort); extern sqd_uint32 sre_hton32(sqd_uint32 hostlong); #endif /*!USE_HOST_BYTESWAP_FUNCTIONS*/ extern sqd_uint64 sre_ntoh64(sqd_uint64 net_int64); extern sqd_uint64 sre_hton64(sqd_uint64 host_int64); /* * from weight.c */ extern void GSCWeights(char **aseq, int nseq, int alen, float *wgt); extern void VoronoiWeights(char **aseq, int nseq, int alen, float *wgt); extern void BlosumWeights(char **aseq, int nseq, int alen, float blosumlevel, float *wgt); extern void PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt); extern void FilterAlignment(MSA *msa, float cutoff, MSA **ret_new); extern void SampleAlignment(MSA *msa, int sample, MSA **ret_new); extern void SingleLinkCluster(char **aseq, int nseq, int alen, float maxid, int **ret_c, int *ret_nc); /* from wuss.c */ extern int WUSS2ct(char *ss, int len, int allow_pseudoknots, int **ret_ct); extern void WUSStoKHS(char *ss); extern void KHStoWUSS(char *ss); #endif /* SQFUNCSH_INCLUDED */ squid/sre_random.h0000644000175000017520000000106210463223377014420 0ustar naolivbiolinux/* sre_random.h * Header file for sre_random.c * * SRE, Tue Oct 1 15:24:29 2002 * CVS $Id: sre_random.h,v 1.2 2003/10/27 21:08:13 eddy Exp $ */ extern double sre_random(void); extern void sre_srandom(int seed); extern double sre_random_positive(void); extern double ExponentialRandom(void); extern double Gaussrandom(double mean, double stddev); extern int DChoose(double *p, int N); extern int FChoose(float *p, int N); extern void SampleCountvector(double *p, int K, int ctot, double *c); #define CHOOSE(a) ((int) (sre_random() * (a))) squid/sre_stack.h0000644000175000017520000000446510463223377014257 0ustar naolivbiolinux/* sre_stack.h * * Pushdown stack implementations, for integers, for objects, and characters. * * nstack - SRE 1 March 2000. [Seattle] * mstack - SRE, Fri Oct 10 10:18:16 2003 [St. Louis] * cstack - SRE, Mon Oct 13 12:57:56 2003 [St. Louis] * * CVS $Id: sre_stack.h,v 1.3 2003/10/13 23:07:56 eddy Exp $ ***************************************************************** * @LICENSE@ ***************************************************************** */ #ifndef SRE_STACKH_INCLUDED #define SRE_STACKH_INCLUDED typedef struct nstack_s { int *data; /* the data stack */ int n; /* current (topmost) elem in data */ int nalloc; /* # of elems allocated right now */ int memblock; /* memory allocation block size, # of elems */ } Nstack_t; typedef struct mstack_s { void **data; /* the data stack */ int n; /* current (topmost) elem in data */ int nalloc; /* # of elems allocated right now */ int memblock; /* memory allocation block size, # of elems */ } Mstack_t; typedef struct cstack_s { char *data; /* the data stack */ int n; /* current (topmost) elem in data */ int nalloc; /* # of elems allocated right now */ int memblock; /* memory allocation block size, # of elems */ } Cstack_t; extern Nstack_t *CreateNstack(void); extern int PushNstack(Nstack_t *ns, int x); extern int PopNstack(Nstack_t *ns, int *ret_x); extern void FreeNstack(Nstack_t *ns); extern int NstackIsEmpty(Nstack_t *ns); extern void NstackSetBlocksize(Nstack_t *ns, int newsize); extern Mstack_t *CreateMstack(void); extern int PushMstack(Mstack_t *ms, void *obj); extern void *PopMstack(Mstack_t *ms); extern void FreeMstack(Mstack_t *ms); extern int MstackIsEmpty(Mstack_t *ms); extern void MstackSetBlocksize(Mstack_t *ms, int newsize); extern Cstack_t *CreateCstack(void); extern int PushCstack(Cstack_t *cs, char c); extern int PopCstack(Cstack_t *cs, char *ret_c); extern void FreeCstack(Cstack_t *cs); extern int CstackIsEmpty(Cstack_t *cs); extern void CstackSetBlocksize(Cstack_t *cs, int newsize); extern char *CstackString(Cstack_t *cs); #endif /*SRE_STACKH_INCLUDED*/ squid/ssi.h0000640000175000017520000001626410463223377013073 0ustar naolivbiolinux/***************************************************************** * @LICENSE@ *****************************************************************/ #ifndef SSIH_INCLUDED #define SSIH_INCLUDED /* ssi.h * Database indexing (SSI format support) * CVS $Id: ssi.h,v 1.8 2003/04/14 16:00:16 eddy Exp $ * * See: ssi_format.tex in Docs/ */ #include "squidconf.h" #include #include "squid.h" /* Limits */ #define SSI_MAXFILES 32767 /* 2^15-1 */ #define SSI_MAXKEYS 2147483647L /* 2^31-1 */ #define SSI_MAXRAM 200 /* allow 200MB indexes before external sort mode */ /* typedef: SSIOFFSET * Use the union to save space, since the two offset types are * mutually exclusive, controlled by "mode" */ struct ssioffset_s { char mode; /* GSI_OFFSET_I32, for example */ union { sqd_uint32 i32; /* an offset that fseek() can use */ sqd_uint64 i64; /* an offset that e.g. fseeko64() can use */ } off; }; typedef struct ssioffset_s SSIOFFSET; #define SSI_OFFSET_I32 0 #define SSI_OFFSET_I64 1 /* Structure: SSIFILE * xref: SSI API documentation in ssi-format.tex */ struct ssifile_s { FILE *fp; /* open SSI index file */ sqd_uint32 flags; /* optional behavior flags */ sqd_uint16 nfiles; /* number of files = 16 bit int */ sqd_uint32 nprimary; /* number of primary keys */ sqd_uint32 nsecondary; /* number of secondary keys */ sqd_uint32 flen; /* length of filenames (inc '\0') */ sqd_uint32 plen; /* length of primary keys (inc '\0') */ sqd_uint32 slen; /* length of secondary keys (inc '\0') */ sqd_uint32 frecsize; /* # bytes in a file record */ sqd_uint32 precsize; /* # bytes in a primary key record */ sqd_uint32 srecsize; /* # bytes in a secondary key record */ SSIOFFSET foffset; /* disk offset, start of file records */ SSIOFFSET poffset; /* disk offset, start of pri key recs */ SSIOFFSET soffset; /* disk offset, start of sec key recs */ char imode; /* mode for index file offsets, 32 v. 64 bit */ char smode; /* mode for sequence file offsets, 32 v. 64 bit */ /* File information: */ char **filename; /* list of file names [0..nfiles-1] */ sqd_uint32 *fileformat; /* file formats */ sqd_uint32 *fileflags; /* optional per-file behavior flags */ sqd_uint32 *bpl; /* bytes per line in file */ sqd_uint32 *rpl; /* residues per line in file */ }; typedef struct ssifile_s SSIFILE; /* optional per-index behavior flags in SSIFILE structure's flags: */ #define SSI_USE64 1<<0 /* seq offsets are 64-bit */ #define SSI_USE64_INDEX 1<<1 /* index file offsets are 64-bit */ /* optional per-file behavior flags in fileflags */ #define SSI_FAST_SUBSEQ 1<<0 /* can do subseq lookup in this file */ /* Structure: SSIINDEX * * Used when building up an index and writing it to disk */ struct ssipkey_s { /* Primary key data: */ char *key; /* key name */ sqd_uint16 fnum; /* file number */ SSIOFFSET r_off; /* record offset */ SSIOFFSET d_off; /* data offset */ sqd_uint32 len; /* sequence length */ }; struct ssiskey_s { /* Secondary key data: */ char *key; /* secondary key name */ char *pkey; /* primary key name */ }; struct ssiindex_s { int smode; /* sequence mode: SSI_OFFSET_I32 or _I64 */ int imode; /* index mode: SSI_OFFSET_I32 or _I64 */ int external; /* TRUE if pkeys and skeys are on disk */ int max_ram; /* maximum RAM in MB before switching to external */ char **filenames; sqd_uint32 *fileformat; sqd_uint32 *bpl; sqd_uint32 *rpl; sqd_uint32 flen; /* length of longest filename, inc '\0' */ sqd_uint16 nfiles; struct ssipkey_s *pkeys; sqd_uint32 plen; /* length of longest pkey, including '\0' */ sqd_uint32 nprimary; char *ptmpfile; /* name of tmp file, for external sort mode */ FILE *ptmp; /* handle on open ptmpfile */ struct ssiskey_s *skeys; sqd_uint32 slen; /* length of longest skey, including '\0' */ sqd_uint32 nsecondary; char *stmpfile; /* name of tmp file, for external sort mode */ FILE *stmp; /* handle on open ptmpfile */ }; typedef struct ssiindex_s SSIINDEX; /* These control malloc and realloc chunk sizes in the index * construction code. */ #define SSI_FILE_BLOCK 10 #define SSI_KEY_BLOCK 100 /* Error codes set by the API */ #define SSI_ERR_OK 0 #define SSI_ERR_NODATA 1 /* no data? an fread() failed */ #define SSI_ERR_NO_SUCH_KEY 2 /* that key's not in the index */ #define SSI_ERR_MALLOC 3 #define SSI_ERR_NOFILE 4 /* no such file? an fopen() failed */ #define SSI_ERR_BADMAGIC 5 /* magic number mismatch in GSIOpen() */ #define SSI_ERR_BADFORMAT 6 /* didn't read what I expected to fread() */ #define SSI_ERR_NO64BIT 7 /* needed 64-bit support and didn't have it */ #define SSI_ERR_SEEK_FAILED 8 /* an fseek() (or similar) failed */ #define SSI_ERR_TELL_FAILED 9 /* an ftell() (or similar) failed */ #define SSI_ERR_NO_SUBSEQS 10 /* fast subseq is disallowed */ #define SSI_ERR_RANGE 11 /* subseq requested is out of range */ #define SSI_ERR_BADARG 12 /* something wrong with a function argument */ #define SSI_ERR_TOOMANY_FILES 13 /* ran out of range for files in an index */ #define SSI_ERR_TOOMANY_KEYS 14 /* ran out of range for keys in an index */ #define SSI_ERR_FWRITE 15 #define SSI_ERR_EXTERNAL_SORT 16 /* external sort failed */ /* The SSI file reading API: */ extern int SSIOpen(char *filename, SSIFILE **ret_sfp); extern int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh, SSIOFFSET *ret_offset); extern int SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh, SSIOFFSET *ret_offset); extern int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start, int *ret_fh, SSIOFFSET *record_offset, SSIOFFSET *data_offset, int *ret_actual_start); extern int SSISetFilePosition(FILE *fp, SSIOFFSET *offset); extern int SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format); extern void SSIClose(SSIFILE *sfp); /* The SSI index file writing API: */ extern int SSIRecommendMode(char *file); extern SSIINDEX *SSICreateIndex(int mode); extern int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset); extern int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh); extern int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl); extern int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh, SSIOFFSET *r_off, SSIOFFSET *d_off, int L); extern int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey); extern int SSIWriteIndex(char *file, SSIINDEX *g); extern void SSIFreeIndex(SSIINDEX *g); /* The SSI misc. functions API: */ extern char *SSIErrorString(int n); /* The SSI debugging API: */ extern void SSIForceExternalSort(SSIINDEX *g); #endif /*SSIH_INCLUDED*/ squid/stockholm.h0000640000175000017520000000351410463223377014272 0ustar naolivbiolinux#ifndef STOCKHOLM_H_INCLUDED #define STOCKHOLM_H_INCLUDED #include "gki.h" typedef struct { int *linetype; /* e.g. STOCKHOLM_GF_LINE; always valid */ int *featurecode; /* all markup codes: e.g. STOCKHOLM_GF_ID; nonmarkup: always set to STOCKHOLM_UNPARSED */ char **featurename; /* all unparsed markup codes: string, e.g. "ID"; all other lines: NULL */ int *seqidx; /* all GS, GR, GC, sequence lines: which sequence; other lines: 0 */ int *len; /* all GR, GC, sequence lines: length of text field; other lines: 0 */ char **text; /* all unparsed nonblank lines: rest of data other lines: NULL */ int nseqalloc; /* current nseqs allocated for in aseqs and ainfo */ int nlines; /* number of lines in this skel */ int nlinealloc; /* current # of lines allocated for in this skel */ int overall_line; /* line # in file (important in files w/ >1 ali)*/ } alifile_skeleton; #define STOCKHOLM_GF_LINE 0 #define STOCKHOLM_GS_LINE 1 #define STOCKHOLM_GC_LINE 2 #define STOCKHOLM_GR_LINE 3 #define STOCKHOLM_SEQ_LINE 4 #define STOCKHOLM_BLANK_LINE 5 #define STOCKHOLM_COMMENT_LINE 6 #define STOCKHOLM_UNPARSED 0 #define STOCKHOLM_GF_ID 1 #define STOCKHOLM_GF_AC 2 #define STOCKHOLM_GF_DE 3 #define STOCKHOLM_GF_AU 4 #define STOCKHOLM_GF_GA 5 #define STOCKHOLM_GF_NC 6 #define STOCKHOLM_GF_TC 7 #define STOCKHOLM_GS_WT 100 #define STOCKHOLM_GS_AC 101 #define STOCKHOLM_GS_DE 102 #define STOCKHOLM_GC_CS 200 #define STOCKHOLM_GC_RF 201 #define STOCKHOLM_GR_SS 300 #define STOCKHOLM_GR_SA 301 #define SKEL_NSEQLUMP 10 /* allocate for new seqs in blocks of this size */ #define SKEL_LUMPSIZE 100 /* allocate for new lines in skel in blocks of this size */ #endif /*STOCKHOLM_H_INCLUDED*/ squid/stopwatch.h0000640000175000017520000000325010463223377014300 0ustar naolivbiolinux/* stopwatch.h * SRE, Fri Nov 26 14:54:21 1999 [St. Louis] [HMMER] * SRE, Thu Aug 3 08:00:35 2000 [St. Louis] [moved to SQUID] * CVS $Id: stopwatch.h,v 1.4 2003/06/13 20:05:31 eddy Exp $ * * Header file for stopwatch.c module: * reporting of cpu/system/elapsed time used by a process. * See stopwatch.c comments for documentation of compile-time * configuration options and API. * ***************************************************************** * @LICENSE@ ***************************************************************** */ #include "squidconf.h" #include #include #ifndef SRE_STRICT_ANSI #include #endif #ifndef STOPWATCH_H_INCLUDED #define STOPWATCH_H_INCLUDED struct stopwatch_s { time_t t0; /* Wall clock time, ANSI time() */ #ifdef SRE_STRICT_ANSI clock_t cpu0; /* CPU time, ANSI clock() */ #else struct tms cpu0; /* CPU/system time, POSIX times()*/ #endif double elapsed; /* elapsed time, seconds */ double user; /* CPU time, seconds */ double sys; /* system time, seconds */ }; typedef struct stopwatch_s Stopwatch_t; extern void StopwatchStart(Stopwatch_t *w); extern void StopwatchStop(Stopwatch_t *w); extern void StopwatchInclude(Stopwatch_t *w1, Stopwatch_t *w2); extern Stopwatch_t *StopwatchCreate(void); extern void StopwatchZero(Stopwatch_t *w); extern void StopwatchCopy(Stopwatch_t *w1, Stopwatch_t *w2); extern void StopwatchFree(Stopwatch_t *w); extern void StopwatchDisplay(FILE *fp, char *s, Stopwatch_t *w); #ifdef SRE_ENABLE_PVM extern void StopwatchPVMPack(Stopwatch_t *w); extern void StopwatchPVMUnpack(Stopwatch_t *w); #endif /* SRE_ENABLE_PVM */ #endif /*STOPWATCH_H_INCLUDED*/ squid/vectorops.h0000644000175000017520000000275510463223377014325 0ustar naolivbiolinux/* vectorops.h * Header file for vectorops.c * * SRE, Tue Oct 1 15:23:37 2002 [St. Louis] * CVS $Id: vectorops.h,v 1.4 2004/05/24 15:49:07 eddy Exp $ */ extern void DSet(double *vec, int n, double value); extern void FSet(float *vec, int n, float value); extern void DScale(double *vec, int n, double scale); extern void FScale(float *vec, int n, float scale); extern double DSum(double *vec, int n); extern float FSum(float *vec, int n); extern void DAdd(double *vec1, double *vec2, int n); extern void FAdd(float *vec1, float *vec2, int n); extern void DCopy(double *vec1, double *vec2, int n); extern void FCopy(float *vec1, float *vec2, int n); extern double DDot(double *vec1, double *vec2, int n); extern float FDot(float *vec1, float *vec2, int n); extern double DMax(double *vec, int n); extern float FMax(float *vec, int n); extern double DMin(double *vec, int n); extern float FMin(float *vec, int n); extern int DArgMax(double *vec, int n); extern int FArgMax(float *vec, int n); extern int DArgMin(double *vec, int n); extern int FArgMin(float *vec, int n); extern void DNorm(double *vec, int n); extern void FNorm(float *vec, int n); extern void DLog(double *vec, int n); extern void FLog(float *vec, int n); extern void DExp(double *vec, int n); extern void FExp(float *vec, int n); extern double DLogSum(double *vec, int n); extern float FLogSum(float *vec, int n); extern double DEntropy(double *p, int n); extern float FEntropy(float *p, int n);