debian/0000755000000000000000000000000012214273044007165 5ustar debian/control0000644000000000000000000000301312214272745010574 0ustar Source: embassy-domsearch Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~), libx11-dev, libgd2-xpm-dev, libmysqlclient-dev, libpq-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/embassy-domsearch/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/embassy-domsearch/trunk/ Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH Package: embassy-domsearch Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.6.0-1~), emboss-lib (<< 6.6.1~) Recommends: emboss Suggests: embassy Description: Extra EMBOSS commands to search for protein domains The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. . Applications in this DOMSEARCH release are seqfraggle (removes fragment sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove ambiguous classified sequences from DHF files) and seqwords (Generates DHF files from keyword search of UniProt). debian/embassy-domsearch.manpages0000644000000000000000000000021311430506065014305 0ustar debian/manpages/seqfraggle.1e debian/manpages/seqnr.1e debian/manpages/seqsearch.1e debian/manpages/seqsort.1e debian/manpages/seqwords.1e debian/rules0000755000000000000000000000043511771050574010257 0ustar #!/usr/bin/make -f CFLAGS += -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib LDFLAGS += -Wl,--as-needed %: dh $@ override_dh_auto_configure: dh_auto_configure -- --enable-systemlibs debian/manpages/0000755000000000000000000000000012214272446010765 5ustar debian/manpages/seqwords.1e0000644000000000000000000000666111430506065013070 0ustar '\" t .\" Title: SEQWORDS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMSEARCH 0.1.0++20100721 .\" Language: English .\" .TH "SEQWORDS" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqwords \- Generates DHF files from keyword search of UniProt\&. .SH "SYNOPSIS" .HP \w'\fBseqwords\fR\ 'u \fBseqwords\fR \fB\-keyfile\ \fR\fB\fIinfile\fR\fR \fB\-spfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqwords\fR\ 'u \fBseqwords\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqwords\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-keyfile\fR \fIinfile\fR .RS 4 This option specifies the name of keywords file (input)\&. This contains a list of keywords specific to a number of SCOP or CATH families and superfamilies used by SEQWORDS to search a sequence database\&. .RE .PP \fB\-spfile\fR \fIinfile\fR .RS 4 This option specifies the name of the sequence database (input) to search\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This option specifies the name of the DHF file (domain hits file) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqwords is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqsearch.1e0000644000000000000000000001220011430506065013161 0ustar '\" t .\" Title: SEQSEARCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMSEARCH 0.1.0++20100721 .\" Language: English .\" .TH "SEQSEARCH" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqsearch \- Generate PSI\-BLAST hits (DHF file) from a DAF file\&. .SH "SYNOPSIS" .HP \w'\fBseqsearch\fR\ 'u \fBseqsearch\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-inseqspath\ \fR\fB\fIdirlist\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-evalue\ \fR\fB\fIfloat\fR\fR \fB\-maxhits\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqsearch\fR\ 'u \fBseqsearch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqsearch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-mode\fR \fIlist\fR .RS 4 This option specifies the mode of SEQSEARCH operation\&. SEQSEARCH takes as input a directory of either i\&. single sequences, ii\&. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\&. The user has to specify which\&. Default value: 1 .RE .PP \fB\-inseqspath\fR \fIdirlist\fR .RS 4 This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ .RE .PP \fB\-database\fR \fIstring\fR .RS 4 Default value: swissprot .RE .SS "Required section" .PP \fB\-niter\fR \fIinteger\fR .RS 4 This option specifies the number of PSIBLAST iterations\&. This option specifies the number of PSIBLAST iterations that are performed in a search\&. Default value: 1 .RE .PP \fB\-evalue\fR \fIfloat\fR .RS 4 This option specifies the threshold E\-value for inclusion in family\&. This option specifies the threshold E\-value for a PSIBLAST hit to be retained\&. Default value: 0\&.001 .RE .PP \fB\-maxhits\fR \fIinteger\fR .RS 4 This option specifies the maximum number of hits\&. This option specifies the maximum number of PSIBLAST hit that are retained\&. It should normally be set high so that nothing is discarded\&. Default value: 1000 .RE .SS "Output section" .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA format\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while SEQSEARCH ran\&. Default value: seqsearch\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqsearch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqnr.1e0000644000000000000000000002227511430506065012350 0ustar '\" t .\" Title: SEQNR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMSEARCH 0.1.0++20100721 .\" Language: English .\" .TH "SEQNR" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqnr \- Removes redundancy from DHF files\&. .SH "SYNOPSIS" .HP \w'\fBseqnr\fR\ 'u \fBseqnr\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dosing\ \fR\fB\fItoggle\fR\fR \fB\-singletsdir\ \fR\fB\fIdirectory\fR\fR \fB\-dosets\ \fR\fB\fItoggle\fR\fR \fB\-insetsdir\ \fR\fB\fIdirectory\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-thresh\ \fR\fB\fIfloat\fR\fR \fB\-threshlow\ \fR\fB\fIfloat\fR\fR \fB\-threshup\ \fR\fB\fIfloat\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-dored\ \fR\fB\fItoggle\fR\fR \fB\-redoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqnr\fR\ 'u \fBseqnr\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqnr\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dhfinpath\fR \fIdirlist\fR .RS 4 This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .PP \fB\-dosing\fR \fItoggle\fR .RS 4 This option specifies whether to use singlet sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y .RE .PP \fB\-singletsdir\fR \fIdirectory\fR .RS 4 This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .PP \fB\-dosets\fR \fItoggle\fR .RS 4 This option specifies whether to use sets of sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y .RE .PP \fB\-insetsdir\fR \fIdirectory\fR .RS 4 This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ .RE .PP \fB\-matrix\fR \fImatrixf\fR .RS 4 This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62 .RE .SS "Required section" .PP \fB\-mode\fR \fIlist\fR .RS 4 This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\&. All permutations of pair\-wise sequence alignments are calculated for each set of input sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1 .RE .PP \fB\-thresh\fR \fIfloat\fR .RS 4 This option specifies the % sequence identity redundancy threshold\&. The % sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0 .RE .PP \fB\-threshlow\fR \fIfloat\fR .RS 4 This option specifies the % sequence identity redundancy threshold (lower limit)\&. The % sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0 .RE .PP \fB\-threshup\fR \fIfloat\fR .RS 4 This option specifies the % sequence identity redundancy threshold (upper limit)\&. The % sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0 .RE .SS "Additional section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 This option specifies the gap insertion penalty\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 This option specifies the gap extension penalty\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5 .RE .SS "Output section" .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .PP \fB\-dored\fR \fItoggle\fR .RS 4 This option specifies whether to retain redundant sequences\&. If this option is set a DHF file (domain hits file) of redundant sequences is written\&. Default value: N .RE .PP \fB\-redoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 This option specifies the name of SEQNR log file (output)\&. The log file contains messages about any errors arising while SEQNR ran\&. Default value: seqnr\&.log .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqnr is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqfraggle.1e0000644000000000000000000000772411430506065013342 0ustar '\" t .\" Title: SEQFRAGGLE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMSEARCH 0.1.0++20100721 .\" Language: English .\" .TH "SEQFRAGGLE" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqfraggle \- Removes fragment sequences from DHF files\&. .SH "SYNOPSIS" .HP \w'\fBseqfraggle\fR\ 'u \fBseqfraggle\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-thresh\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBseqfraggle\fR\ 'u \fBseqfraggle\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqfraggle\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dhfinpath\fR \fIdirlist\fR .RS 4 This option specifies the location of DHF files (domain hits files) or other sequence files (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./ .RE .SS "Required section" .PP \fB\-thresh\fR \fIinteger\fR .RS 4 This option specifies the percentage of median length for definition of fragments\&. SEQFRAGGLE first determines the median length of all the sequences in the input file, then discards any hit sequences which are not within a threshold percentage of the median length\&. The remaining sequences are written to the output file\&. Default value: 50 .RE .SS "Output section" .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./ .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqfraggle is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqsort.1e0000644000000000000000000001353011430506065012712 0ustar '\" t .\" Title: SEQSORT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 08/11/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: DOMSEARCH 0.1.0++20100721 .\" Language: English .\" .TH "SEQSORT" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqsort \- Remove ambiguous classified sequences from DHF files\&. .SH "SYNOPSIS" .HP \w'\fBseqsort\fR\ 'u \fBseqsort\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-dofamilies\ \fR\fB\fItoggle\fR\fR \fB\-doambiguities\ \fR\fB\fItoggle\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-hitsfile\ \fR\fB\fIoutfile\fR\fR \fB\-ambigfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqsort\fR\ 'u \fBseqsort\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqsort\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dhfindir\fR \fIdirectory\fR .RS 4 This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .SS "Required section" .PP \fB\-overlap\fR \fIinteger\fR .RS 4 This option specifies the number of overlapping residues required for merging of two hits\&. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user\-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits\&. Default value: 10 .RE .PP \fB\-dofamilies\fR \fItoggle\fR .RS 4 This option specifies to write a domain families file\&. If this option is set a domain families file is written\&. Default value: N .RE .PP \fB\-doambiguities\fR \fItoggle\fR .RS 4 This option specifies whether to write a domain ambiguities file\&. If this option is set a domain ambiguities file is written\&. Default value: N .RE .SS "Output section" .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ .RE .PP \fB\-hitsfile\fR \fIoutfile\fR .RS 4 This option specifies the name of domain families file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf .RE .PP \fB\-ambigfile\fR \fIoutfile\fR .RS 4 This option specifies the name of domain ambiguities file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqsort is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/watch0000644000000000000000000000015111450303733010213 0ustar version=3 opts=dversionmangle=s/\+\+\d+// \ ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-(.*).tar.gz debian/embassy-domsearch.lintian-overrides0000644000000000000000000000026711567121432016163 0ustar # The embassy packages use privately some of the EMBOSS libraries. They have # the same upstream authors and are released together. embassy-domsearch: binary-or-shlib-defines-rpath * debian/copyright0000644000000000000000000000236511771053045011132 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: DOMSEARCH Source: ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.0.tar.gz Files: * Copyright: Jon Ison (jison@ebi.ac.uk) Matt Blades Ranjeeva Ranasinghe License: GPL-2+ Files: debian/* Copyright: 2007-2011 Charles Plessy 2012 Andreas Tille License: GPL-2+ License: GPL-2+ This package 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 package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. debian/source/0000755000000000000000000000000012214272446010472 5ustar debian/source/format0000644000000000000000000000001411507156767011713 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000570312214273044011044 0ustar embassy-domsearch (1:0.1.650-1) unstable; urgency=low * New upstream version * debian/control: - cme fix dpkg-control - Bumped versioned depends from emboss-lib - anonscm in VCS fields -- Andreas Tille Thu, 12 Sep 2013 10:03:31 +0200 embassy-domsearch (1:0.1.0+20110714-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.3 (no changes needed) - debhelper version 9 - Adapted versioned (build-)depends to latest emboss version * added debian/compat: 9 * debian/source/format: 3.0 (quilt) * debian/rules: short dh * debian/copyright: DEP5 fixes -- Andreas Tille Fri, 22 Jun 2012 10:03:24 +0200 embassy-domsearch (0.1.0++20100721-3) unstable; urgency=low * Corrected version mangling in debian/watch. * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. (debian/rules) Closes: #625193, LP: #771001. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * Updated debian/embassy-domsearch.lintian-overrides for lintian 2.5. * debian/copyright validated with config-edit. -- Charles Plessy Wed, 11 May 2011 18:52:14 +0900 embassy-domsearch (0.1.0++20100721-2) unstable; urgency=low * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions lower than 6.3.2, because backwards compatibility is sometimes broken (debian/control, debian/rules). * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private libraries (debian/rules, debian/embassy-domsearch.lintian-overrides). * Refreshed debian/copyright to test the latest DEP-5 format. -- Charles Plessy Thu, 23 Sep 2010 13:04:32 +0900 embassy-domsearch (0.1.0++20100721-1) unstable; urgency=low * New upstream release in which the version number was unchanged. * Build-Depends on emboss 6.3.1 (debian/control, debian/rules, closes: #591121). * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). -- Charles Plessy Wed, 11 Aug 2010 20:33:08 +0900 embassy-domsearch (0.1.0++20100115-1) unstable; urgency=low * New upstream release in which the version number was unchanged. (I chose a strange version number to avoid an epoch because of the typo in the previous number). * debian/control: - Build against EMBOSS 6.2 (Closes: #587119). - Checked conformance with Policy 3.8.4 (no changes needed). * debian/*manpages* refreshed. -- Charles Plessy Sat, 26 Jun 2010 22:58:36 +0900 embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low * Initial release (Closes: #537204). -- Charles Plessy Mon, 20 Jul 2009 10:43:26 +0900 debian/compat0000644000000000000000000000000211770332430010364 0ustar 9