debian/0000755000000000000000000000000012233472330007165 5ustar debian/control0000644000000000000000000000330312233471060010566 0ustar Source: biosquid Maintainer: Debian-Med Packaging Team Uploaders: Nelson A. de Oliveira , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), autoconf, autotools-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biosquid/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biosquid/trunk/ Package: biosquid Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: hmmer Description: utilities for biological sequence analysis SQUID is a library of C code functions for sequence analysis. It also includes a number of small utility programs to convert, show statistics, manipulate and do other functions on sequence files. . The original name of the package is "squid", but since there is already a squid on the archive (a proxy cache), it was renamed to "biosquid". . This package contains some tools to demonstrate the features of the SQUID library. Package: biosquid-dev Architecture: any Section: devel Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: biosquid Description: headers and static library for biological sequence analysis SQUID is a library of C code functions for sequence analysis. It also includes a number of small utility programs to convert, show statistics, manipulate and do other functions on sequence files. . The original name of the package is "squid", but since there is already a squid on the archive (a proxy cache), it was renamed to "biosquid". . This package contains the header files and the static SQUID library. debian/stranslate.10000644000000000000000000000332512214301066011426 0ustar .TH STRANSLATE 1 "Mon, 01 Aug 2005 15:28:08 -0300" .SH NAME stranslate \- translate a nucleic acid sequence to protein ORFs .SH SYNOPSIS .B stranslate .RI "[-options] " .SH DESCRIPTION This manual page documents briefly the .B stranslate command. .PP \fBstranslate\fP is a program that creates a file of all possible protein ORFs, given an input nucleic acid sequence. .SH OPTIONS Available options: .TP .B \-a Translate in full, with stops; no individual ORFs. .TP .B \-h Help; show brief usage and version info. .TP .B \-l Report only ORFs greater than minlen (default 20). .TP .B \-m Require ORFs to start with AUG/Met. .TP .B \-o Save results in output file. .TP .B \-q Quiet; silence banner, for piping or redirection. .TP .B \-s With \fB-a\fP, set stop character to . .TP .B \-\-tetrahymena Use the Tetrahymena/Oxytricha genetic code. .TP .B \-\-watson Only do the top strand (frames 0/1/2). .TP .B \-\-crick Only do the bottom strand (frames 3/4/5). .SH NOTE TO DEBIAN USERS The original program name is \fBtranslate\fP. It was renamed to \fBstranslate\fP to avoid conflict with another program of the same name. .SH SEE ALSO .BR afetch (1), .BR alistat (1), .BR compalign (1), .BR compstruct (1), .BR revcomp (1), .BR seqsplit (1), .BR seqstat (1), .BR sfetch (1), .BR shuffle (1), .BR sindex (1), .BR sreformat (1), .BR weight (1). .br .SH AUTHOR .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 .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/biosquid.README.Debian0000644000000000000000000000102112214301066013032 0ustar biosquid for Debian ------------------- The original name of the package is "squid", but since there is already a squid on the archive (a proxy cache) it was renamed to "biosquid", as suggested by Sean Eddy, upstream author of the program. Biosquid was compiled with LFS (Large File Support) enabled. Also, the "translate" binary was renamed to "stranslate", avoiding conflict with the binary of the same name, from the "translate" package. -- Nelson A. de Oliveira Fri, 04 Aug 2006 17:53:28 -03000 debian/biosquid.manpages0000644000000000000000000000013212214301066012511 0ustar debian/compalign.1 debian/revcomp.1 debian/seqsplit.1 debian/stranslate.1 debian/weight.1 debian/weight.10000644000000000000000000000277212214301066010542 0ustar .TH WEIGHT 1 "Mon, 01 Aug 2005 15:28:08 -0300" .SH NAME weight \- calculates sequence weights for an alignment .SH SYNOPSIS .B weight .RI "[-options] " .SH DESCRIPTION This manual page documents briefly the .B weight command. .PP \fBweight\fP is a program that calculates weights for a sequence alignment. .SH OPTIONS Available options: .TP .B \-b Use BLOSUM weighting scheme at fractional identity. .TP .B \-f Filter out seqs w/ fractional ident > [0-1]. .TP .B \-h Help; print version and usage info. .TP .B \-o Save weight-annotated alignment in . .TP .B \-p Use position based weight scheme (Henikoff & Henikoff). .TP .B \-s Sample sequences at random into a new alignment. .TP .B \-v Use Voronoi weight scheme (Sibbald & Argos). .TP .B \-\-informat Specify alignment file format . .br Allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP. .TP .B \-\-quiet Suppress verbose banner. .SH SEE ALSO .BR afetch (1), .BR alistat (1), .BR compalign (1), .BR compstruct (1), .BR revcomp (1), .BR seqsplit (1), .BR seqstat (1), .BR sfetch (1), .BR shuffle (1), .BR sindex (1), .BR sreformat (1), .BR stranslate (1), .br .SH AUTHOR .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 .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/biosquid-dev.README.Debian0000644000000000000000000000035012214301066013612 0ustar biosquid-dev for Debian ----------------------- All the header files are installed on /usr/include/biosquid/ instead being installed on /usr/include/ -- Nelson A. de Oliveira Fri, 04 Aug 2006 17:53:28 -03000 debian/rules0000755000000000000000000000105512233466047010256 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 %: dh $@ --with autotools_dev override_dh_auto_clean: dh_auto_clean rm -f configure override_dh_auto_configure: # autoreconf && true autoconf dh_auto_configure -- --enable-lfs override_dh_auto_install: dh_auto_install -- prefix=$(CURDIR)/debian/tmp/usr override_dh_install: mv $(CURDIR)/debian/tmp/usr/bin/translate $(CURDIR)/debian/tmp/usr/bin/stranslate dh_install override_dh_auto_test: chmod u+x Testsuite/x-base-* Testsuite/bug-1-sfetch* dh_auto_test debian/watch0000644000000000000000000000015312214301066010211 0ustar version=3 opts="dversionmangle=s/\+.*//" \ ftp://selab.janelia.org/pub/software/squid/ squid-(.*)\.tar\.gz debian/biosquid.install0000644000000000000000000000003412233466004012372 0ustar usr/bin usr usr/share/ usr debian/copyright0000644000000000000000000000475512233472110011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: SQUID Upstream-Contact: Sean Eddy Remark: The original homepage vanished - so most probably the author will have changed his e-mail address Source: http://selab.wustl.edu/cgi-bin/selab.pl?mode=software Remark: This page is not available any more Files: * Copyright: 1992-2006 Sean Eddy Washington University School of Medicine License: GPLv2 License: GPLv2 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. . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: debian/* Copyright: © 2005-2008 Nelson A. de Oliveira 2008-2013 Andreas Tille License: GPLv2 debian/source/0000755000000000000000000000000012214301202010451 5ustar debian/source/format0000644000000000000000000000001412214301202011657 0ustar 3.0 (quilt) debian/biosquid-dev.install0000644000000000000000000000006012233465764013161 0ustar usr/include/* usr/include/biosquid usr/lib/ usr debian/revcomp.10000644000000000000000000000172112214301066010717 0ustar .TH REVCOMP 1 "Mon, 01 Aug 2005 15:28:08 -0300" .SH NAME revcomp \- reverse complement a nucleic acid sequence .SH SYNOPSIS .B revcomp .RI "[-options] " .SH DESCRIPTION This manual page documents briefly the .B revcomp command. .PP \fBrevcomp\fP is a program that generates reverse complement of sequences. .SH OPTIONS Available options: .TP .B \-h Help; print version and usage info. .SH SEE ALSO .BR afetch (1), .BR alistat (1), .BR compalign (1), .BR compstruct (1), .BR seqsplit (1), .BR seqstat (1), .BR sfetch (1), .BR shuffle (1), .BR sindex (1), .BR sreformat (1), .BR stranslate (1), .BR weight (1). .br .SH AUTHOR .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 .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/changelog0000644000000000000000000000203712233472262011045 0ustar biosquid (1.9g+cvs20050121-3) unstable; urgency=low * debian/control: - added myself to uploaders - cme fix dpkg-control - debhelper 9 - Homepage field droped since homepage vanished - canonical Vcs fields - enhanced long description * debian/source/format: 3.0 (quilt) * debian/rules: use dh instead of cdbs * debian/copyright: DEP5 -- Andreas Tille Mon, 28 Oct 2013 14:04:02 +0100 biosquid (1.9g+cvs20050121-2) unstable; urgency=low [ Andreas Tille ] * Use Homepage tag control field instead of putting it into long description (Closes: #466005). [ Nelson A. de Oliveira ] * Update watch file (Closes: #453579); * Updated Standards-Version; * Changed Maintainer to the Debian-Med Packaging Team; * Added Vcs-* fields. -- Nelson A. de Oliveira Thu, 21 Feb 2008 22:41:01 -0300 biosquid (1.9g+cvs20050121-1) unstable; urgency=low * Initial release (Closes: #319945). -- Nelson A. de Oliveira Sat, 5 Aug 2006 01:03:52 -0300 debian/patches/0000755000000000000000000000000012233461164010617 5ustar debian/patches/afetch.man.patch0000644000000000000000000000172112233461056013645 0ustar --- a/Man/afetch.man +++ b/Man/afetch.man @@ -1,4 +1,4 @@ -.TH "afetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "afetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -67,15 +67,23 @@ file to prepare it for all future afetch .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). +.BR alistat (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR sfetch (1), +.BR shuffle (1), +.BR sindex (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/sindex.man.patch0000644000000000000000000000153212233461163013704 0ustar --- a/Man/sindex.man +++ b/Man/sindex.man @@ -1,4 +1,4 @@ -.TH "sindex" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "sindex" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -83,12 +83,24 @@ and accession (as a secondary key). .SH SEE ALSO .PP -@SEEALSO@ + +.BR afetch (1), +.BR alistat (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR sfetch (1), +.BR shuffle (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/seqstat.man.patch0000644000000000000000000000224112233461063014073 0ustar --- a/Man/seqstat.man +++ b/Man/seqstat.man @@ -1,4 +1,4 @@ -.TH "seqstat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "seqstat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -16,7 +16,7 @@ reads a sequence file .I seqfile and shows a number of simple statistics about it. -.pp +.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 @@ -69,13 +69,23 @@ and date, the parameters and options in .SH SEE ALSO -.PP -@SEEALSO@ +.BR afetch (1), +.BR alistat (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR sfetch (1), +.BR shuffle (1), +.BR sindex (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/compstruct.man.patch0000644000000000000000000000155512233461062014620 0ustar --- a/Man/compstruct.man +++ b/Man/compstruct.man @@ -1,4 +1,4 @@ -.TH "compstruct" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "compstruct" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -116,13 +116,23 @@ Don't print any verbose header informati .SH SEE ALSO -.PP -@SEEALSO@ +.BR afetch (1), +.BR alistat (1), +.BR compalign (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR sfetch (1), +.BR shuffle (1), +.BR sindex (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/sreformat.man.patch0000644000000000000000000000225312233461164014416 0ustar --- a/Man/sreformat.man +++ b/Man/sreformat.man @@ -1,4 +1,4 @@ -.TH "sreformat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "sreformat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -43,7 +43,7 @@ include .I raw (raw sequence, no other information). -.pp +.PP The available aligned output file format codes include .I stockholm @@ -59,7 +59,7 @@ codes include .I selex (the old SELEX/HMMER/Pfam annotated alignment format); -.pp +.PP All thee codes are interpreted case-insensitively (e.g. MSF, Msf, or msf all work). @@ -231,13 +231,23 @@ markup. .SH SEE ALSO -.PP -@SEEALSO@ +.BR afetch (1), +.BR alistat (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR sfetch (1), +.BR shuffle (1), +.BR sindex (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/series0000644000000000000000000000024412233461156012035 0ustar afetch.man.patch alistat.man.patch compstruct.man.patch Makefile.in.patch seqstat.man.patch sfetch.man.patch shuffle.man.patch sindex.man.patch sreformat.man.patch debian/patches/shuffle.man.patch0000644000000000000000000000327712233461162014055 0ustar --- a/Man/shuffle.man +++ b/Man/shuffle.man @@ -1,4 +1,4 @@ -.TH "shuffle" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "shuffle" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -19,7 +19,7 @@ in FASTA format on standard output. The are unchanged; this allows you to track down the source of each randomized sequence if necessary. -.pp +.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 @@ -27,7 +27,7 @@ composition exactly, use the .I -d option. -.pp +.PP The .I -0 and @@ -44,7 +44,7 @@ the generated sequence has the same 1st Markov properties as the input sequence (e.g. the same disymbol frequencies). -.pp +.PP Note that the default and .I -0, or @@ -56,7 +56,7 @@ composition exactly, while the Markov al only expect to generate a sequence of similar composition on average. -.pp +.PP Other shuffling algorithms are also available, as documented below in the options. @@ -175,13 +175,23 @@ the same output in subsequent runs with .SH SEE ALSO -.PP -@SEEALSO@ +.BR afetch (1), +.BR alistat (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR sfetch (1), +.BR sindex (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/alistat.man.patch0000644000000000000000000000153312233461060014050 0ustar --- a/Man/alistat.man +++ b/Man/alistat.man @@ -1,4 +1,4 @@ -.TH "alistat" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "alistat" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -109,13 +109,23 @@ Babelfish autodetection option. .SH SEE ALSO -.PP -@SEEALSO@ +.BR afetch (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR sfetch (1), +.BR shuffle (1), +.BR sindex (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/patches/Makefile.in.patch0000644000000000000000000000646212233461063013770 0ustar --- a/Makefile.in +++ b/Makefile.in @@ -75,10 +75,12 @@ PROGS = afetch\ MANS = afetch\ alistat\ + compstruct\ seqstat\ sfetch\ shuffle\ - sreformat\ + sindex\ + sreformat READMES = 00README INSTALL Makefile.in @@ -103,51 +105,80 @@ HDRS = dirichlet.h\ stopwatch.h\ vectorops.h -OBJS = a2m.o\ - aligneval.o\ +COMMON_OBJS = \ + a2m.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\ + types.o\ + vectorops.o + +OBJS = $(COMMON_OBJS)\ + aligneval.o\ + cluster.o\ + dayhoff.o\ + dirichlet.o\ + eps.o\ + iupac.o\ + revcomp.o\ + rk.o\ + seqencode.o\ + shuffle.o\ + sre_math.o\ + sre_stack.o\ stopwatch.o\ translate.o\ - types.o\ - vectorops.o\ weight.o\ wuss.o +MAINS = afetch_main.o\ + alistat_main.o\ + compalign_main.o\ + compstruct_main.o\ + revcomp_main.o\ + seqsplit_main.o\ + seqstat_main.o\ + sfetch_main.o\ + shuffle_main.o\ + sindex_main.o\ + sreformat_main.o\ + translate_main.o\ + weight_main.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} ${LIBS} +$(PROGS): @EXEC_DEPENDENCY@ ${OBJS} ${MAINS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o afetch afetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o alistat aligneval.o cluster.o sre_math.o sre_stack.o alistat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compalign aligneval.o compalign_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compstruct sre_math.o sre_stack.o wuss.o compstruct_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o revcomp revcomp.o shuffle.o revcomp_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqsplit seqsplit_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqstat seqstat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sfetch revcomp.o shuffle.o sfetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o shuffle iupac.o shuffle.o shuffle_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sindex sindex_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sreformat eps.o shuffle.o sre_stack.o wuss.o sreformat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o translate iupac.o revcomp.o shuffle.o sre_stack.o translate.o translate_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o weight aligneval.o cluster.o iupac.o sre_math.o sre_stack.o weight.o weight_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} .c.o: ${CC} ${CFLAGS} ${CPPFLAGS} ${PVMINCDIR} ${DEFS} -c $< debian/patches/sfetch.man.patch0000644000000000000000000000176212233461160013670 0ustar --- a/Man/sfetch.man +++ b/Man/sfetch.man @@ -1,4 +1,4 @@ -.TH "sfetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual" +.TH "sfetch" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual" .SH NAME .TP @@ -64,7 +64,7 @@ databases. The program .B sindex creates SSI indexes for any sequence file. -.pp +.PP .B sfetch was originally named .B getseq, @@ -191,13 +191,23 @@ Babelfish autodetection option. .SH SEE ALSO -.PP -@SEEALSO@ +.BR afetch (1), +.BR alistat (1), +.BR compalign (1), +.BR compstruct (1), +.BR revcomp (1), +.BR seqsplit (1), +.BR seqstat (1), +.BR shuffle (1), +.BR sindex (1), +.BR sreformat (1), +.BR stranslate (1), +.BR weight (1). .SH AUTHOR -@PACKAGE@ and its documentation are @COPYRIGHT@ -@LICENSE@ +Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine +Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. .nf debian/compat0000644000000000000000000000000212233460432010363 0ustar 9 debian/compalign.10000644000000000000000000000435612214301066011224 0ustar .TH COMPALIGN 1 "Mon, 01 Aug 2005 15:28:08 -0300" .SH NAME compalign \- compare two multiple alignments .SH SYNOPSIS .B compalign .RI "[-options] " .SH DESCRIPTION .PP \fBcompalign\fP calculates 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. .sp 1 The identity of the multiple sequence alignments is defined as the averaged identity over all N(N-1)/2 pairwise alignments. .sp 1 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): .sp 1 .nf 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. .fi 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. .SH OPTIONS Available options: .TP .B \-h Print short help and usage info. .TP .B \-c Only compare under marked #=CS consensus structure. .TP .B \-\-informat Specify that both alignments are in format (MSF, for instance). .TP .B \-\-quiet Suppress verbose header (used in regression testing). .SH SEE ALSO .BR afetch (1), .BR alistat (1), .BR compstruct (1), .BR revcomp (1), .BR seqsplit (1), .BR seqstat (1), .BR sfetch (1), .BR shuffle (1), .BR sindex (1), .BR sreformat (1), .BR stranslate (1), .BR weight (1). .br .SH AUTHOR .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 .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others). debian/seqsplit.10000644000000000000000000000274712214301066011121 0ustar .TH SEQSPLIT 1 "Mon, 01 Aug 2005 15:28:08 -0300" .SH NAME seqsplit \- split seqs into chunks of defined size and overlap .SH SYNOPSIS .B seqsplit .RI "[-options] " .SH DESCRIPTION This manual page documents briefly the .B seqsplit command. .PP \fBseqsplit\fP is a program that splits sequences into smaller chunks of defined size and overlap; output a FASTA file. .SH OPTIONS .TP .B \-h Help; display usage and version. .TP .B \-o Output the new FASTA file to . .TP .B \-\-fragfile Save one-line-per-frag coord summary file to . .TP .B \-\-informat Specify sequence file format . .TP .B \-\-length Set max length of each unique seq frag to . .TP .B \-\-overlap Set overlap length to (total frag size = length+overlap). .TP .B \-\-shortnames Use short "frag1" names, not "/-". .SH LIMITATIONS Still working in 32 bits -- no sequence can be more than 2 GB in size. .SH SEE ALSO .BR afetch (1), .BR alistat (1), .BR compalign (1), .BR compstruct (1), .BR revcomp (1), .BR seqstat (1), .BR sfetch (1), .BR shuffle (1), .BR sindex (1), .BR sreformat (1), .BR stranslate (1), .BR weight (1). .br .SH AUTHOR .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 .PP This manual page was written by Nelson A. de Oliveira , for the Debian project (but may be used by others).