[med-svn] r822 - in trunk/packages/readseq: . tags tags/1-7 tags/1-7/debian tags/1-7/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Sat Nov 17 23:38:59 UTC 2007
Author: tille
Date: 2007-11-17 23:38:59 +0000 (Sat, 17 Nov 2007)
New Revision: 822
Added:
trunk/packages/readseq/tags/
trunk/packages/readseq/tags/1-7/
trunk/packages/readseq/tags/1-7/debian/
trunk/packages/readseq/tags/1-7/debian/README.debian
trunk/packages/readseq/tags/1-7/debian/changelog
trunk/packages/readseq/tags/1-7/debian/compat
trunk/packages/readseq/tags/1-7/debian/control
trunk/packages/readseq/tags/1-7/debian/copyright
trunk/packages/readseq/tags/1-7/debian/dirs
trunk/packages/readseq/tags/1-7/debian/docs
trunk/packages/readseq/tags/1-7/debian/get-orig-source
trunk/packages/readseq/tags/1-7/debian/install
trunk/packages/readseq/tags/1-7/debian/links
trunk/packages/readseq/tags/1-7/debian/manpages
trunk/packages/readseq/tags/1-7/debian/patches/
trunk/packages/readseq/tags/1-7/debian/patches/00list
trunk/packages/readseq/tags/1-7/debian/patches/20-Formats.dpatch
trunk/packages/readseq/tags/1-7/debian/patches/20-Makefile.dpatch
trunk/packages/readseq/tags/1-7/debian/patches/30-arb-code-patches.dpatch
trunk/packages/readseq/tags/1-7/debian/readseq.1
trunk/packages/readseq/tags/1-7/debian/rules
trunk/packages/readseq/tags/1-7/debian/translate.patch
Log:
Tagged readseq 1-7
Added: trunk/packages/readseq/tags/1-7/debian/README.debian
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/README.debian (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/README.debian 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,49 @@
+readseq for DEBIAN
+------------------
+
+This version is built against the NCBI libraries but it seems
+quite buggy: please report any problem with ASN/1 conversions
+<http://bugs.debian.org/>.
+
+I need this package to build Arb (http://www.arb-home.de).
+There was a bug report (#43372) about a new version (version 2).
+I decided to use the latest sources of version 1 which are in C
+because I need exactly this C version. I will not package version 2
+for the following reasons:
+ - Java adds en extra dependency of java-virtual-machine which
+ would bother my users and me
+ - most certainly it would let readseq go to contrib which I want
+ to avoid (not checked)
+ - I really need the C version for Arb.
+
+If somebody really wants to have readseq Version 2 packaged (which
+might make sense for sure) this should be made as separate package
+readseq2. In this case please double check, whether it can go into
+main.
+
+The new version can be found at
+
+ ftp://ftp.bio.indiana.edu/molbio/readseq/version2
+
+Quote from the documentation of version 2:
+
+ This release version 2, first available in 1999, continues support for
+ the "classic" C version, in that it supports the same command-line
+ options, but has extensions for sequence documentation, feature table
+ and other additions, plus new sequence format conversions, and a lot
+ of bug fixing. This java version is also more efficient, working
+ faster than the compiled C classic version. It still isn't efficient
+ enough to handle large sequences (genome sized or full GenBank/EMBL
+ data release files).
+
+Andreas Tille <tille at debian.org> Thu, 25 Oct 2001 09:42:26 +0200
+
+Starting with readseq 1-4, support for two more sequence formats was added:
+
+LinAll format: used by the 'LinAll' and 'ConStruct' RNA structure packages
+from the Duesseldorf biophysics group.
+
+Vienna RNA format: used by the Vienna RNA package avaiable from the
+Theoretical Chemistry group at Vienna University.
+
+Michael Schmitz <schmitz at debian.org> Wed, 11 Dec 2002 13:38:05 +0200
Added: trunk/packages/readseq/tags/1-7/debian/changelog
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/changelog (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/changelog 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,115 @@
+readseq (1-7) unstable; urgency=low
+
+ * Group maintainance by Debian-Med packaging group
+ * Build-Depends: debhelper (>= 5.0)
+ * Standards-Version: 3.7.2 (no changes necessary)
+ * Switched to dpatch, cdbs
+ * Added get-orig-source target
+ * Moved manpage to Debian directory
+ * debian/control: Homepage tag
+
+ -- Andreas Tille <tille at debian.org> Sat, 17 Nov 2007 23:04:00 +0100
+
+readseq (1-6) unstable; urgency=low
+
+ * Fixed amd64 bug (segfaults when command line options given), thanks to
+ a hint by the ncbi6 maintainer. Closes: #269643.
+
+ -- Michael Schmitz <schmitz at debian.org> Tue, 26 Oct 2004 18:12:15 +0100
+
+readseq (1-5) unstable; urgency=low
+
+ * Fixed bug in format detection that did result in readseq incorrectly
+ claiming LinAll format files whose title begins with a number as
+ Phylip format. Bug spotted locally and fixed by Gerhard Steger
+ <steger at biophys.uni-duesseldorf.de>.
+
+ -- Michael Schmitz <schmitz at debian.org> Thu, 12 Jun 2003 17:55:15 +0100
+
+readseq (1-4) unstable; urgency=low
+
+ * New Maintainer (took over from Andreas Tille 'cuz readseq is actually
+ in use at our site).
+
+ * Added LinAll and Vienna RNA formats.
+
+ -- Michael Schmitz <schmitz at debian.org> Thu, 07 Nov 2002 16:55:05 +0100
+
+readseq (1-3) unstable; urgency=low
+
+ * Corrected spelling bug (Thanks to Matt Zimmerman <mdz at debian.org>)
+ closes: #125305
+
+ -- Andreas Tille <tille at debian.org> Tue, 18 Dec 2001 12:03:25 +0100
+
+readseq (1-2) unstable; urgency=low
+
+ * compile explicitely with -lncbiid1 and -lnetcli according to a hint of
+ ncbi-tools6 maintainer Aaron M. Ucko <ucko at debian.org>
+ (Thanks Aaron)
+ closes: #119586
+
+ -- Andreas Tille <tille at debian.org> Thu, 15 Nov 2001 17:01:18 +0100
+
+readseq (1-1) unstable; urgency=low
+
+ * New Maintainer
+ closes: #100257
+ * New upstream release
+ * Applied Bugfix 20Apr93
+ * Applied fixes from former versions
+ * Added debian/translate.patch to the sources for those brave people
+ who want to test it (please report if I should apply it to the binary)
+ * Replaced a gets call by fgets to avoid buffer overflow
+ * increased p.namewidth from 8 to 10 in ureadseq.h because Arb need this
+ * Added patch by o. strunk (ARB) to allow numbers in genbank sequences
+ to ureadseq.c
+ * Added an undocumented ARB patch which seems to fix a problem with older
+ Phylip versions.
+ * Added a further patch from ARB. Patches can be undone by just
+ undefining ARB.
+ * I did not apply the patch of the ARB version which wrapped isdigit by
+ by rs_isdigit in readseq.c.
+ * Declared in README.Debian that this is the packaged version 1 of
+ readseq by certain reasons. Because I really need this version I
+ close the "new version available" bug. If somebody really wants
+ the new version please file an RFP bug against wnpp. Make sure
+ to read /usr/share/doc/readseq/README.Debian before.
+ closes: #43372
+ * Added URL to the package description because I consider this as
+ "good style" to have an upstream link without installing the package.
+ * Install Readseq.help as NCBI Vibrant Toolkit compatible helpfile
+ instead of just putting it just into /usr/share/doc/readseq.
+
+ -- Andreas Tille <tille at debian.org> Mon, 5 Nov 2001 08:43:12 +0100
+
+readseq (0.0-4) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Fri, 24 Aug 2001 23:51:22 +0200
+
+readseq (0.0-3) unstable; urgency=low
+
+ * Adopted by new maintainer; closes: #92801
+ * Updated to latest standards version and added Build-Depends;
+ closes: #84541, #91036, #91640
+ * Corrected doc path in Makefile and manpage.
+ * Moved from section misc to science.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Thu, 19 Apr 2001 20:05:45 +0200
+
+readseq (0.0-2) unstable; urgency=low
+
+ * Manual page. Closes #33772
+ * Now linked with the NCBI libraries an therefore depends on
+ ncbi-tools.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Sat, 6 Mar 1999 22:44:04 +0100
+
+readseq (0.0-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Fri, 5 Feb 1999 16:58:28 +0100
+
Added: trunk/packages/readseq/tags/1-7/debian/compat
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/compat (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/compat 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1 @@
+5
Added: trunk/packages/readseq/tags/1-7/debian/control
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/control (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/control 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,17 @@
+Source: readseq
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael Schmitz <schmitz at debian.org>, Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 5.0), cdbs, dpatch, ncbi-tools-dev
+Standards-Version: 3.7.2
+Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/
+
+Package: readseq
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: [Biology] Conversion between sequence formats
+ Reads and writes nucleic/protein sequences in various
+ formats. Data files may have multiple sequences.
+ Readseq is particularly useful as it automatically detects many
+ sequence formats, and converts between them.
Added: trunk/packages/readseq/tags/1-7/debian/copyright
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/copyright (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/copyright 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,38 @@
+This package was debianized by Andreas Tille tille at debian.org on
+Thu, 25 Oct 2001 09:42:26 +0200.
+
+It was downloaded from
+ http://iubio.bio.indiana.edu/soft/molbio/readseq/version1/src/
+
+Upstream Author: D. Gilbert <gilbertd at bio.indiana.edu>
+
+Copyright: 1990-1993 D. Gilbert
+
+(From the Readme:)
+
+ * Copyright 1990 by d.g.gilbert
+ * biology dept., indiana university, bloomington, in 47405
+ * e-mail: gilbertd at bio.indiana.edu
+ *
+ * This program may be freely copied and used by anyone.
+ * Developers are encourged to incorporate parts in their
+ * programs, rather than devise their own private sequence
+ * format.
+
+
+From gilbertd at bio.indiana.edu Tue Oct 30 08:18:23 2001
+Date: Mon, 29 Oct 2001 13:07:26 -0500 (EST)
+From: Don Gilbert <gilbertd at bio.indiana.edu>
+To: TilleA at rki.de
+Subject: Re: [ITA] Intent To Adopt Readseq
+
+Andreas,
+
+Please feel free to use readseq code as you like; I've placed
+it in the public domain.
+
+- Don
+
+The Debian packaging is (C) 2001-2007 Andreas Tille <tille at debian.org>
+and is licensed under the GPL which is available at
+`/usr/share/common-licenses/GPL'.
Added: trunk/packages/readseq/tags/1-7/debian/dirs
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/dirs (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/dirs 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,4 @@
+usr/bin
+usr/share/doc/readseq
+usr/share/doc/readseq/tests
+usr/share/man/man1
Added: trunk/packages/readseq/tags/1-7/debian/docs
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/docs (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/docs 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,4 @@
+Formats
+Readme
+Stdfiles
+Readseq.help
Added: trunk/packages/readseq/tags/1-7/debian/get-orig-source
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/get-orig-source (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/get-orig-source 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,38 @@
+#!/bin/sh
+prog=readseq
+version=1
+dir="$prog"-"$version"
+tardir=`pwd`/../tarballs/"$dir"
+# url="ftp://ftp.bio.indiana.edu/molbio/readseq/version1/src"
+url="http://iubio.bio.indiana.edu/soft/molbio/readseq/version1/src/"
+
+mkdir -p "$tardir"
+cd "$tardir"
+
+files="add.gdemenu
+ alphabet.std
+ Formats
+ macinit.c
+ macinit.r
+ Make.com
+ Makefile
+ Make.ncbi
+ multi.std
+ nucleic.std
+ Readme
+ readseq.c
+ Readseq.help
+ readseqSIOW.make
+ Stdfiles
+ upper.std
+ ureadasn.c
+ ureadseq.c
+ ureadseq.h"
+
+for file in $files ; do
+ wget "$url/$file"
+done
+
+cd ..
+GZIP=-9 tar -czf "$prog"_"$version".orig.tar.gz "$dir"
+rm -rf "$dir"
Added: trunk/packages/readseq/tags/1-7/debian/install
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/install (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/install 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,3 @@
+readseq usr/bin
+Makefile usr/share/doc/readseq/tests
+*.std usr/share/doc/readseq/tests
Added: trunk/packages/readseq/tags/1-7/debian/links
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/links (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/links 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1 @@
+usr/share/doc/readseq/Readseq.help usr/share/readseq/readseq_help
Added: trunk/packages/readseq/tags/1-7/debian/manpages
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/manpages (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/manpages 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1 @@
+debian/readseq.1
Added: trunk/packages/readseq/tags/1-7/debian/patches/00list
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/patches/00list (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/patches/00list 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,3 @@
+20-Formats.dpatch
+20-Makefile.dpatch
+30-arb-code-patches.dpatch
Added: trunk/packages/readseq/tags/1-7/debian/patches/20-Formats.dpatch
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/patches/20-Formats.dpatch (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/patches/20-Formats.dpatch 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,30 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_Format.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Add new Formats for ARB
+
+ at DPATCH@
+
+--- readseq-1/Formats.orig 1992-12-30 01:00:00.000000000 +0100
++++ readseq-1/Formats 2007-11-14 12:14:36.000000000 +0100
+@@ -978,3 +978,19 @@
+ hist Seq-hist OPTIONAL } -- sequence history
+
+ ------------------------------------------------
++
++||||||||||| LinAll sequence file format
++----------------------------------------
++
++1234 seq1-id (1234 is sequence length, right justified)
++abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzab
++cdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyz
++(80 characters per line, one sequence per file)
++
++||||||||||| Vienna RNA sequence file format
++--------------------------------------------
++
++> seq1-id
++jsdhkasjlhsdlkjcbsd ... (one single line)
++> seq2-id
++odjgoirhggonavdskgj ... (one single line)
Added: trunk/packages/readseq/tags/1-7/debian/patches/20-Makefile.dpatch
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/patches/20-Makefile.dpatch (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/patches/20-Makefile.dpatch 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,147 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_Makefile.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Enhanced Makefile
+
+ at DPATCH@
+
+--- readseq-1/Makefile.orig 1992-12-30 01:00:00.000000000 +0100
++++ readseq-1/Makefile 2007-11-17 21:31:39.000000000 +0100
+@@ -10,7 +10,7 @@
+ #CC=cc # SGI Irix
+ #CC=vcc # some DEC Ultrix
+
+-CFLAGS=
++CFLAGS= -g -O2
+ #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
+ # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+
+@@ -29,63 +29,66 @@
+ LIB2=-lncbiobj
+ LIB3=-lncbicdr
+ LIB4=-lvibrant
+-INCPATH=$(NCBI)/include
+-LIBPATH=$(NCBI)/lib
++LIB5=-lncbimmdb -lncbiid1 -lnetcli
++LIB6=-lncbiacc
++LIB7=-lncbitool
++INCPATH=/usr/include/ncbi
++#LIBPATH=$(NCBI)/lib
+ NCFLAGS=$(CFLAGS) -DNCBI -I$(INCPATH)
+-NLDFLAGS=-I$(INCPATH) -L$(LIBPATH)
+-NLIBS=$(LIB1) $(LIB2) $(OTHERLIBS)
++NLDFLAGS=-I$(INCPATH)
++NLIBS=$(LIB1) $(LIB2) $(LIB3) $(LIB6) $(LIB7) $(LIB5) $(OTHERLIBS)
++ARBFLAGS=-DARB
+
++all: build
+
+-all: build test
+-
+-build: $(SOURCES)
+- @echo "Compiling readseq..."
+- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
++#build: $(SOURCES)
++# @echo "Compiling readseq..."
++# $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
+
+ # if using NCBI, uncomment these lines in place of build: above
+-#build: $(SOURCES)
+-# @echo "Compiling readseq with NCBI toolkit support...";
+-# $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
++build: $(SOURCES)
++ @echo "Compiling readseq with NCBI toolkit support and ARB patches";
++ $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
+
+-test: $(SOURCES) readseq
++test:
+ @echo ""
+ @echo "Test for general read/write of all chars:"
+- ./readseq -p alphabet.std -otest.alpha
++ readseq -p alphabet.std -otest.alpha
+ -diff test.alpha alphabet.std
+
+ @echo ""
+ @echo "Test for valid format conversions:"
+- ./readseq -v -p -f=ig nucleic.std -otest.ig
+- ./readseq -v -p -f=gb test.ig -otest.gb
+- ./readseq -v -p -f=nbrf test.gb -otest.nbrf
+- ./readseq -v -p -f=embl test.nbrf -otest.embl
+- ./readseq -v -p -f=gcg test.embl -otest.gcg
+- ./readseq -v -p -f=strider test.gcg -otest.strider
+- ./readseq -v -p -f=fitch test.strider -otest.fitch
+- ./readseq -v -p -f=fasta test.fitch -otest.fasta
+- ./readseq -v -p -f=pir test.fasta -otest.pir
+- ./readseq -v -p -f=ig test.pir -otest.ig-b
++ readseq -v -p -f=ig nucleic.std -otest.ig
++ readseq -v -p -f=gb test.ig -otest.gb
++ readseq -v -p -f=nbrf test.gb -otest.nbrf
++ readseq -v -p -f=embl test.nbrf -otest.embl
++ readseq -v -p -f=gcg test.embl -otest.gcg
++ readseq -v -p -f=strider test.gcg -otest.strider
++ readseq -v -p -f=fitch test.strider -otest.fitch
++ readseq -v -p -f=fasta test.fitch -otest.fasta
++ readseq -v -p -f=pir test.fasta -otest.pir
++ readseq -v -p -f=ig test.pir -otest.ig-b
+ -diff test.ig test.ig-b
+
+ @echo ""
+ @echo "Test for multiple-sequence format conversions:"
+- ./readseq -p -f=ig multi.std -otest.m-ig
+- ./readseq -p -f=gb test.m-ig -otest.m-gb
+- ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
+- ./readseq -p -f=embl test.m-nbrf -otest.m-embl
+- ./readseq -p -f=fasta test.m-embl -otest.m-fasta
+- ./readseq -p -f=pir test.m-fasta -otest.m-pir
+- ./readseq -p -f=msf test.m-pir -otest.m-msf
+- ./readseq -p -f=paup test.m-msf -otest.m-paup
+- ./readseq -p -f=ig test.m-paup -otest.m-ig-b
++ readseq -p -f=ig multi.std -otest.m-ig
++ readseq -p -f=gb test.m-ig -otest.m-gb
++ readseq -p -f=nbrf test.m-gb -otest.m-nbrf
++ readseq -p -f=embl test.m-nbrf -otest.m-embl
++ readseq -p -f=fasta test.m-embl -otest.m-fasta
++ readseq -p -f=pir test.m-fasta -otest.m-pir
++ readseq -p -f=msf test.m-pir -otest.m-msf
++ readseq -p -f=paup test.m-msf -otest.m-paup
++ readseq -p -f=ig test.m-paup -otest.m-ig-b
+ -diff test.m-ig test.m-ig-b
+ #
+ # if using NCBI, uncomment these lines
+-# @echo ""
+-# @echo "Test of NCBI ASN.1 conversions:"
+-# ./readseq -p -f=asn test.m-ig -otest.m-asn
+-# ./readseq -p -f=ig test.m-asn -otest.m-ig-c
+-# -diff test.m-ig test.m-ig-c
++ @echo ""
++ @echo "Test of NCBI ASN.1 conversions:"
++ readseq -p -f=asn test.m-ig -otest.m-asn
++ readseq -p -f=ig test.m-asn -otest.m-ig-c
++ -diff test.m-ig test.m-ig-c
+ #
+ @echo ""
+ @echo "Expect differences in the header lines due to"
+@@ -97,8 +100,13 @@
+ @echo " make clean"
+
+
++install:
++ install readseq $(DESTDIR)/usr/bin
++ install *.std $(DESTDIR)/usr/share/doc/readseq/tests
++ install Makefile $(DESTDIR)/usr/share/doc/readseq/tests
++
+ clean:
+- rm -f *.o core test.*
++ rm -f *.o core test.* readseq
+
+ shar:
+ @echo "shell archiving files..."
+@@ -109,3 +117,7 @@
+ shar -v readseqd > readseq.shar
+ rm -rf readseqd
+
++
++
++
++
Added: trunk/packages/readseq/tags/1-7/debian/patches/30-arb-code-patches.dpatch
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/patches/30-arb-code-patches.dpatch (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/patches/30-arb-code-patches.dpatch 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,558 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 30_arb_changes.dpatch by <tille at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Several patches for arb that enable new formats and contain other
+## DP: needed fixes
+
+ at DPATCH@
+
+diff -ubrN readseq-1.orig/readseq.c readseq-1/readseq.c
+--- readseq-1.orig/readseq.c 1993-02-01 01:00:00.000000000 +0100
++++ readseq-1/readseq.c 2007-11-14 12:14:36.000000000 +0100
+@@ -93,6 +93,10 @@
+ = fix bug for possible memory overrun when truncating seqs for
+ Phylip or Paup formats (thanks Anthony Persechini)
+
++ 13 Sep 96 GSt + RL (Steger at biophys.uni-duesseldorf.de)
++ * real time in MSF format (Main); #include <time.h>
++ + added VIE multi sequence file format
++ + added LinAll sequence file format
+ */
+
+
+@@ -169,8 +173,11 @@
+
+
+ #include <stdio.h>
++#include <stdlib.h> /* MSch */
+ #include <string.h>
+ #include <ctype.h>
++#include <time.h> /* RL */
++#include <ncbi.h>
+
+ #include "ureadseq.h"
+
+@@ -199,9 +206,11 @@
+ "16. ASN.1",
+ "17. PAUP/NEXUS",
+ "18. Pretty (out-only)",
++ "19. LinAll",
++ "20. Vienna",
+ "" };
+
+-#define kFormCount 30
++#define kFormCount 32
+ #define kMaxFormName 15
+
+ const struct formatTable {
+@@ -238,6 +247,8 @@
+ {"paup", kPAUP},
+ {"nexus", kPAUP},
+ {"pretty", kPretty},
++ {"linall", kLINALL},
++ {"vie", kVIE},
+ };
+
+ const char *kASN1headline = "Bioseq-set ::= {\nseq-set {\n";
+@@ -415,7 +426,7 @@
+ fprintf( stderr, " %-20s %-20s\n",
+ formats[i], formats[midi+i]);
+ fprintf(stderr,"\nChoose an output format (name or #): \n");
+- gets(sform);
++ fgets(sform, 127, stdin);
+ outform = parseformat(sform);
+ if (outform == kNoformat) outform = kPearson;
+ return outform;
+@@ -708,8 +719,12 @@
+ #else
+ #define Exit(a) exit(a)
+
++#ifdef NCBI
++Nlm_Int2 Nlm_Main(void)
++#else
+ main( int argc, char *argv[])
+ #endif
++#endif
+ {
+ boolean closein = false;
+ short ifile, nseq, atseq, format, err = 0, seqtype = kDNA,
+@@ -721,6 +736,14 @@
+ char stempstore[256], *stemp = stempstore;
+ FILE *ftmp, *fin, *fout;
+ long outindexmax= 0, noutindex= 0, *outindex = NULL;
++time_t time_val; /* GSt + RL */
++size_t size_timestr = 50;/* GSt + RL */
++char timestr[50]; /* GSt + RL */
++
++#ifdef NCBI
++int argc;
++char** argv;
++#endif
+
+ #define exit_main(err) { \
+ if (closeout) fclose(fout); \
+@@ -739,6 +762,10 @@
+
+
+ resetGlobals();
++#if NCBI
++ argc = Nlm_GetArgc();
++ argv = Nlm_GetArgv();
++#endif
+ foo = stdout;
+ progname = argv[0];
+ *oname = 0;
+@@ -764,7 +791,7 @@
+
+ quietly = (dopipe || (gotinputfile && (listonly || whichSeq != 0)));
+
+- if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title);
++ //if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, "%s\n", title);
+ ifile = 1;
+
+ /* UI: Choose output */
+@@ -1003,6 +1030,13 @@
+ else if (dolower)
+ for (i = 0; i<seqlen; i++) seq[i] = to_lower(seq[i]);
+
++/* This is an undocumented patch from ARB which hopefully does no harm A. Tille */
++#ifdef ARB
++ if (outform==kPhylip){
++ for (i = 0; i<seqlen; i++) if (seq[i] == '.') seq[i] = '?';
++ }
++#endif
++
+ if (doreverse) {
+ long j, k;
+ char ctemp;
+@@ -1014,8 +1048,15 @@
+ }
+
+ if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq != NULL) {
++#ifdef ARB
++ for (i=0; i<seqlen; i++){
++ if (seq[i] == gPretty.matchchar) seq[i] = 'o';
++ if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
++ }
++#else
+ for (i=0; i<seqlen; i++)
+ if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
++#endif
+ }
+
+
+@@ -1070,9 +1111,15 @@
+ }
+
+ if (outform == kMSF) {
++ time(&time_val); /* GSt + RL */
++ strftime(timestr, size_timestr, "%B %e, %Y %H:%M", localtime(&time_val)); /* GSt + RL */
+ if (*oname) cp= oname; else cp= inputfile;
++ fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */
++ cp, seqlen, timestr, checkall);
++/*
+ fprintf(foo,"\n %s MSF: %d Type: N January 01, 1776 12:00 Check: %d ..\n\n",
+ cp, seqlen, checkall);
++*/
+ }
+
+ if (outform == kPAUP) {
+diff -ubrN readseq-1.orig/ureadseq.c readseq-1/ureadseq.c
+--- readseq-1.orig/ureadseq.c 1998-09-03 02:00:00.000000000 +0200
++++ readseq-1/ureadseq.c 2007-11-14 12:14:36.000000000 +0100
+@@ -18,11 +18,14 @@
+
+
+ #include <stdio.h>
++#define __NO_CTYPE
++#include <stdlib.h> /* MSch */
+ #include <ctype.h>
+ #include <string.h>
+
+ #define UREADSEQ_G
+ #include "ureadseq.h"
++/* changed according to original which is the same with the changed header (at) */
+
+ #pragma segment ureadseq
+
+@@ -66,7 +69,7 @@
+ # define Local static /* local functions */
+ #endif
+
+-#define kStartLength 500
++#define kStartLength 500000 /* 20Apr93 temp. bug fix */
+
+ const char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
+ const char *primenuc = "ACGTU";
+@@ -101,6 +104,9 @@
+ long linestart;
+ char s[256], *sp;
+
++#ifdef ARB
++ int (*isseqcharfirst8)(); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/
++#endif
+ int (*isseqchar)();
+ /* int (*isseqchar)(int c); << sgi cc hates (int c) */
+ };
+@@ -150,9 +156,23 @@
+ Local void addseq(char *s, struct ReadSeqVars *V)
+ {
+ char *ptr;
++#ifdef ARB
++ /* Patch by o. strunk (ARB) to allow numbers in genbank sequences */
++ int count = 0;
++#endif
+
++#ifdef ARB
++ if (V->addit){
++ for (;*s != 0;s++,count++) {
++ if (count < 9 && V->isseqcharfirst8) {
++ if (!(V->isseqcharfirst8) (*s)) continue;
++ }else{
++ if (!(V->isseqchar) (*s)) continue;
++ }
++#else
+ if (V->addit) while (*s != 0) {
+ if ((V->isseqchar)(*s)) {
++#endif
+ if (V->seqlen >= V->maxseq) {
+ V->maxseq += kStartLength;
+ ptr = (char*) realloc(V->seq, V->maxseq+1);
+@@ -164,7 +184,9 @@
+ }
+ V->seq[(V->seqlen)++] = *s;
+ }
++#ifndef ARB
+ s++;
++#endif
+ }
+ }
+
+@@ -324,6 +346,11 @@
+ Local void readGenBank(struct ReadSeqVars *V)
+ { /*GenBank -- many seqs/file */
+
++#ifdef ARB
++ /* Patch by o. strunk (ARB) to allow numbers in genbank sequences */
++ V->isseqchar = isSeqNumChar;
++ V->isseqcharfirst8 = isSeqChar;
++#endif
+ while (!V->allDone) {
+ strcpy(V->seqid, (V->s)+12);
+ while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
+@@ -337,9 +364,44 @@
+ }
+ if (feof(V->f)) V->allDone = true;
+ }
++#ifdef ARB
++ V->isseqchar = isSeqChar;
++ V->isseqcharfirst8 = 0;
++#endif
+ }
+
+
++Local boolean endVIE( boolean *addend, boolean *ungetend, struct ReadSeqVars *V) /* GSt + RL */
++{
++ if (*V->s == '>') { /* start of next seq */
++ *addend = false;
++ *ungetend= true;
++ return(true);
++ }
++ else
++ return(false);
++}
++
++
++Local void readVIE(struct ReadSeqVars *V) /* GSt + RL */
++{
++ while (!V->allDone) {
++ strcpy(V->seqid, (V->s)+2);
++ readLoop(0, false, endVIE, V);
++ if (feof(V->f)) V->allDone = true;
++ }
++/*
++ printf("readVIE: V->nseq = %d\n",V->nseq);
++ printf("readVIE: V->choice = %d\n",V->choice);
++ printf("readVIE: V->addit = %d\n",V->addit);
++ printf("readVIE: V->seqlen = %ld\n",V->seqlen);
++ printf("readVIE: V->seqid = %s\n",V->seqid);
++ printf("readVIE: V->s = %s\n",V->s);
++ printf("readVIE: V->seqid = %s\n",V->seqid);
++ printf("readVIE: V->s = %s\n<<<last action\n",V->s);
++*/
++}
++
+ Local boolean endNBRF( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
+ {
+ char *a;
+@@ -449,6 +511,46 @@
+ }
+ }
+
++Local void readLINALL(struct ReadSeqVars *V) /* GSt */
++{
++ /* SeqLen[I4] Label[Char*60]
++ Seq[Char*70 per line]
++ */
++ int laenge;
++ int i;
++
++ V->nseq++; /* but there is only a single sequence ? */
++ // dprintf(("readLINALL: V->nseq = %d\n",V->nseq));
++ /* V->addit = (V->choice > 0); */ /* what's that for ???? */
++ // dprintf(("readLINALL: V->choice = %d\n",V->choice));
++ // dprintf(("readLINALL: V->addit = %d\n",V->addit));
++ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
++ // dprintf(("readLINALL: V->s = %s\n",V->s));
++ /* if (V->addit) V->seqlen = 0; */ /* what's that for ???? */
++ sscanf(V->s, "%4d", &laenge); /* seqlen is in 1st 4 chars of 1st line */
++ // dprintf(("readLINALL: laenge = %d\n",laenge));
++ // fflush(stdout);
++ strcpy(V->seqid, (V->s)+5); /* label starts after 5th char of 1st line */
++ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
++ // fflush(stdout);
++ do {
++ V->done = feof(V->f);
++ getline(V);
++ if (!V->done) addseq((V->s), V);
++ } while ( !(V->done) && (V->seqlen)<=laenge );
++ V->seqlen = laenge; /* only laenge chars are relevant for V->seq */
++ // dprintf(("readLINALL: V->s = %s\n",V->s));
++ /* if (V->choice == kListSequences) addinfo(V->seqid, V); */ /* what's that for ???? */
++ // dprintf(("readLINALL: V->seqid = %s\n",V->seqid));
++ // dprintf(("readLINALL: V->seqlen = %ld\n",V->seqlen));
++ // dprintf(("readLINALL: V->seq =>"));
++ // for ( i=0; i<V->seqlen; i++ ) dprintf(("%c",V->seq[i]));
++ // dprintf(("<\n"));
++ // dprintf(("readLINALL: V->s = %s\n<<<last action\n",V->s));
++ V->allDone = true;
++
++}
++
+
+
+ Local boolean endFitch( boolean *addend, boolean *ungetend, struct ReadSeqVars *V)
+@@ -956,6 +1058,8 @@
+ case kZuker : readZuker(V); break;
+ case kOlsen : readOlsen(V); break;
+ case kMSF : readMSF(V); break;
++ case kLINALL: readLINALL(V); break;
++ case kVIE : readVIE(V); break;
+
+ case kPAUP : {
+ boolean done= false;
+@@ -1049,6 +1153,9 @@
+ V.err = 0;
+ V.nseq = 0;
+ V.isseqchar = isSeqChar;
++#ifdef ARB
++ V.isseqcharfirst8 = 0;
++#endif
+ if (V.choice == kListSequences) ; /* leave as is */
+ else if (V.choice <= 0) V.choice = 1; /* default ?? */
+ V.addit = (V.choice > 0);
+@@ -1092,6 +1199,9 @@
+ V.err = 0;
+ V.nseq = 0;
+ V.isseqchar = isSeqChar;
++#ifdef ARB
++ V.isseqcharfirst8 = 0;
++#endif
+ if (V.choice == kListSequences) ; /* leave as is */
+ else if (V.choice <= 0) V.choice = 1; /* default ?? */
+ V.addit = (V.choice > 0);
+@@ -1152,6 +1262,7 @@
+ boolean foundDNA= false, foundIG= false, foundStrider= false,
+ foundGB= false, foundPIR= false, foundEMBL= false, foundNBRF= false,
+ foundPearson= false, foundFitch= false, foundPhylip= false, foundZuker= false,
++ foundLINALL= false, foundVIE= false,
+ gotolsen= false, gotpaup = false, gotasn1 = false, gotuw= false, gotMSF= false,
+ isfitch= false, isphylip= false, done= false;
+ short format= kUnknown;
+@@ -1159,6 +1270,8 @@
+ char sp[256];
+ long linestart=0;
+ int maxlines2check=500;
++ int linallSeqLen;
++ char linallHeader[60];
+
+ #define ReadOneLine(sp) \
+ { done |= (feof(fseq)); \
+@@ -1225,8 +1338,9 @@
+ foundPIR= true;
+
+ else if (*sp == '>') {
+- if (sp[3] == ';') foundNBRF= true;
+- else foundPearson= true;
++ if (sp[3] == ';') foundNBRF= true; /* {foundNBRF= true; printf("foundNBRF\n");} */
++ else if (sp[1] == ' ') foundVIE= true; /* {foundVIE= true; printf("foundVIE\n");} */
++ else foundPearson= true; /* {foundPearson= true; printf("foundPearson\n");} */
+ }
+
+ else if (strstr(sp,"ID ") == sp)
+@@ -1239,9 +1353,16 @@
+
+ else {
+ if (nlines - *skiplines == 1) {
+- int ispp= 0, ilen= 0;
+- sscanf( sp, "%d%d", &ispp, &ilen);
+- if (ispp > 0 && ilen > 0) isphylip= true;
++ int ispp= 0, ilen= 0, icnt=0;
++ char junkstr[120];
++ memset(junkstr,0,120);
++ icnt= sscanf( sp, "%d%d%c", &ispp, &ilen, junkstr);
++ if (icnt == 2 && ispp > 0 && ilen > 0) {
++ isphylip= true;
++ }
++ else if (icnt==3 && ispp > 0 && ilen > 0 && *junkstr == ' ') {
++ isphylip= true;
++ }
+ }
+ else if (isphylip && nlines - *skiplines == 2) {
+ int tseq;
+@@ -1257,6 +1378,65 @@
+ }
+ if (isfitch & (splen > 20)) foundFitch= true;
+
++#ifdef DEBUG_LINALL
++ dprintf(("Check for LINALL\n"));
++ dprintf(("\tstrtol(sp,NULL,0) = %d\n",strtol(sp,NULL,0)));
++ dprintf(("\tnlines = %d\n",nlines));
++ dprintf(("\tisphylip = %d\n",isphylip));
++ dprintf(("\tfoundPhylip = %d\n",foundPhylip));
++ dprintf(("\tisfitch = %d\n",isfitch));
++ dprintf(("\tfoundFitch = %d\n",foundFitch));
++#endif
++
++ /*
++ * This format detection was highly bogus ...
++ * Lesson 1: always initialize variables (in case the conversion fails...)
++ * Lesson 2: strings are passed to sscanf _without_ & (string variable is a pointer already)
++ * Lesson 3: forget to check return codes from syscalls: you lose.
++ */
++
++ if (nlines==1) {
++ int rv;
++#ifdef DEBUG_LINALL
++ int i, sane=1;
++ char *spp;
++
++ /*
++ * possible sanity check, for losers (see above)
++ */
++ for (spp=sp, i=0; i<4; i++, spp++)
++ if (!(isspace(*spp) || isdigit(*spp))) {
++ dprintf(("bogus linall format header: %s\n", sp));
++ sane=0;
++ break;
++ }
++#endif
++
++ linallSeqLen = 0;
++ *linallHeader = '\0';
++ rv = sscanf( sp, "%d %s", &linallSeqLen, linallHeader);
++
++#ifdef DEBUG_LINALL
++ dprintf(("\tsscanf rval = %d\n",rv));
++ dprintf(("\tlinallSeqLen = %d\n",linallSeqLen));
++ dprintf(("\tlinallHeader = %s\n",linallHeader));
++ dprintf(("\tlinallHeader = %d\n",strlen(linallHeader)));
++#endif
++
++ if (rv > 0 && linallSeqLen>0 &&
++ strlen(linallHeader)>0 &&
++ !(isphylip || foundPhylip)) {
++ /* !(isphylip || foundPhylip || isfitch || foundFitch)) { */
++ foundLINALL= true; /* The 1st line contains the seqlength (4 digits), a blank, and a label (up to 60 char). */
++ /* The following lines contain the sequence with 70 chars per line. */
++#ifdef DEBUG_LINALL
++ dprintf(("debug: foundLINALL: %ld<\n",strtol(sp,NULL,0)));
++ dprintf(("debug: sp:%s<\n\n",sp));
++#endif
++ }
++
++ }
++
+ /* kRNA && kDNA are fairly certain...*/
+ switch (getseqtype( sp, splen)) {
+ case kOtherSeq: otherlines++; break;
+@@ -1302,6 +1482,16 @@
+ done= true;
+ }
+
++ else if (foundLINALL) {
++ format= kLINALL;
++ done= true;
++ }
++
++ else if (foundVIE) {
++ format= kVIE;
++ done= true;
++ }
++
+ else if ((dnalines > 1) || done || (nlines > maxlines2check)) {
+ /* decide on most likely format */
+ /* multichar idents: */
+@@ -1785,6 +1975,27 @@
+ linesout += 2;
+ break;
+
++ case kLINALL: /* GSt */
++ fprintf(outf,"%4d %-60s\n",seqlen,seqname);
++ strcpy(endstr,"\n");
++ linesout++;
++ width = 70;
++ tab = 0;
++ spacer = 0;
++ nameleft = false;
++ nameright = false;
++ numleft = false;
++ numright = false;
++ break;
++
++ case kVIE: /* GSt + RL */
++ if ( strchr(seqname,' ') != NULL ) seqname[strchr(seqname,' ')-seqname] = '\0'; /* no blanks in label line */
++ fprintf(outf,"> %-s\n", seqname);
++ linesout++;
++ fprintf(outf,"%s\n\n",seq); /* complete sequence in one line; additional blank line before next sequence */
++ return linesout; /* thus, do nothing else */
++ break;
++
+ default :
+ case kZuker: /* don't attempt Zuker's ftn format */
+ case kPearson:
+@@ -1841,7 +2052,8 @@
+ s[l++] = ' ';
+ if (!baseonlynum) ibase++;
+ else if (0==strchr(nocountsymbols,seq[i])) ibase++;
+- s[l++] = seq[i++];
++ if (outform==kLINALL) { s[l++] = to_upper(seq[i]); i++; } /* GSt */
++ else s[l++] = seq[i++] ;
+ }
+
+ if (l1 == width || i == seqlen) {
+diff -ubrN readseq-1.orig/ureadseq.h readseq-1/ureadseq.h
+--- readseq-1.orig/ureadseq.h 1992-12-30 01:00:00.000000000 +0100
++++ readseq-1/ureadseq.h 2007-11-14 12:14:36.000000000 +0100
+@@ -66,8 +66,10 @@
+ #define kASN1 16
+ #define kPAUP 17
+ #define kPretty 18
++#define kLINALL 19
++#define kVIE 20
+
+-#define kMaxFormat 18
++#define kMaxFormat 20
+ #define kMinFormat 1
+ #define kNoformat -1 /* format not tested */
+ #define kUnknown 0 /* format not determinable */
+@@ -100,7 +102,7 @@
+ p.noleaves= p.domatch= p.degap= false;\
+ p.matchchar='.';\
+ p.gapchar='-';\
+- p.namewidth=8;\
++ p.namewidth=10;\
+ p.numwidth=5;\
+ p.interline=1;\
+ p.spacer=10;\
Added: trunk/packages/readseq/tags/1-7/debian/readseq.1
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/readseq.1 (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/readseq.1 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,212 @@
+.TH READSEQ 1
+.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
+.\" other parms are allowed: see man(7), man(1)
+
+.SH NAME
+readseq \- Reads and writes nucleic/protein sequences in various formats
+
+.SH SYNOPSIS
+.B readseq
+.I "[-options] in.seq > out.seq"
+
+.SH "DESCRIPTION"
+This manual page documents briefly the
+.BR readseq
+command.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in text form, see below.
+.PP
+.B readseq
+reads and writes biosequences (nucleic/protein) in various formats.
+Data files may have multiple sequences.
+.B readseq
+is particularly useful as it automatically detects many
+sequence formats, and interconverts among them.
+
+.SH FORMATS
+.TP
+Formats which readseq currently understands:
+
+.PD 0
+.TP
+ * IG/Stanford, used by Intelligenetics and others
+.TP
+ * GenBank/GB, genbank flatfile format
+.TP
+ * NBRF format
+.TP
+ * EMBL, EMBL flatfile format
+.TP
+ * GCG, single sequence format of GCG software
+.TP
+ * DNAStrider, for common Mac program
+.TP
+ * Fitch format, limited use
+.TP
+ * Pearson/Fasta, a common format used by Fasta programs and others
+.TP
+ * Zuker format, limited use. Input only.
+.TP
+ * Olsen, format printed by Olsen VMS sequence editor. Input only.
+.TP
+ * Phylip3.2, sequential format for Phylip programs
+.TP
+ * Phylip, interleaved format for Phylip programs (v3.3, v3.4)
+.TP
+ * Plain/Raw, sequence data only (no name, document, numbering)
+.TP
+ + MSF multi sequence format used by GCG software
+.TP
+ + PAUP's multiple sequence (NEXUS) format
+.TP
+ + PIR/CODATA format used by PIR
+.TP
+ + ASN.1 format used by NCBI
+.TP
+ + Pretty print with various options for nice looking output. Output only.
+.TP
+ + LinAll format, limited use (LinAll and ConStruct programs)
+.TP
+ + Vienna format used by ViennaRNA programs
+.PD 1
+
+.TP
+See the included "Formats" file for detail on file formats.
+
+.SH OPTIONS
+
+.PD 0
+
+.TP
+.B \-help
+Show summary of options.
+
+.TP
+.B \-a[ll]
+Select All sequences
+
+.TP
+.B \-c[aselower]
+Change to lower case
+
+.TP
+.B \-C[ASEUPPER]
+Change to UPPER CASE
+
+.TP
+.B \-degap[=-]
+Remove gap symbols
+
+.TP
+.B \-i[tem=2,3,4]
+Select Item number(s) from several
+
+.TP
+.B \-l[ist]
+List sequences only
+
+.TP
+.B \-o[utput=]out.seq
+Redirect Output
+
+.TP
+.B \-p[ipe]
+Pipe (command line, <stdin, >stdout)
+
+.TP
+.B \-r[everse]
+Change to Reverse-complement
+
+.TP
+.B \-v[erbose]
+Verbose progress
+
+.TP
+.B \-f[ormat=]# Format number for output, or
+ -f[ormat=]Name Format name for output:
+ 1. IG/Stanford 11. Phylip3.2
+ 2. GenBank/GB 12. Phylip
+ 3. NBRF 13. Plain/Raw
+ 4. EMBL 14. PIR/CODATA
+ 5. GCG 15. MSF
+ 6. DNAStrider 16. ASN.1
+ 7. Fitch 17. PAUP/NEXUS
+ 8. Pearson/Fasta 18. Pretty (out-only)
+ 9. Zuker (in-only) 19. LinAll
+ 10. Olsen (in-only) 20. Vienna
+
+Pretty format options:
+
+.TP
+.B \-wid[th]=#
+Sequence line width
+
+.TP
+.B \-tab=#
+Left indent
+
+.TP
+.B \-col[space]=#
+Column space within sequence line on output
+
+.TP
+.B \-gap[count]
+Count gap chars in sequence numbers
+
+.TP
+.B \-nameleft, -nameright[=#]
+Name on left/right side [=max width]
+
+.TP
+.B \-nametop
+Name at top/bottom
+
+.TP
+.B \-numleft, -numright
+Seq index on left/right side
+
+.TP
+.B \-numtop, -numbot
+Index on top/bottom
+
+.TP
+.B \-match[=.]
+Use match base for 2..n species
+
+.TP
+.B \-inter[line=#]
+Blank line(s) between sequence blocks
+
+.PD 1
+
+.SH EXAMPLES
+.PD 0
+.TP
+ readseq
+ -- for interactive use
+
+.TP
+ readseq my.1st.seq my.2nd.seq -all -format=genbank -output=my.gb
+ -- convert all of two input files to one genbank format output file
+
+.TP
+ readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match
+ -- output to standard output a file in a pretty format
+
+.TP
+ readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev
+ -- select 4 items from input, degap, reverse, and uppercase them
+
+.TP
+ cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
+ -- pipe a bunch of data thru readseq, converting all to asn
+.PD 1
+
+.SH "SEE ALSO"
+The programs are documented fully in text form. See the files in
+.I /usr/share/doc/readseq
+
+.SH AUTHOR
+This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/readseq/tags/1-7/debian/rules
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/rules (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/rules 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+# debian/rules for readseq using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+include /usr/share/cdbs/1/rules/dpatch.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_COMPRESS_EXCLUDE := help
+
+clean::
+ rm -f readseq
+
+get-orig-source:
+ . debian/get-orig-source
Property changes on: trunk/packages/readseq/tags/1-7/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/readseq/tags/1-7/debian/translate.patch
===================================================================
--- trunk/packages/readseq/tags/1-7/debian/translate.patch (rev 0)
+++ trunk/packages/readseq/tags/1-7/debian/translate.patch 2007-11-17 23:38:59 UTC (rev 822)
@@ -0,0 +1,126 @@
+
+##
+## Patch to readseq to allow input sequence symbols to be translated
+## to different output sequence symbols. This has not been tested,
+## as of 22 Dec 94. D.Gilbert
+##
+
+diff -bwrc old/Makefile rtrans/Makefile
+*** old/Makefile Thu Dec 22 08:58:41 1994
+--- rtrans/Makefile Thu Dec 22 08:58:31 1994
+***************
+*** 13,21 ****
+ CFLAGS=
+ #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
+ # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+
+ SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
+! DOCS= Readme Readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
+
+
+ # NCBI toolkit support for ASN.1 reader
+--- 13,23 ----
+ CFLAGS=
+ #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
+ # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
++ #CFLAGS= -DTRANSLATE # if you want option to translate certain input sequence symbols
++ # to a different output sequence symbols
+
+ SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
+! DOCS= Readme readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
+
+
+ # NCBI toolkit support for ASN.1 reader
+
+
+diff -bwrc old/readseq.c rtrans/readseq.c
+*** old/readseq.c Thu Dec 22 08:58:41 1994
+--- rtrans/readseq.c Thu Dec 22 09:01:05 1994
+***************
+*** 338,343 ****
+--- 338,347 ----
+ fprintf(stderr, " -o[utput=]out.seq redirect Output\n");
+ fprintf(stderr, " -p[ipe] Pipe (command line, <stdin, >stdout)\n");
+ fprintf(stderr, " -r[everse] change to Reverse-complement\n");
++ #ifdef TRANSLATE
++ fprintf(stderr, " -t[ranslate=]io translate input symbol [i] to output symbol [o] \n");
++ fprintf(stderr, " use several -tio to translate several symbols \n");
++ #endif
+ fprintf(stderr, " -v[erbose] Verbose progress\n");
+ fprintf(stderr, " -f[ormat=]# Format number for output, or\n");
+ fprintf(stderr, " -f[ormat=]Name Format name for output:\n");
+***************
+*** 474,479 ****
+--- 478,486 ----
+ foo = NULL;
+
+ gPrettyInit(gPretty);
++ #ifdef TRANSLATE
++ gTranslateInit();
++ #endif
+ }
+
+
+***************
+*** 590,595 ****
+--- 597,615 ----
+ outform = parseformat( sparam);
+ return kOptOkay;
+ }
++
++ #ifdef TRANSLATE
++ if (checkopt( false, sopt, "-translate", 3)) {/* -translate=io */
++ if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }
++ if (*sparam) gTranslate[*sparam]= sparam[1];
++ return kOptOkay;
++ }
++ if (checkopt( false, sopt, "-t", 2)) { /* shorthand is -tio */
++ if (*sparam==0) sparam= sopt+2;
++ if (*sparam) gTranslate[*sparam]= sparam[1];
++ return kOptOkay;
++ }
++ #endif
+
+ if (checkopt( false, sopt, "-output", 3)) {/* -output=myseq */
+ if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }
+
+
+diff -bwrc old/ureadseq.c rtrans/ureadseq.c
+*** old/ureadseq.c Thu Dec 22 08:58:41 1994
+--- rtrans/ureadseq.c Thu Dec 22 09:01:43 1994
+***************
+*** 162,168 ****
+--- 162,172 ----
+ }
+ else V->seq = ptr;
+ }
++ #ifdef TRANSLATE
++ V->seq[(V->seqlen)++] = gTranslate[*s];
++ #else
+ V->seq[(V->seqlen)++] = *s;
++ #endif
+ }
+ s++;
+ }
+
+
+diff -bwrc old/ureadseq.h rtrans/ureadseq.h
+*** old/ureadseq.h Thu Dec 22 08:58:41 1994
+--- rtrans/ureadseq.h Thu Dec 22 08:58:28 1994
+***************
+*** 113,118 ****
+--- 113,126 ----
+ extern prettyopts gPretty;
+ #endif
+
++ #ifdef TRANSLATE
++ #ifdef UREADSEQ_G
++ char gTranslate[256];
++ #else
++ extern char gTranslate[256];
++ #endif
++ #define gTranslateInit() { short c; for(c=0; c<256; c++) gTranslate[c]= c; }
++ #endif
+
+ #ifdef __cplusplus
+ extern "C" {
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