[med-svn] r11551 - in trunk/packages/seg/trunk/debian: . patches source
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed Jul 4 20:48:00 UTC 2012
Author: lkajan-guest
Date: 2012-07-04 20:47:59 +0000 (Wed, 04 Jul 2012)
New Revision: 11551
Added:
trunk/packages/seg/trunk/debian/README.source
trunk/packages/seg/trunk/debian/patches/
trunk/packages/seg/trunk/debian/patches/autotools
trunk/packages/seg/trunk/debian/patches/example
trunk/packages/seg/trunk/debian/patches/genwin.c
trunk/packages/seg/trunk/debian/patches/makefile
trunk/packages/seg/trunk/debian/patches/seg.c
trunk/packages/seg/trunk/debian/patches/seg.pod
trunk/packages/seg/trunk/debian/patches/series
trunk/packages/seg/trunk/debian/seg.examples
trunk/packages/seg/trunk/debian/seg.install
trunk/packages/seg/trunk/debian/source/
trunk/packages/seg/trunk/debian/source/format
trunk/packages/seg/trunk/debian/upstream
Modified:
trunk/packages/seg/trunk/debian/
trunk/packages/seg/trunk/debian/changelog
trunk/packages/seg/trunk/debian/compat
trunk/packages/seg/trunk/debian/control
trunk/packages/seg/trunk/debian/copyright
trunk/packages/seg/trunk/debian/rules
Log:
lintian clean
Property changes on: trunk/packages/seg/trunk/debian
___________________________________________________________________
Added: svn:ignore
+ autoreconf.*
Added: mergeWithUpstream
+ 1
Added: trunk/packages/seg/trunk/debian/README.source
===================================================================
--- trunk/packages/seg/trunk/debian/README.source (rev 0)
+++ trunk/packages/seg/trunk/debian/README.source 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,19 @@
+seg for Debian
+==============
+
+COPYING
+-------
+Licensing information was provided by John C. Wootton, see his email at [1].
+
+[1] http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016269.html
+
+Repackaged Upstream Source
+--------------------------
+Upstream comes as a bunch of files at ftp://ftp.ncbi.nih.gov/pub/seg/seg/.
+There is no upstream tarball at all. The orig.tar.gz can be generated using
+the get-orig-source of debian/rules.
+
+debian/watch
+------------
+The upstream is not versioned, there is no upstream tarball. There can be no
+watch file.
Modified: trunk/packages/seg/trunk/debian/changelog
===================================================================
--- trunk/packages/seg/trunk/debian/changelog 2012-07-04 19:27:02 UTC (rev 11550)
+++ trunk/packages/seg/trunk/debian/changelog 2012-07-04 20:47:59 UTC (rev 11551)
@@ -1,25 +1,6 @@
-lowcompseg (19973009.1) UNRELEASED; urgency=low
+seg (1994101801-1) UNRELEASED; urgency=low
- * rpm spec file
- * updated man page example
+ * Initial version. (Closes: #680233)
- -- Laszlo Kajan <lkajan at rostlab.org> Sun, 10 Jul 2011 23:29:45 +0200
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 04 Jul 2012 16:11:12 +0000
-lowcompseg (19973009-rg1-2) unstable; urgency=low
-
- * version apt goes up to
-
- -- Laszlo Kajan <lkajan at rostlab.org> Tue, 01 Mar 2011 14:29:55 +0100
-
-lowcompseg (19973009-rg2) unstable; urgency=low
-
- * debian native
-
- -- Laszlo Kajan <lkajan at rostlab.org> Fri, 18 Feb 2011 16:30:17 +0100
-
-lowcompseg (1.0.0)
-
- * Initial version.
-
- -- Guy Yachdav <gyahcdav at rostlab.org> Thu, 17 Dec 2009 14:35:44 +0100
-
Modified: trunk/packages/seg/trunk/debian/compat
===================================================================
--- trunk/packages/seg/trunk/debian/compat 2012-07-04 19:27:02 UTC (rev 11550)
+++ trunk/packages/seg/trunk/debian/compat 2012-07-04 20:47:59 UTC (rev 11551)
@@ -1 +1 @@
-7
+8
Modified: trunk/packages/seg/trunk/debian/control
===================================================================
--- trunk/packages/seg/trunk/debian/control 2012-07-04 19:27:02 UTC (rev 11550)
+++ trunk/packages/seg/trunk/debian/control 2012-07-04 20:47:59 UTC (rev 11551)
@@ -1,23 +1,36 @@
-Source: lowcompseg
+Source: seg
Section: science
Priority: extra
-Maintainer: Guy Yachdav <gyachdav at rostlab.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 7)
-Standards-Version: 3.9.1
-Homepage:
+Build-Depends: debhelper (>= 8), dh-autoreconf
+Standards-Version: 3.9.3
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seg/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seg/trunk/
+DM-Upload-Allowed: yes
-Package: lowcompseg
+Package: seg
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: segment sequence(s) by local complexity
- Segment sequence(s) by local complexity. lowcompseg divides sequences into
- contrasting segments of low-complexity and high-complexity.
+Description: masking of segments of low compositional complexity in amino acid sequences
+ SEG is a program for identifying and masking segments of low compositional
+ complexity in amino acid sequences.
+ .
+ seg divides sequences into contrasting segments of low-complexity and
+ high-complexity. Low-complexity segments defined by the
+ algorithm represent "simple sequences" or "compositionally-biased regions".
+ .
+ This program is inappropriate for masking nucleotide sequences and, in fact,
+ may strip some nucleotide ambiguity codes from nt. sequences as they are being
+ read.
-Package: lowcompseg-dbg
+Package: seg-dbg
Section: debug
Architecture: any
Priority: extra
-Depends: ${shlibs:Depends}, ${misc:Depends}, lowcompseg (= ${binary:Version})
-Description: debug files for lowcompseg
- This package contains the stripped debugging symbols for lowcompseg.
+Depends: ${shlibs:Depends}, ${misc:Depends}, seg (= ${binary:Version})
+Description: debug symbols for seg
+ SEG is a program for identifying and masking segments of low compositional
+ complexity in amino acid sequences.
+ .
+ This package contains detached debug symbols for seg.
Modified: trunk/packages/seg/trunk/debian/copyright
===================================================================
--- trunk/packages/seg/trunk/debian/copyright 2012-07-04 19:27:02 UTC (rev 11550)
+++ trunk/packages/seg/trunk/debian/copyright 2012-07-04 20:47:59 UTC (rev 11551)
@@ -1,43 +1,54 @@
-This package was debianized by Guy Yachdav <gyachdav at rostlab.org> on
-Tue, 15 Dec 2009 12:40:35 +0100
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: seg
+Upstream-Contact: John Wootton <wootton at ncbi.nlm.nih.gov>
+Source: ftp://ftp.ncbi.nih.gov/pub/seg/seg/
-Upstream Authors:
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>
+License: GPL-3+
- John Wootton, Scott Federhen
+Files: *
+Copyright: public-domain
+License: public-domain
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the authors' official duties as United States Government employees and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite the authors in any work or product based on this material.
+ .
+ Authors: John C. Wootton, Scott Federhen
+ National Center For Biotechnology Information
+ National Library of Medicine
+ National Institutes of Health
-Copyright:
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 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 program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
- National Center for Biotechnology Information (1994)(1997)
-
-License:
-
- PUBLIC DOMAIN NOTICE
- National Center for Biotechnology Information
-
- This software/database is a "United States Government Work" under the
- terms of the United States Copyright Act. It was written as part of
- the authors' official duties as United States Government employees and
- thus cannot be copyrighted. This software/database is freely available
- to the public for use. The National Library of Medicine and the U.S.
- Government have not placed any restriction on its use or reproduction.
-
- Although all reasonable efforts have been taken to ensure the accuracy
- and reliability of the software and data, the NLM and the U.S.
- Government do not and cannot warrant the performance or results that
- may be obtained by using this software or data. The NLM and the U.S.
- Government disclaim all warranties, express or implied, including
- warranties of performance, merchantability or fitness for any particular
- purpose.
-
- Please cite the authors in any work or product based on this material.
-
- Authors: John C. Wootton, Scott Federhen
- National Center For Biotechnology Information
- National Library of Medicine
- National Institutes of Health
-
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is (C) 2009, Guy Yachdav <gyachdav at rostlab.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Added: trunk/packages/seg/trunk/debian/patches/autotools
===================================================================
--- trunk/packages/seg/trunk/debian/patches/autotools (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/autotools 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,132 @@
+Index: seg-1994101801/configure.ac
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/configure.ac 2012-07-04 20:31:38.946824368 +0000
+@@ -0,0 +1,7 @@
++AC_INIT([seg], [1994101801])
++AC_CONFIG_SRCDIR([seg.c])
++AM_INIT_AUTOMAKE
++AC_CONFIG_FILES([Makefile])
++AC_PROG_CC
++
++AC_OUTPUT
+Index: seg-1994101801/Makefile.am
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/Makefile.am 2012-07-04 20:31:38.946824368 +0000
+@@ -0,0 +1,14 @@
++man_MANS = seg.1
++
++bin_PROGRAMS = seg
++
++seg_SOURCES = seg.c genwin.c genwin.h lnfac.h
++
++LDADD = -lm
++
++seg.1: seg.pod
++ sed -e 's|__datadir__|$(datadir)|g;s|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__PREFIX__|$(prefix)|g;s|__sysconfdir__|$(sysconfdir)|g;s|__VERSION__|$(VERSION)|g;' "$<" | \
++ pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') > "$@"
++
++clean-local:
++ rm -f $(man_MANS)
+Index: seg-1994101801/AUTHORS
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/AUTHORS 2012-07-04 20:31:38.946824368 +0000
+@@ -0,0 +1,4 @@
++John C. Wootton, Scott Federhen
++National Center For Biotechnology Information
++National Library of Medicine
++National Institutes of Health
+Index: seg-1994101801/ChangeLog
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/ChangeLog 2012-07-04 20:31:38.950824087 +0000
+@@ -0,0 +1,52 @@
++
++This directory contains C language source code for the SEG program of Wootton
++and Federhen, for identifying and masking segments of low compositional
++complexity in amino acid sequences. This program is inappropriate for
++masking nucleotide sequences and, in fact, may strip some nucleotide
++ambiguity codes from nt. sequences as they are being read.
++
++The SEG program can be used as a plug-in filter of query sequences used in the
++NCBI BLAST programs. See the -filter and -echofilter options described in the
++BLAST software's manual page.
++
++Input to SEG must be sequences in FASTA format. Output can be produced in a
++variety of formats, with FASTA format being one of them when the -x option is
++used. The file seg.doc includes a copy of the man page for the seg program.
++
++
++References:
++Wootton, J. C. and S. Federhen (1993). Statistics of local complexity in amino
++acid sequences and sequence databases. Computers and Chemistry 17:149-163.
++
++
++MODIFICATION HISTORY
++10/18/94
++Fixed a bug in the boundary conditions for the alphabet assignments
++(colorings) calculations. This condition seems not to arise in the
++current protein sequence databases, but does appear when the algorithm
++is customized for the nucleic acid alphabet.
++
++4/2/94
++Fixed a bug in the reading of input sequence files. B, Z, and U letters found
++in the IUB amino acid alphabet and the NCBI standard amino acid alphabet
++were being stripped.
++
++3/30/94
++WRG improved speed by about 3X (roughly 5X overall since 3/21/94), due in part
++to the elimination of nearly all log() function calls, plus the removal of much
++unused or unnecessary code.
++
++3/21/94
++Included support for the special characters "*" (translation stop) and "-"
++(gap) which are found in some NCBI standard amino acid alphabets.
++
++WRG replaced repetitive dynamic calls to log(2.) and log(20.) with precomputed
++values, yielding a 33-50% speed improvement.
++
++WRG added EOF checks in several places, the lack of which could produce
++infinite looping.
++
++The previous version of seg is archived beneath the archive subdirectory.
++
++9/30/97
++HMF5 plugged a memory leak.
+Index: seg-1994101801/NEWS
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/NEWS 2012-07-04 20:31:38.950824087 +0000
+@@ -0,0 +1 @@
++2012-07-04 Debianization of seg.
+Index: seg-1994101801/COPYING
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/COPYING 2012-07-04 20:32:08.274824880 +0000
+@@ -0,0 +1,24 @@
++ PUBLIC DOMAIN NOTICE
++ National Center for Biotechnology Information
++
++ This software/database is a "United States Government Work" under the
++ terms of the United States Copyright Act. It was written as part of
++ the authors' official duties as United States Government employees and
++ thus cannot be copyrighted. This software/database is freely available
++ to the public for use. The National Library of Medicine and the U.S.
++ Government have not placed any restriction on its use or reproduction.
++
++ Although all reasonable efforts have been taken to ensure the accuracy
++ and reliability of the software and data, the NLM and the U.S.
++ Government do not and cannot warrant the performance or results that
++ may be obtained by using this software or data. The NLM and the U.S.
++ Government disclaim all warranties, express or implied, including
++ warranties of performance, merchantability or fitness for any particular
++ purpose.
++
++ Please cite the authors in any work or product based on this material.
++
++ Authors: John C. Wootton, Scott Federhen
++ National Center For Biotechnology Information
++ National Library of Medicine
++ National Institutes of Health
Added: trunk/packages/seg/trunk/debian/patches/example
===================================================================
--- trunk/packages/seg/trunk/debian/patches/example (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/example 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,11 @@
+Index: seg-1994101801/prion.fa
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/prion.fa 2012-07-04 19:08:07.066840944 +0000
+@@ -0,0 +1,6 @@
++>PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
++MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP
++HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA
++VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
++NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV
++ILLISFLIFLIVG
Added: trunk/packages/seg/trunk/debian/patches/genwin.c
===================================================================
--- trunk/packages/seg/trunk/debian/patches/genwin.c (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/genwin.c 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,42 @@
+Index: seg-1994101801/genwin.c
+===================================================================
+--- seg-1994101801.orig/genwin.c 2012-07-04 18:15:40.000000000 +0000
++++ seg-1994101801/genwin.c 2012-07-04 18:48:41.414821989 +0000
+@@ -5,6 +5,7 @@
+
+ /*--------------------------------------------------------------(includes)---*/
+
++#include <string.h>
+ #include "genwin.h"
+
+ /*---------------------------------------------------------------(defines)---*/
+@@ -53,7 +54,7 @@
+
+ #define TESTMAX 1000
+ void *tmalloc();
+-int record_ptrs[TESTMAX] = {0,0,0,0};
++void *record_ptrs[TESTMAX] = {NULL,NULL,NULL,NULL};
+ int rptr = 0;
+
+ /*------------------------------------------------------------(genwininit)---*/
+@@ -850,7 +851,7 @@
+ exit(2);
+ }
+
+- record_ptrs[rptr] = (int) ptr;
++ record_ptrs[rptr] = ptr;
+ rptr++;
+
+ return(ptr);
+@@ -865,9 +866,9 @@
+
+ for (i=0; i<rptr; i++)
+ {
+- if (record_ptrs[i]==(int)ptr)
++ if (record_ptrs[i]==ptr)
+ {
+- record_ptrs[i] = 0;
++ record_ptrs[i] = NULL;
+ break;
+ }
+ }
Added: trunk/packages/seg/trunk/debian/patches/makefile
===================================================================
--- trunk/packages/seg/trunk/debian/patches/makefile (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/makefile 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,40 @@
+Index: seg-1994101801/makefile
+===================================================================
+--- seg-1994101801.orig/makefile 2012-07-04 19:09:41.530825609 +0000
++++ /dev/null 1970-01-01 00:00:00.000000000 +0000
+@@ -1,15 +0,0 @@
+-
+-all : seg
+-
+-seg : seg.c lnfac.h genwin.h genwin.o
+- cc -O -o seg seg.c genwin.o -lm
+-
+-hiseg : hiseg.c lnfac.h genwin.h genwin.o
+- cc -O -o hiseg hiseg.c genwin.o -lm
+-
+-genwin.o : genwin.c genwin.h
+- cc -O -c genwin.c
+-
+-clean:
+- rm -f seg seg.o genwin.o
+-
+Index: seg-1994101801/makefile.old
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/makefile.old 2012-07-04 19:09:41.530825609 +0000
+@@ -0,0 +1,15 @@
++
++all : seg
++
++seg : seg.c lnfac.h genwin.h genwin.o
++ cc -O -o seg seg.c genwin.o -lm
++
++hiseg : hiseg.c lnfac.h genwin.h genwin.o
++ cc -O -o hiseg hiseg.c genwin.o -lm
++
++genwin.o : genwin.c genwin.h
++ cc -O -c genwin.c
++
++clean:
++ rm -f seg seg.o genwin.o
++
Added: trunk/packages/seg/trunk/debian/patches/seg.c
===================================================================
--- trunk/packages/seg/trunk/debian/patches/seg.c (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/seg.c 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,12 @@
+Index: seg-1994101801/seg.c
+===================================================================
+--- seg-1994101801.orig/seg.c 2012-07-04 18:15:49.000000000 +0000
++++ seg-1994101801/seg.c 2012-07-04 18:47:15.222835801 +0000
+@@ -6,6 +6,7 @@
+
+ /*--------------------------------------------------------------(includes)---*/
+
++#include <string.h>
+ #include "genwin.h"
+ #include "lnfac.h"
+
Added: trunk/packages/seg/trunk/debian/patches/seg.pod
===================================================================
--- trunk/packages/seg/trunk/debian/patches/seg.pod (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/seg.pod 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,535 @@
+Index: seg-1994101801/seg.pod
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ seg-1994101801/seg.pod 2012-07-04 20:45:27.206822408 +0000
+@@ -0,0 +1,290 @@
++=head1 NAME
++
++seg - segment sequence(s) by local complexity
++
++=head1 SYNOPSIS
++
++seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]
++
++=head1 DESCRIPTION
++
++seg divides sequences into contrasting segments of low-complexity
++and high-complexity. Low-complexity segments defined by the
++algorithm represent "simple sequences" or "compositionally-biased
++regions".
++
++Locally-optimized low-complexity segments are produced at defined
++levels of stringency, based on formal definitions of local
++compositional complexity (Wootton & Federhen, 1993). The segment
++lengths and the number of segments per sequence are determined
++automatically by the algorithm.
++
++The input is a FASTA-formatted sequence file, or a database file
++containing many FASTA-formatted sequences. seg is tuned for amino
++acid sequences. For nucleotide sequences, see EXAMPLES OF
++PARAMETER SETS below.
++
++The stringency of the search for low-complexity segments is
++determined by three user-defined parameters, trigger window length
++[ W ], trigger complexity [ K(1) ] and extension complexity [ K(2)]
++(see below under PARAMETERS ). The defaults provided are suitable
++for low-complexity masking of database search query sequences [ -x
++option required, see below].
++
++
++=head1 OUTPUTS AND APPLICATIONS
++
++(1) Readable segmented sequence [Default]. Regions of contrasting
++complexity are displayed in "tree format". See EXAMPLES.
++
++(2) Low-complexity masking (see Altschul et al, 1994). Produce a
++masked FASTA-formatted file, ready for input as a query sequence for
++database search programs such as BLAST or FASTA. The amino acids in
++low-complexity regions are replaced with "x" characters [-x option].
++See EXAMPLES.
++
++(3) Database construction. Produce FASTA-formatted files containing
++low-complexity segments [-l option], or high-complexity segments
++[-h option], or both [-a option]. Each segment is a separate
++sequence entry with an informative header line.
++
++=head1 ALGORITHM
++
++The SEG algorithm has two stages. First, identification of
++approximate raw segments of low- complexity; second local
++optimization.
++
++At the first stage, the stringency and resolution of the search for
++low-complexity segments is determined by the W, K(1) and K(2)
++parameters. All trigger windows are defined, including overlapping
++windows, of length W and complexity less than or equal to K(1).
++"Complexity" here is defined by equation (3) of Wootton & Federhen
++(1993). Each trigger window is then extended into a contig in both
++directions by merging with extension windows, which are overlapping
++windows of length W and complexity less than or equal to K(2).
++Each contig is a raw segment.
++
++At the second stage, each raw segment is reduced to a single
++optimal low-complexity segment, which may be the entire raw
++segment but is usually a subsequence. The optimal subsequence has
++the lowest value of the probability P(0) (equation (5) of Wootton
++& Federhen, 1993).
++
++=head1 PARAMETERS
++
++These three numeric parameters are in obligatory order after the
++sequence file name.
++
++Trigger window length [ W ]. An integer greater than zero [ Default
++12 ].
++
++Trigger complexity. [ K1 ]. The maximum complexity of a trigger
++window in units of bits. K1 must be equal to or greater than zero.
++The maximum value is 4.322 (log[base 2]20) for amino acid
++sequences [ Default 2.2 ].
++
++Extension complexity [ K2 ]. The maximum complexity of an extension
++window in units of bits. Only values greater than K1 are effective
++in extending triggered windows. Range of possible values is as for
++K1 [ Default 2.5 ].
++
++
++=head1 OPTIONS
++
++The following options may be placed in any order in the command
++line after the W, K1 and K2 parameters:
++
++=over
++
++=item -a
++
++Output both low-complexity and high-complexity segments in a
++FASTA-formatted file, as a set of separate entries with header
++lines.
++
++=item -c [characters-per-line]
++
++Number of sequence characters per line of
++output [Default 60]. Other characters, such as residue numbers, are additional.
++
++=item -h
++
++Output only the high-complexity segments in a FASTA-formatted
++file, as a set of separate entries with header lines.
++
++=item -l
++
++Output only the low-complexity segments in a FASTA-formatted
++file, as a set of separate entries with header lines.
++
++=item -m [length]
++
++Minimum length in residues for a high-complexity
++segment [default 0]. Shorter segments are merged with adjacent
++low-complexity segments.
++
++=item -o
++
++Show all overlapping, independently-triggered low-complexity
++segments [these are merged by default].
++
++=item -q
++
++Produce an output format with the sequence in a numbered block
++with markings to assist residue counting. The low-complexity and
++high-complexity segments are in lower- and upper-case characters
++respectively.
++
++=item -t [length]
++
++"Maximum trim length" parameter [default 100]. This
++controls the search space (and search time) during the
++optimization of raw segments (see ALGORITHM above). By default,
++subsequences 100 or more residues shorter than the raw segment are
++omitted from the search. This parameter may be increased to give
++a more extensive search if raw segments are longer than 100 residues.
++
++=item -x
++
++The masking option for amino acid sequences. Each input
++sequence is represented by a single output sequence in FASTA-format
++with low-complexity regions replaced by strings of "x" characters.
++
++=back
++
++=head1 EXAMPLES OF PARAMETER SETS
++
++Default parameters are given by 'seg sequence' (equivalent to 'seg
++sequence 12 2.2 2.5'). These parameters are appropriate for low-
++complexity masking of many amino acid sequences [with -x option ].
++
++=head2 Database-database comparisons:
++
++More stringent (lower) complexity parameters are suitable when
++masked sequences are compared with masked sequences. For example,
++for BLAST or FASTA searches that compare two amino acid sequence
++databases, the following masking may be applied to both databases:
++
++ seg database 12 1.8 2.0 -x
++
++=head2 Homopolymer analysis:
++
++To examine all homopolymeric subsequences of length (for example)
++7 or greater:
++
++ seg sequence 7 0 0
++
++=head2 Non-globular regions of protein sequences:
++
++Many long non-globular domains may be diagnosed at longer window
++lengths, typically:
++
++ seg sequence 45 3.4 3.75
++
++For some shorter non-globular domains, the following set is
++appropriate:
++
++ seg sequence 25 3.0 3.3
++
++=head2 Nucleotide sequences:
++
++The maximum value of the complexity parameters is 2 (log[base 2]4).
++For masking, the following is approximately equivalent in effect
++to the default parameters for amino acid sequences:
++
++ seg sequence.na 21 1.4 1.6
++
++=head1 EXAMPLES
++
++The following is a file named 'prion' in FASTA format:
++
++ >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
++ MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP
++ HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA
++ VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
++ NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV
++ ILLISFLIFLIVG
++
++The command line:
++
++ seg __docdir__/examples/prion.fa
++
++gives the standard output below
++
++
++ >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
++
++ 1-49 MANLGCWMLVLFVATWSDLGLCKKRPKPGG
++ WNTGGSRYPGQGSPGGNRY
++ ppqggggwgqphgggwgqphgggwgqphgg 50-94
++ gwgqphgggwgqggg
++ 95-112 THSQWNKPSKPKTNMKHM
++ agaaaagavvgglggymlgsams 113-135
++ 136-187 RPIIHFGSDYEDRYYRENMHRYPNQVYYRP
++ MDEYSNQNNFVHDCVNITIKQH
++ tvttttkgenftet 188-201
++ 202-236 DVKMMERVVEQMCITQYERESQAYYQRGSS
++ MVLFS
++ sppvillisflifliv 237-252
++ 253-253 G
++
++The low-complexity sequences are on the left (lower case) and
++high-complexity sequences are on the right (upper case). All
++sequence segments read from left to right and their order in the
++sequence is from top to bottom, as shown by the central column of
++residue numbers.
++
++The command line:
++
++ seg __docdir__/examples/prion.fa -x
++
++gives the following FASTA-formatted file:-
++
++ >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
++ MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYxxxxxxxxxxx
++ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTHSQWNKPSKPKTNMKHMxxxxxxxx
++ xxxxxxxxxxxxxxxRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
++ NITIKQHxxxxxxxxxxxxxxDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSxxxx
++ xxxxxxxxxxxxG
++
++=head1 SEE ALSO
++
++segn(1), blast(1), saps(1), xnu(1)
++
++=head1 AUTHORS
++
++John Wootton: wootton at ncbi.nlm.nih.gov
++
++Scott Federhen: federhen at ncbi.nlm.nih.gov
++
++ National Center for Biotechnology Information
++ Building 38A, Room 8N805
++ National Library of Medicine
++ National Institutes of Health
++ Bethesda, Maryland, MD 20894
++ U.S.A.
++
++
++=head1 PRIMARY REFERENCE
++
++Wootton, J.C., Federhen, S. (1993) Statistics of local complexity
++in amino acid sequences and sequence databases. Computers &
++Chemistry 17: 149-163.
++
++
++=head1 OTHER REFERENCES
++
++Wootton, J.C. (1994) Non-globular domains in protein sequences:
++automated segmentation using complexity measures. Computers &
++Chemistry 18: (in press).
++
++Altschul, S.F., Boguski, M., Gish, W., Wootton, J.C. (1994) Issues
++in searching molecular sequence databases. Nature Genetics 6:
++119-129.
++
++Wootton, J.C. (1994) Simple sequences of protein and DNA. In:
++Nucleic Acid and Protein Sequence Analysis: A Practical Approach.
++(Second Edition, Chapter 8, Bishop, M.J. and Rawlings, C.R. Eds.
++IRL Press, Oxford) (In press).
++
++
+Index: seg-1994101801/seg.doc
+===================================================================
+--- seg-1994101801.orig/seg.doc 2012-07-04 20:45:24.878825058 +0000
++++ seg-1994101801/seg.doc 2012-07-04 20:45:27.206822408 +0000
+@@ -13,12 +13,12 @@
+ seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ]
+
+
+-DESCRIPTION
++DESCRIPTION
+ -----------
+
+ seg divides sequences into contrasting segments of low-complexity
+ and high-complexity. Low-complexity segments defined by the
+-algorithm represent "simple sequences" or "compositionally-biased
++algorithm represent "simple sequences" or "compositionally-biased
+ regions".
+
+ Locally-optimized low-complexity segments are produced at defined
+@@ -29,36 +29,36 @@
+
+ The input is a FASTA-formatted sequence file, or a database file
+ containing many FASTA-formatted sequences. seg is tuned for amino
+-acid sequences. For nucleotide sequences, see EXAMPLES OF
++acid sequences. For nucleotide sequences, see EXAMPLES OF
+ PARAMETER SETS below.
+
+ The stringency of the search for low-complexity segments is
+ determined by three user-defined parameters, trigger window length
+-[ W ], trigger complexity [ K(1) ] and extension complexity [ K(2)]
++[ W ], trigger complexity [ K(1) ] and extension complexity [ K(2)]
+ (see below under PARAMETERS ). The defaults provided are suitable
+ for low-complexity masking of database search query sequences [ -x
+ option required, see below].
+
+
+-OUTPUTS AND APPLICATIONS
++OUTPUTS AND APPLICATIONS
+ ------------------------
+
+ (1) Readable segmented sequence [Default]. Regions of contrasting
+ complexity are displayed in "tree format". See EXAMPLES.
+
+-(2) Low-complexity masking (see Altschul et al, 1994). Produce a
++(2) Low-complexity masking (see Altschul et al, 1994). Produce a
+ masked FASTA-formatted file, ready for input as a query sequence for
+-database search programs such as BLAST or FASTA. The amino acids in
+-low-complexity regions are replaced with "x" characters [-x option].
++database search programs such as BLAST or FASTA. The amino acids in
++low-complexity regions are replaced with "x" characters [-x option].
+ See EXAMPLES.
+
+ (3) Database construction. Produce FASTA-formatted files containing
+ low-complexity segments [-l option], or high-complexity segments
+-[-h option], or both [-a option]. Each segment is a separate
++[-h option], or both [-a option]. Each segment is a separate
+ sequence entry with an informative header line.
+
+
+-ALGORITHM
++ALGORITHM
+ ---------
+
+ The SEG algorithm has two stages. First, identification of
+@@ -81,7 +81,7 @@
+ the lowest value of the probability P(0) (equation (5) of Wootton
+ & Federhen, 1993).
+
+-PARAMETERS
++PARAMETERS
+ ----------
+
+ These three numeric parameters are in obligatory order after the
+@@ -92,16 +92,16 @@
+
+ Trigger complexity. [ K1 ]. The maximum complexity of a trigger
+ window in units of bits. K1 must be equal to or greater than zero.
+-The maximum value is 4.322 (log[base 2]20) for amino acid
++The maximum value is 4.322 (log[base 2]20) for amino acid
+ sequences [ Default 2.2 ].
+
+ Extension complexity [ K2 ]. The maximum complexity of an extension
+ window in units of bits. Only values greater than K1 are effective
+-in extending triggered windows. Range of possible values is as for
++in extending triggered windows. Range of possible values is as for
+ K1 [ Default 2.5 ].
+
+
+-OPTIONS
++OPTIONS
+ -------
+
+ The following options may be placed in any order in the command
+@@ -112,7 +112,7 @@
+ lines.
+
+ -c [characters-per-line] Number of sequence characters per line of
+- output [Default 60]. Other characters, such as residue numbers,
++ output [Default 60]. Other characters, such as residue numbers,
+ are additional.
+
+ -h Output only the high-complexity segments in a FASTA-formatted
+@@ -122,7 +122,7 @@
+ file, as a set of separate entries with header lines.
+
+ -m [length] Minimum length in residues for a high-complexity
+- segment [default 0]. Shorter segments are merged with adjacent
++ segment [default 0]. Shorter segments are merged with adjacent
+ low-complexity segments.
+
+ -o Show all overlapping, independently-triggered low-complexity
+@@ -130,7 +130,7 @@
+
+ -q Produce an output format with the sequence in a numbered block
+ with markings to assist residue counting. The low-complexity and
+- high-complexity segments are in lower- and upper-case characters
++ high-complexity segments are in lower- and upper-case characters
+ respectively.
+
+ -t [length] "Maximum trim length" parameter [default 100]. This
+@@ -145,7 +145,7 @@
+ with low-complexity regions replaced by strings of "x" characters.
+
+
+-EXAMPLES OF PARAMETER SETS
++EXAMPLES OF PARAMETER SETS
+ --------------------------
+
+ Default parameters are given by 'seg sequence' (equivalent to 'seg
+@@ -154,48 +154,48 @@
+
+ Database-database comparisons:
+ -----------------------------
+-More stringent (lower) complexity parameters are suitable when
+-masked sequences are compared with masked sequences. For example,
+-for BLAST or FASTA searches that compare two amino acid sequence
++More stringent (lower) complexity parameters are suitable when
++masked sequences are compared with masked sequences. For example,
++for BLAST or FASTA searches that compare two amino acid sequence
+ databases, the following masking may be applied to both databases:
+
+ seg database 12 1.8 2.0 -x
+
+ Homopolymer analysis:
+ --------------------
+-To examine all homopolymeric subsequences of length (for example)
++To examine all homopolymeric subsequences of length (for example)
+ 7 or greater:
+
+- seg sequence 7 0 0
++ seg sequence 7 0 0
+
+ Non-globular regions of protein sequences:
+ -----------------------------------------
+-Many long non-globular domains may be diagnosed at longer window
++Many long non-globular domains may be diagnosed at longer window
+ lengths, typically:
+
+ seg sequence 45 3.4 3.75
+
+-For some shorter non-globular domains, the following set is
++For some shorter non-globular domains, the following set is
+ appropriate:
+
+ seg sequence 25 3.0 3.3
+
+ Nucleotide sequences:
+ --------------------
+-The maximum value of the complexity parameters is 2 (log[base 2]4).
+-For masking, the following is approximately equivalent in effect
++The maximum value of the complexity parameters is 2 (log[base 2]4).
++For masking, the following is approximately equivalent in effect
+ to the default parameters for amino acid sequences:
+
+ seg sequence.na 21 1.4 1.6
+
+-EXAMPLES
++EXAMPLES
+ The following is a file named 'prion' in FASTA format:
+
+ >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
+-MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP
+-HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA
+-VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
+-NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV
++MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP
++HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA
++VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
++NITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPV
+ ILLISFLIFLIVG
+
+ The command line:
+@@ -221,8 +221,8 @@
+ sppvillisflifliv 237-252
+ 253-253 G
+
+-The low-complexity sequences are on the left (lower case) and
+-high-complexity sequences are on the right (upper case). All
++The low-complexity sequences are on the left (lower case) and
++high-complexity sequences are on the right (upper case). All
+ sequence segments read from left to right and their order in the
+ sequence is from top to bottom, as shown by the central column of
+ residue numbers.
+@@ -234,21 +234,21 @@
+ gives the following FASTA-formatted file:-
+
+ >PRIO_HUMAN MAJOR PRION PROTEIN PRECURSOR
+-MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYxxxxxxxxxxx
+-xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTHSQWNKPSKPKTNMKHMxxxxxxxx
+-xxxxxxxxxxxxxxxRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
+-NITIKQHxxxxxxxxxxxxxxDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSxxxx
++MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYxxxxxxxxxxx
++xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTHSQWNKPSKPKTNMKHMxxxxxxxx
++xxxxxxxxxxxxxxxRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV
++NITIKQHxxxxxxxxxxxxxxDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSxxxx
+ xxxxxxxxxxxxG
+
+
+
+-SEE ALSO
++SEE ALSO
+ --------
+
+ segn, blast, saps, xnu
+
+
+-AUTHORS
++AUTHORS
+ -------
+
+ John Wootton: wootton at ncbi.nlm.nih.gov
+@@ -262,7 +262,7 @@
+ U.S.A.
+
+
+-PRIMARY REFERENCE
++PRIMARY REFERENCE
+ -----------------
+
+ Wootton, J.C., Federhen, S. (1993) Statistics of local complexity
Added: trunk/packages/seg/trunk/debian/patches/series
===================================================================
--- trunk/packages/seg/trunk/debian/patches/series (rev 0)
+++ trunk/packages/seg/trunk/debian/patches/series 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,6 @@
+makefile
+example
+seg.c
+genwin.c
+autotools
+seg.pod
Modified: trunk/packages/seg/trunk/debian/rules
===================================================================
--- trunk/packages/seg/trunk/debian/rules 2012-07-04 19:27:02 UTC (rev 11550)
+++ trunk/packages/seg/trunk/debian/rules 2012-07-04 20:47:59 UTC (rev 11551)
@@ -1,106 +1,39 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-
# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+export DH_VERBOSE=1
+export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-# These are used for cross-compiling and for saving the configure script
-# from having to guess our platform (since we know it already)
-DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
-DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-ifneq ($(DEB_HOST_GNU_TYPE),$(DEB_BUILD_GNU_TYPE))
-CROSS= --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE)
-else
-CROSS= --build $(DEB_BUILD_GNU_TYPE)
-endif
+.PHONY: get-orig-source
+get-orig-source:
+ set -e; \
+ v="1994101801"; \
+ t=$$(mktemp -d) || exit 1; \
+ trap "rm -rf -- '$$t'" EXIT; \
+ d="$$t/seg-$${v}.orig"; \
+ mkdir "$$d"; \
+ ( cd "$$d"; \
+ wget \
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/README\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/genwin.c\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/genwin.h\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/hiseg.c\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/lnfac.h\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/makefile\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/seg.c\
+ ftp://ftp.ncbi.nih.gov/pub/seg/seg/seg.doc; \
+ ); \
+ GZIP=--best tar -czf "./seg_$${v}.orig.tar.gz" -C "$$t" "seg-$${v}.orig"
+.PHONY: override_dh_autoreconf
+override_dh_autoreconf:
+ dh_autoreconf -X./COPYING
+.PHONY: override_dh_strip
+override_dh_strip:
+ dh_strip --dbg-package=seg-dbg
-config.status: configure
- dh_testdir
- # Add here commands to configure the package.
-ifneq "$(wildcard /usr/share/misc/config.sub)" ""
- cp -f /usr/share/misc/config.sub config.sub
-endif
-ifneq "$(wildcard /usr/share/misc/config.guess)" ""
- cp -f /usr/share/misc/config.guess config.guess
-endif
- ./configure $(CROSS) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info --sysconfdir=/etc --with-pppopconspool=/var/spool/pp-popcon CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="-Wl,-z,defs"
-
-
-build: build-stamp
-
-build-stamp: config.status
- dh_testdir
-
- # Add here commands to compile the package.
- $(MAKE)
- #docbook-to-man debian/lowcompseg.sgml > lowcompseg.1
-
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp
-
- # Add here commands to clean up after the build process.
- [ ! -f Makefile ] || $(MAKE) distclean
- rm -f config.sub config.guess
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
-
- # Add here commands to install the package into debian/lowcompseg.
- $(MAKE) DESTDIR=$(CURDIR)/debian/lowcompseg install
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs ChangeLog
- dh_installdocs
- dh_lintian
- dh_installexamples
-# dh_install
-# dh_installmenu
-# dh_installdebconf
-# dh_installlogrotate
-# dh_installemacsen
-# dh_installpam
-# dh_installmime
-# dh_python
-# dh_installinit
- dh_installcron
-# dh_installinfo
- dh_installman
- dh_link
- dh_strip --dbg-package=lowcompseg-dbg
- dh_compress
- dh_fixperms
-# dh_perl
-# dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
+%:
+ dh $@ --with autoreconf
Added: trunk/packages/seg/trunk/debian/seg.examples
===================================================================
--- trunk/packages/seg/trunk/debian/seg.examples (rev 0)
+++ trunk/packages/seg/trunk/debian/seg.examples 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1 @@
+prion.fa
Added: trunk/packages/seg/trunk/debian/seg.install
===================================================================
--- trunk/packages/seg/trunk/debian/seg.install (rev 0)
+++ trunk/packages/seg/trunk/debian/seg.install 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share
Added: trunk/packages/seg/trunk/debian/source/format
===================================================================
--- trunk/packages/seg/trunk/debian/source/format (rev 0)
+++ trunk/packages/seg/trunk/debian/source/format 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/seg/trunk/debian/upstream
===================================================================
--- trunk/packages/seg/trunk/debian/upstream (rev 0)
+++ trunk/packages/seg/trunk/debian/upstream 2012-07-04 20:47:59 UTC (rev 11551)
@@ -0,0 +1,9 @@
+Name: seg
+Reference:
+ Author: Wootton, J.C. and Federhen, S.
+ Title: 'Statistics of local complexity in amino acid sequences and sequence databases.'
+ Journal: 'Computers & Chemistry'
+ Year: 1993
+ Volume: 17
+ Pages: 149-163
+ DOI: 10.1016/0097-8485(93)85006-X
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