Author: lkajan-guest Date: 2012-07-05 13:55:25 +0000 (Thu, 05 Jul 2012) New Revision: 11573
Added: trunk/packages/seg/trunk/debian/ncbi-seg.examples trunk/packages/seg/trunk/debian/ncbi-seg.install Removed: trunk/packages/seg/trunk/debian/seg.examples trunk/packages/seg/trunk/debian/seg.install Modified: trunk/packages/seg/trunk/debian/README.source trunk/packages/seg/trunk/debian/changelog trunk/packages/seg/trunk/debian/control trunk/packages/seg/trunk/debian/patches/autotools trunk/packages/seg/trunk/debian/patches/seg.pod trunk/packages/seg/trunk/debian/rules trunk/packages/seg/trunk/debian/upstream Log: changed version to 0.0.20000620; change package and binary name to ncbi-seg; changed get-orig-source back to static version and package name Modified: trunk/packages/seg/trunk/debian/README.source =================================================================== --- trunk/packages/seg/trunk/debian/README.source 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/README.source 2012-07-05 13:55:25 UTC (rev 11573) @@ -1,5 +1,5 @@ -seg for Debian -============== +ncbi-seg for Debian +=================== COPYING ------- Modified: trunk/packages/seg/trunk/debian/changelog =================================================================== --- trunk/packages/seg/trunk/debian/changelog 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/changelog 2012-07-05 13:55:25 UTC (rev 11573) @@ -1,4 +1,4 @@ -seg (1994101801-1) UNRELEASED; urgency=low +ncbi-seg (0.0.20000620-1) UNRELEASED; urgency=low * Initial version. (Closes: #680233) Modified: trunk/packages/seg/trunk/debian/control =================================================================== --- trunk/packages/seg/trunk/debian/control 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/control 2012-07-05 13:55:25 UTC (rev 11573) @@ -1,4 +1,4 @@ -Source: seg +Source: ncbi-seg Section: science Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> @@ -10,14 +10,14 @@ DM-Upload-Allowed: yes Homepage: ftp://ftp.ncbi.nih.gov/pub/seg/seg/ -Package: seg +Package: ncbi-seg Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} -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. +Description: tool to mask segments of low compositional complexity in amino acid sequences + ncbi-seg (a.k.a. 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 + ncbi-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". . @@ -25,12 +25,12 @@ may strip some nucleotide ambiguity codes from nt. sequences as they are being read. -Package: seg-dbg +Package: ncbi-seg-dbg Section: debug Architecture: any -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. +Depends: ${shlibs:Depends}, ${misc:Depends}, ncbi-seg (= ${binary:Version}) +Description: debug symbols for ncbi-seg + ncbi-seg (a.k.a. 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. + This package contains detached debug symbols for ncbi-seg. Copied: trunk/packages/seg/trunk/debian/ncbi-seg.examples (from rev 11572, trunk/packages/seg/trunk/debian/seg.examples) =================================================================== --- trunk/packages/seg/trunk/debian/ncbi-seg.examples (rev 0) +++ trunk/packages/seg/trunk/debian/ncbi-seg.examples 2012-07-05 13:55:25 UTC (rev 11573) @@ -0,0 +1 @@ +prion.fa Copied: trunk/packages/seg/trunk/debian/ncbi-seg.install (from rev 11572, trunk/packages/seg/trunk/debian/seg.install) =================================================================== --- trunk/packages/seg/trunk/debian/ncbi-seg.install (rev 0) +++ trunk/packages/seg/trunk/debian/ncbi-seg.install 2012-07-05 13:55:25 UTC (rev 11573) @@ -0,0 +1,2 @@ +usr/bin +usr/share Modified: trunk/packages/seg/trunk/debian/patches/autotools =================================================================== --- trunk/packages/seg/trunk/debian/patches/autotools 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/patches/autotools 2012-07-05 13:55:25 UTC (rev 11573) @@ -3,50 +3,42 @@ From: Laszlo Kajan <[email protected]> Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016275.html -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 +--- /dev/null ++++ b/configure.ac @@ -0,0 +1,7 @@ -+AC_INIT([seg], [1994101801]) ++AC_INIT([ncbi-seg], [0.0.20000620]) +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 +--- /dev/null ++++ b/Makefile.am @@ -0,0 +1,14 @@ -+man_MANS = seg.1 ++man_MANS = ncbi-seg.1 + -+bin_PROGRAMS = seg ++bin_PROGRAMS = ncbi-seg + -+seg_SOURCES = seg.c genwin.c genwin.h lnfac.h ++ncbi_seg_SOURCES = seg.c genwin.c genwin.h lnfac.h + +LDADD = -lm + -+seg.1: seg.pod ++ncbi-seg.1: ncbi-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 +--- /dev/null ++++ b/AUTHORS @@ -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 +--- /dev/null ++++ b/ChangeLog @@ -0,0 +1,52 @@ + +This directory contains C language source code for the SEG program of Wootton @@ -100,16 +92,12 @@ + +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 +--- /dev/null ++++ b/NEWS @@ -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 ++2012-07-04 Debianization of seg as ncbi-seg. +--- /dev/null ++++ b/COPYING @@ -0,0 +1,24 @@ + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information Modified: trunk/packages/seg/trunk/debian/patches/seg.pod =================================================================== --- trunk/packages/seg/trunk/debian/patches/seg.pod 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/patches/seg.pod 2012-07-05 13:55:25 UTC (rev 11573) @@ -3,22 +3,20 @@ From: Laszlo Kajan <[email protected]> Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-July/016275.html -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 +--- /dev/null ++++ b/ncbi-seg.pod @@ -0,0 +1,290 @@ +=head1 NAME + -+seg - segment sequence(s) by local complexity ++ncbi-seg - segment sequence(s) by local complexity + +=head1 SYNOPSIS + -+seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ] ++ncbi-seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ] + +=head1 DESCRIPTION + -+seg divides sequences into contrasting segments of low-complexity ++ncbi-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". @@ -30,7 +28,7 @@ +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 ++containing many FASTA-formatted sequences. ncbi-seg is tuned for amino +acid sequences. For nucleotide sequences, see EXAMPLES OF +PARAMETER SETS below. + @@ -164,7 +162,7 @@ + +=head1 EXAMPLES OF PARAMETER SETS + -+Default parameters are given by 'seg sequence' (equivalent to 'seg ++Default parameters are given by 'ncbi-seg sequence' (equivalent to 'ncbi-seg +sequence 12 2.2 2.5'). These parameters are appropriate for low- +complexity masking of many amino acid sequences [with -x option ]. + @@ -175,26 +173,26 @@ +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 ++ ncbi-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 ++ ncbi-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 ++ ncbi-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 ++ ncbi-seg sequence 25 3.0 3.3 + +=head2 Nucleotide sequences: + @@ -202,7 +200,7 @@ +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 ++ ncbi-seg sequence.na 21 1.4 1.6 + +=head1 EXAMPLES + @@ -217,7 +215,7 @@ + +The command line: + -+ seg __docdir__/examples/prion.fa ++ ncbi-seg __docdir__/examples/prion.fa + +gives the standard output below + @@ -246,7 +244,7 @@ + +The command line: + -+ seg __docdir__/examples/prion.fa -x ++ ncbi-seg __docdir__/examples/prion.fa -x + +gives the following FASTA-formatted file:- + @@ -298,10 +296,8 @@ +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 +--- a/seg.doc ++++ b/seg.doc @@ -13,12 +13,12 @@ seg sequence [ W ] [ K(1) ] [ K(2) ] [ -x ] [ options ] Modified: trunk/packages/seg/trunk/debian/rules =================================================================== --- trunk/packages/seg/trunk/debian/rules 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/rules 2012-07-05 13:55:25 UTC (rev 11573) @@ -6,8 +6,8 @@ export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -ver := $(shell dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d- -f1 ) -pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') +ver := 0.0.20000620 +pkg := ncbi-seg .PHONY: get-orig-source get-orig-source: Deleted: trunk/packages/seg/trunk/debian/seg.examples =================================================================== --- trunk/packages/seg/trunk/debian/seg.examples 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/seg.examples 2012-07-05 13:55:25 UTC (rev 11573) @@ -1 +0,0 @@ -prion.fa Deleted: trunk/packages/seg/trunk/debian/seg.install =================================================================== --- trunk/packages/seg/trunk/debian/seg.install 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/seg.install 2012-07-05 13:55:25 UTC (rev 11573) @@ -1,2 +0,0 @@ -usr/bin -usr/share Modified: trunk/packages/seg/trunk/debian/upstream =================================================================== --- trunk/packages/seg/trunk/debian/upstream 2012-07-05 11:24:46 UTC (rev 11572) +++ trunk/packages/seg/trunk/debian/upstream 2012-07-05 13:55:25 UTC (rev 11573) @@ -1,4 +1,4 @@ -Name: seg +Name: ncbi-seg Reference: Author: John C. Wootton and Scott Federhen Title: 'Statistics of local complexity in amino acid sequences and sequence databases.' _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
