[med-svn] r8319 - in trunk/packages/coils/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Oct 27 16:47:34 UTC 2011
Author: lkajan-guest
Date: 2011-10-27 16:47:34 +0000 (Thu, 27 Oct 2011)
New Revision: 8319
Added:
trunk/packages/coils/trunk/debian/patches/coils-wrap
Removed:
trunk/packages/coils/trunk/debian/patches/xyz.diff
Modified:
trunk/packages/coils/trunk/debian/README.source
trunk/packages/coils/trunk/debian/changelog
trunk/packages/coils/trunk/debian/control
trunk/packages/coils/trunk/debian/copyright
trunk/packages/coils/trunk/debian/patches/series
trunk/packages/coils/trunk/debian/rules
trunk/packages/coils/trunk/debian/upstream-metadata.yaml
Log:
2002-3: perl script coils-wrap.pl moved from doc to /usr/bin as 'coils-wrap'; improved man pages; updated upstream URL; removed requirement to define COILSDIR env var
Modified: trunk/packages/coils/trunk/debian/README.source
===================================================================
--- trunk/packages/coils/trunk/debian/README.source 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/README.source 2011-10-27 16:47:34 UTC (rev 8319)
@@ -1,6 +1,17 @@
coils for Debian
================
+coils-wrap.patch
+----------------
+* coils-wrap now uses Getopt::Long
+* coils-wrap now also writes out raw prediction
+* coils-wrap input file format recognition improved
+* ncoils.c does not require the env var COILSDIR defined any more
+* -max_seq_len is not a cmd line argument any more
+* added coils-wrap.pod and ncoils.pod
+
+strcpy.patch
+------------
The source is left untouched, except for
* the removal of the ncoils-linux binary.
* some compiler warnings
Modified: trunk/packages/coils/trunk/debian/changelog
===================================================================
--- trunk/packages/coils/trunk/debian/changelog 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/changelog 2011-10-27 16:47:34 UTC (rev 8319)
@@ -1,3 +1,12 @@
+coils (2002-3) unstable; urgency=low
+
+ * perl script coils-wrap.pl moved from doc to /usr/bin as 'coils-wrap'
+ * improved man pages
+ * updated upstream URL
+ * removed requirement to define COILSDIR env var
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 27 Oct 2011 12:25:48 +0200
+
coils (2002-2) unstable; urgency=low
* debian/control:
Modified: trunk/packages/coils/trunk/debian/control
===================================================================
--- trunk/packages/coils/trunk/debian/control 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/control 2011-10-27 16:47:34 UTC (rev 8319)
@@ -4,9 +4,10 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7)
-Standards-Version: 3.9.1
+ Andreas Tille <tille at debian.org>,
+ Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 7), perl
+Standards-Version: 3.9.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/coils/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/coils/trunk/
Homepage: http://www.russelllab.org/coils/
@@ -14,7 +15,7 @@
Package: ncoils
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggested: gnuplot
+Suggests: gnuplot
Description: coiled coil secondary structure prediction
The program predicts the coiled coil secondary structure predictions
from protein sequences. The algorithm was published in
Modified: trunk/packages/coils/trunk/debian/copyright
===================================================================
--- trunk/packages/coils/trunk/debian/copyright 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/copyright 2011-10-27 16:47:34 UTC (rev 8319)
@@ -2,7 +2,7 @@
on Wed Mar 16 23:57:06 CET 2005, saved by Andreas Tille and is now
being completed again by Steffen.
-It was downloaded from <http://www.russell.embl-heidelberg.de/coils/coils.tar.gz>
+It was downloaded from <http://www.russelllab.org/coils/coils.tar.gz>
Copyright: (C) 2002 Robert B. Russel and its employing institute, the
EMBL - European Molecular Biology Lab
Added: trunk/packages/coils/trunk/debian/patches/coils-wrap
===================================================================
--- trunk/packages/coils/trunk/debian/patches/coils-wrap (rev 0)
+++ trunk/packages/coils/trunk/debian/patches/coils-wrap 2011-10-27 16:47:34 UTC (rev 8319)
@@ -0,0 +1,700 @@
+Index: coils-2002/coils-wrap.pl
+===================================================================
+--- coils-2002.orig/coils-wrap.pl 2011-10-27 18:35:51.000000000 +0200
++++ coils-2002/coils-wrap.pl 2011-10-27 18:41:40.855278169 +0200
+@@ -1,6 +1,8 @@
+-#!/usr/local/bin/perl
+-
++#!/usr/bin/perl -w
+ $|=1;
++use Carp qw| cluck :DEFAULT |;
++use Getopt::Long;
++use File::Temp qw||;
+
+
+ # Runs coils multiply to give you a three-window output
+@@ -9,42 +11,75 @@
+ # You may need to change these, in addition
+ # to the "/usr/local/bin/perl" above if necessary
+ #
+-$ENV{"COILSDIR"} = "/data/ATG/coils/";
+-$coils_root = "/data/ATG/coils/";
+-$coils_exec = "/apps/ATG/bin/coils";
++#$ENV{"COILSDIR"} = "__MAKE_PREFIX__/usr/share/coiledcoils";
++$coils_root = "__pkgdatadir__";
++$coils_exec = "ncoils";
+
+-$tmpdir = "/tmp/";
++$tmpdir = File::Temp::tempdir( CLEANUP => 1 );
+
+ undef($in_seq);
+ undef($id);
+ $mode = "threewin";
+ $weighted = "";
+ $matrix = "MTK";
+-$win = "21";
++#$win = "21";
+ $extra = "";
+
+-for($i=0; $i<=$#ARGV; ++$i) {
+- if($ARGV[$i] eq "-m") { # matrix file
+- if(($i+1)>($#ARGV)) { exit_error(); }
+- $matrix = uc($ARGV[$i+1]);
+- $i++;
+- } elsif($ARGV[$i] eq "-w") { # matrix file
+- $weighted = " -w ";
+- } elsif(!defined($fastafile)) {
+- $fastafile = $ARGV[$i];
+- } else {
+- exit_error();
+- }
++$nameScr = $0;
++$nameScr =~ s/.*\///g;
++
++$Lok = GetOptions ("m=s" => \$matrix,
++ "w!" => \$opt_weight,
++ "i=s" => \$fastafile,
++ "o=s" => \$outfile,
++ "r=s" => \$fileRaw,
++ "debug!" => \$dbg
++ #'help' => \$opt_help);
++ );
++
++
++if ( ! $Lok ) {
++ print STDERR
++ "Invalid arguments found, -h or --help for help\n",
++ "Usage: $nameScr [options] -i fastafile -o out_file -r raw_file\n",
++ " -m [matrix type] set matrix (MTK or MTIDK)\n",
++ " -w weight a&d = b,c,e,f&g\n",
++ "Try $nameScr --help for more information\n";
++
++ exit(1);
++}
++
++
++if ( ! $fastafile or ! $outfile ) {
++ print STDERR
++ "Usage: $nameScr [options] -i fastafile -o out_file -r raw_file\n",
++ " -m [matrix type] set matrix (MTK or MTIDK)\n",
++ " -w weight a&d = b,c,e,f&g\n",
++ "Try $nameScr --help for more information\n";
++ exit(1);
++}
++
++if ( ! -f $fastafile ) {
++ print STDERR
++ "input file '$fastafile' not found, exiting..\n";
++ exit(1);
++}
++
++$fileRaw = $outfile."_raw" if ( ! defined $fileRaw );
++
++$matrix = uc($matrix);
++if ( $opt_weight ) {
++ $weighted = " -w ";
+ }
+
+ sub exit_error {
+- print STDERR "coils-wrap.pl [options] [fasta file]\n";
++ print STDERR "coils-wrap.pl [options] [fasta file] [output file]\n";
+ print STDERR " -m [matrix type] set matrix (MTK or MTIDK)\n";
+ print STDERR " -w weight a&d = b,c,e,f&g\n";
+ exit;
+ }
+
+- at data = read_align($fastafile,$type);
++ at data = read_align($fastafile,\$type);
+ if($type ne "f") {
+ die "Error file must be in FASTA format\n";
+ }
+@@ -61,14 +96,14 @@
+
+ $seqs = get_afasta(@data);
+
+-print "What should appear below is the result of running COILS three \n";
+-print "times with windows of 14,21 & 28.\n`frame' denotes the predicted \n";
+-print "position of the heptad repeat for the highest scoring window that \n";
+-print "overlaps each position.\n`prob' gives a single integer value \n";
+-print "representation of P (where 0-9 covers the range 0.0-1.0)\n";
+-print "This will be repeated for each sequence \n\n\n";
++#print "What should appear below is the result of running COILS three \n";
++#print "times with windows of 14,21 & 28.\n`frame' denotes the predicted \n";
++#print "position of the heptad repeat for the highest scoring window that \n";
++#print "overlaps each position.\n`prob' gives a single integer value \n";
++#print "representation of P (where 0-9 covers the range 0.0-1.0)\n";
++#print "This will be repeated for each sequence \n\n\n";
+
+-print "A total of $seqs->{nseq} sequences found in $seqfile\n\n\n";
++#print "A total of $seqs->{nseq} sequences found in $seqfile\n\n\n";
+ for($n=0; $n<$seqs->{nseq}; ++$n) {
+ $id = $seqs->{list}[$n];
+ $in_seq = $seqs->{ids}{$id}{seq};
+@@ -76,7 +111,8 @@
+ # print "ID $id seq $seq\n";
+
+ &write_fasta($seqfile,$id,$in_seq);
+-
++ @result = ();
++ push @result, ">$id\n\n";
+ if($mode eq "threewin") {
+ # Runs threewin style mode
+ # Three windows 14,21,28
+@@ -94,7 +130,10 @@
+ for($i=14; $i<=28; $i+=7) {
+ $j=($i-14)/7;
+ $command = $coils_exec . $extra . " -win " . $i . " < " . $seqfile;
+-# print "Command is $command\n";
++ if ( $i == 28 ) {
++ open (RAW,">$fileRaw") or die "cannot write to $fileRaw:$!";
++ }
++ if($dbg){ cluck("Command is $command"); }
+ open(IN,"$command|");
+
+ $fid = "frame-" . $i;
+@@ -107,7 +146,18 @@
+
+ $p=0;
+ while(<IN>) {
+- if(!/sequences/) {
++ if ( $i == 28 ) { # print the raw file if window is 28
++ print RAW $_;
++ }
++ if ( /^\#/ ) {
++ chomp($result = $_);
++ $result =~ s/.*aas//;
++ $result =~ s/in coil\s*//g;
++ $result = "window size = $i ".$result." residues in coiled coil".
++ " domain\n";
++ push @result, $result;
++ next;
++ } else {
+ $_ =~ s/^ *//;
+ @t=split(/ +/);
+ $align->{ids}{$fid}{seq} .= $t[2];
+@@ -118,18 +168,22 @@
+ else { $sP = substr($P,0,1); }
+ if($sP eq "0") { $sP = "-"; }
+ $align->{ids}{$pid}{seq} .= $sP;
+- } else {
+- print;
+ }
+ }
+ close(IN);
+ }
+- write_clustal($align,"-");
+- }
+-}
+-#unlink $seqfile;
++
++
++ if ( defined($outfile)) { # Write output to file
++ write_clustal($align,\@result, $outfile);
++ } else {
++ write_clustal($align,\@result, "-");
++ }
++ }
++}
++unlink $seqfile;
+
+-exit;
++exit(0);
+
+ sub write_fasta {
+ my($fn,$id,$seq) = @_;
+@@ -139,7 +193,7 @@
+ while($i<length($seq)) {
+ $aa = substr($seq,$i,1);
+ print SEQ $aa;
+- if((($i+1)%60)==0){ print SEQ "\n" }
++ if((($i+1)%50)==0){ print SEQ "\n" }
+ $i++;
+ }
+ print SEQ "\n";
+@@ -150,12 +204,14 @@
+ my($align) = $_[0];
+ my($i,$j,$k,$id);
+
+- my($outfile) = $_[1];
++ my($header)= $_[1];
++ my($outfile) = $_[2];
+ open(OUT,">$outfile") || die "Error opening output file $outfile\n";
+
+-
+-
+ # print OUT "CLUSTAL W(1.60) multiple sequence alignment\n\n";
++
++ print OUT @$header;
++ print OUT "\n";
+
+ foreach $id (keys %{$align->{ids}}) {
+ if(defined($align->{ids}{$id}{start})) {
+@@ -164,24 +220,44 @@
+ $align->{ids}{$id}{newid} .= $align->{ids}{$id}{ranges};
+ }
+ } else {
+- $align->{ids}{$id}{newid} = $id;
+- }
+- }
+- $i=0;
+- while($i<$align->{alen}) {
+- for($k=0; $k<$align->{nseq}; ++$k) {
+- $id = $align->{list}[$k];
+- printf(OUT "%-10s ",$align->{ids}{$id}{newid});
+- for($j=0; $j<60; ++$j) {
+- last if(($i+$j)>=$align->{alen});
+- print OUT substr($align->{ids}{$id}{seq},($i+$j),1);
+- }
+- printf(OUT "\n");
+- }
+- $i+=60;
+- printf(OUT "\n");
++ if ( $id !~ /frame/ and $id !~ /prob/) {
++ $align->{ids}{$id}{newid} = "seq";
++ } else {
++ $align->{ids}{$id}{newid} = $id;
++ }
++ } #
++ }
++ #
++ $i=0;
++
++ while($i<$align->{alen}) {
++ printf OUT "%-10s ", ' ';
++ for ($z = 1; $z <=50; $z++) {
++ if ($z == 50) {
++ print OUT ($i+50)/10 ;
++ } elsif ($z % 10 == 0) {
++ print OUT ":";
++ } elsif ($z % 5 == 0) {
++ print OUT ".";
++ } else {
++ print OUT " ";
++ }
++ }
++ print OUT "\n";
++
++ for($k=0; $k<$align->{nseq}; ++$k) {
++ $id = $align->{list}[$k];
++ printf(OUT "%-10s ",$align->{ids}{$id}{newid});
++ for($j=0; $j<50; ++$j) {
++ last if(($i+$j)>=$align->{alen});
++ print OUT substr($align->{ids}{$id}{seq},($i+$j),1);
++ }
++ print OUT "\n";
++ }
++ $i+=50;
+ }
+- close(OUT);
++ print OUT "// End\n\n";
++ close OUT;
+ }
+
+ sub get_afasta {
+@@ -222,7 +298,7 @@
+ if(defined($align->{ids}{$label})) {
+ $_ =~ s/-/ /g;
+ $align->{ids}{$label}{seq} .= $_;
+- print "Adding $_ to $label\n";
++# print "Adding $_ to $label\n";
+ }
+ }
+ }
+@@ -233,6 +309,7 @@
+ }
+
+ sub read_align { # Just read in text and modify format if necessary
++ #( $fastafile, \$type )
+
+ #
+ # Likely format is determined by looking for signs of one format over another
+@@ -255,7 +332,7 @@
+ my($file) = $_[0];
+ my(@data);
+ my($i,$type);
+- my($winner,$highest);
++ my($winner,$highest) = ('x', 0);
+
+ @data=();
+
+@@ -268,18 +345,19 @@
+
+ for($i=0; $i<=$#data; ++$i) {
+ $_ = $data[$i];
+- if(($i==0) && ($_ =~ / *[0-9]+ +[0-9]+ */)) { $votes{"y"}+=1000; }
++ if( $file =~ /\.fa(sta)?$/oi ){ $votes{"f"}+=1000; last; }
++ elsif(($i==0) && ($_ =~ / *[0-9]+ +[0-9]+ */)) { $votes{"y"}+=1000; }
++ elsif(($i==0) && ($_ =~ /^>/o) && $data[1] && $data[1] =~ /^[a-z]/io ) { $votes{"f"}+=10; }
+ elsif(($_ =~ /^ *Name:/) || ($_ =~ /pileUp/) || ($_ =~ /MSF.*Check.*\.\./)) { $votes{"m"}++; last; }
+ elsif($_ =~ /^CLUSTAL/) { $votes{"c"}+=10; last; }
+ elsif($_ =~ /^>P1;/) { $votes{"p"}+=10; last; }
+- elsif($_ =~ /HMMER/) { $votes{"h"}+=10; last; }
++ elsif($_ =~ /HMMER/o && $data[0] !~ /^>/o) { $votes{"h"}+=10; last; }
+ elsif(($_ =~ /^#=SQ/) || ($_ =~ /^#=RF/)) { $votes{"h"}++; }
+ elsif($_ =~ /^>/) { $votes{"f"}++; $votes{"b"}++; }
+ elsif($_ =~ /^ *\* iteration [0-9]*/) { $votes{"b"}++; $block_start++; }
+ elsif($_ =~ /^ *\*/) { $votes{"b"}++; $block_end++; }
+ elsif(($_ =~ /^ID /) || ($_ =~ /^CC /) || ($_ =~ /^AC /) || ($_ =~ /^SE /)) { $votes{"s"}++; }
+ elsif(($_ =~ /^HSSP .*HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS/)) { $votes{"e"}+=1000; }
+-
+ }
+
+ # Block and FASTA are quite hard to tell apart in a quick parse,
+@@ -289,14 +367,12 @@
+ if($block_end==0) { $votes{"f"}++; }
+ }
+
+- $winner = "x";
+- $highest = 0;
+ foreach $type (keys %votes) {
+ # print $type," ", $votes{$type},"\n";
+ if($votes{$type}>$highest) { $winner = $type; $highest = $votes{$type}; }
+ }
+-# print "File is apparently of type $winner\n";
+- $_[1] = $winner;
++ if( $dbg ){ warn( "File is apparently of type $winner" ); }
++ ${$_[1]} = $winner;
+ return @data;
+ }
+ sub get_print_string {
+@@ -311,3 +387,5 @@
+ }
+ return $max_len;
+ }
++
++# vim:et:ai:
+Index: coils-2002/ncoils.c
+===================================================================
+--- coils-2002.orig/ncoils.c 2011-10-27 18:41:40.839278175 +0200
++++ coils-2002/ncoils.c 2011-10-27 18:41:40.855278169 +0200
+@@ -1,4 +1,5 @@
+ #include <ncoils.h>
++#include <string.h>
+
+ /* Copyright (c) 2002 Robert B. Russell
+ * EMBL, Meyerhofstrasse 1, 69917 Heidelberg, Germany
+@@ -22,16 +23,19 @@
+
+
+ /* Rob Russell's attempt to make a COILS program */
++#ifndef __PKGDATADIR__
++#define __PKGDATADIR__ ""
++#endif
+
+-main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+
+- int i,j,k,l;
++ int i,j;
+ int verb;
+ int window,pt;
+ int which,weighted;
+ int nseq;
+ int t,tc;
+- int seqlen;
++ int seqlen = 0;
+ int mode;
+ int min_seg;
+
+@@ -39,7 +43,8 @@
+ char heptfile[HEPTFILELENGTH];
+ char *buff;
+ static char *env;
+- char *seq,*title,*ident;
++ char *seq = NULL;
++ char *title,*ident;
+
+ float min_P;
+
+@@ -55,10 +60,10 @@
+ mode = 0; /* 0 = column mode, 1 = fasta, 2 = concise */
+ min_P = 0.5;
+
+- if((env=getenv("COILSDIR"))==NULL) {
++ if((env=getenv("COILSDIR"))==NULL) env = __PKGDATADIR__;
++
++ if( env[0] == 0 ){ // empty string
+ fprintf(stderr,"error: environment variable COILSDIR must be set\n");
+- fprintf(stderr," Assuming /usr/share/ncoils\n");
+- env=strdup("/usr/share/ncoils"); // a little leak, tolerated as singleton
+ exit(-1);
+ }
+
+@@ -67,19 +72,19 @@
+
+
+ for(i=1; i<argc; ++i) {
+- if(argv[i][0]!='-') exit_error();
++ if(argv[i][0]!='-') exit_error( env );
+ if(strcmp(&argv[i][1],"m")==0) {
+- if((i+1)>=argc) exit_error();
++ if((i+1)>=argc) exit_error( env );
+ strncpy(&heptfile[0],argv[i+1],HEPTFILELENGTH-1);
+ i++;
+ } else if(strcmp(&argv[i][1],"win")==0) {
+- if((i+1)>=argc) exit_error();
++ if((i+1)>=argc) exit_error( env );
+ sscanf(argv[i+1],"%d",&window);
+ i++;
+ } else if(strcmp(&argv[i][1],"c")==0) {
+ mode=2;
+ } else if(strcmp(&argv[i][1],"min_seg")==0) {
+- if((i+1)>=argc) exit_error();
++ if((i+1)>=argc) exit_error( env );
+ sscanf(argv[i+1],"%d",&min_seg);
+ i++;
+ } else if(strcmp(&argv[i][1],"c")==0) {
+@@ -87,18 +92,18 @@
+ } else if((strcmp(&argv[i][1],"f")==0) || (strcmp(&argv[i][1],"fasta")==0)) {
+ mode=1;
+ } else if((strcmp(&argv[i][1],"min_P")==0)) {
+- if((i+1)>=argc) exit_error();
++ if((i+1)>=argc) exit_error( env );
+ sscanf(argv[i+1],"%f",&min_P);
+ i++;
+ } else if(strcmp(&argv[i][1],"help")==0) {
+- exit_error();
++ exit_error( env );
+ } else if(strcmp(&argv[i][1],"w")==0) {
+ weighted=1;
+ } else if(strcmp(&argv[i][1],"V")==0 || strcmp(&argv[i][1],"v")==0) {
+ verb=1;
+ } else {
+ fprintf(stderr," can't understand flag/field %s\n",argv[i]);
+- exit_error();
++ exit_error( env );
+ }
+ }
+
+@@ -175,14 +180,14 @@
+ pred_coils(seq,ident,title,h,window,which,weighted,mode,min_P,&t,&tc,min_seg);
+ free(seq);
+ }
+- fprintf(stderr,"%8d sequences %8d aas %8d in coil\n",nseq,t,tc);
++ if( verb ) fprintf(stderr,"%8d sequences %8d aas %8d in coil\n",nseq,t,tc);
+ free(title); free(ident);
+
+ exit(0);
+
+ }
+
+-void exit_error() {
++void exit_error( const char* __coilsdir ) {
+ fprintf(stderr,"format: ncoils [options] < [sequence file]\n");
+ fprintf(stderr," -f or -fasta [fasta output - coils as 'x', like '-x' in seg]\n");
+ fprintf(stderr," -c [concise mode - which sequences have any coils (and how many)]\n");
+@@ -191,7 +196,7 @@
+ fprintf(stderr," -win <int> [window size; DEFAULT = 21]\n");
+ fprintf(stderr," -w [weight heptad positions a&d the same as b,c,e,f,g]\n");
+ fprintf(stderr," -v [verbose/debug mode - print extra junk]\n");
+- fprintf(stderr," -max_seq_len <int> [longest sequence tolerated; DEFAULT = 100 000]\n");
++ fprintf(stderr,"Effective COILSDIR: %s\n", __coilsdir );
+ fprintf(stderr,"\n");
+ fprintf(stderr,"NCOILS, Rob Russell and Andrei Lupas, 1999\n");
+ fprintf(stderr," based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164\n");
+@@ -206,7 +211,6 @@
+
+ int i,j;
+ int len,pos,aa_pt;
+- int pt;
+ int total_coil_segments;
+ int are_there_coils;
+
+Index: coils-2002/coils-wrap.pod
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ coils-2002/coils-wrap.pod 2011-10-27 18:41:40.855278169 +0200
+@@ -0,0 +1,77 @@
++=head1 NAME
++
++coils-wrap - runs ncoils three times to give you a three-window output
++
++=head1 SYNOPSIS
++
++coils-wrap [OPTION]
++
++=head1 DESCRIPTION
++
++coils-wrap runs ncoils three times to give you a three-window output.
++
++ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
++
++=head1 OPTIONS
++
++=over
++
++=item -i
++
++input file in FASTA format
++
++=item -o
++
++output file
++
++=item -r
++
++raw output file, default: `<output file>_raw'
++
++=item -m
++
++matrix type; set matrix (MTK or MTIDK)
++
++=item -w
++
++weight a&d = b,c,e,f&g (boolean)
++
++=back
++
++=head1 EXAMPLES
++
++C<coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out -r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt>
++
++C<ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa>
++
++=head1 FILES
++
++=over
++
++=item F</usr/share/coiledcoils/*.mat>
++
++matrix data files
++
++=back
++
++=head1 AUTHOR
++
++R.B. Russell, A.N. Lupas, 1999
++
++=head1 COPYRIGHT AND LICENSE
++
++GPL
++
++Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164
++
++=head1 SEE ALSO
++
++L<ncoils(1)>, L</usr/share/doc/coils/README>, L<http://www.russelllab.org/cgi-bin/coils/coils-svr.pl>
++
++=over
++
++=item A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
++
++=item A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991
++
++=back
+Index: coils-2002/ncoils.pod
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ coils-2002/ncoils.pod 2011-10-27 18:41:40.855278169 +0200
+@@ -0,0 +1,89 @@
++=head1 NAME
++
++ncoils - prediction of coiled-coil secondary structure elements
++
++=head1 SYNOPSIS
++
++ncoils [OPTION] < [FASTA FILE]
++
++ncoils -f < /usr/share/doc/ncoils/1srya.fa
++
++=head1 DESCRIPTION
++
++ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
++
++=head1 OPTIONS
++
++=over
++
++=item -f, -fasta
++
++fasta output - coils as 'x', like '-x' in seg
++
++=item -c
++
++concise mode - which sequences have any coils (and how many)
++
++=item -min_seg <int>
++
++for concise mode - only report sequence if >= min coil segments
++
++=item -min_P <float>
++
++minimum P to define coil segment; DEFAULT = 0.5
++
++=item -win <int>
++
++window size; DEFAULT = 21
++
++=item -w
++
++weight heptad positions a&d the same as b,c,e,f,g
++
++=item -v
++
++verbose/debug mode - print extra junk
++
++=back
++
++=head1 EXAMPLES
++
++C<coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out -r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt>
++
++C<ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa>
++
++=head1 ENVIRONMENT
++
++COILSDIR - specifies the directory containing the file new.mat overriding the default F</usr/share/ncoils>
++
++=head1 FILES
++
++=over
++
++=item F</usr/share/ncoils/*.mat>
++
++matrix data files
++
++=back
++
++=head1 AUTHOR
++
++R.B. Russell, A.N. Lupas
++
++=head1 COPYRIGHT AND LICENSE
++
++GPL
++
++Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164
++
++=head1 SEE ALSO
++
++L<coils-wrap(1)>, L</usr/share/doc/coils/README>, L<http://www.russelllab.org/cgi-bin/coils/coils-svr.pl>
++
++=over
++
++=item A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
++
++=item A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991
++
++=back
+Index: coils-2002/ncoils.h
+===================================================================
+--- coils-2002.orig/ncoils.h 2011-10-27 18:41:40.839278175 +0200
++++ coils-2002/ncoils.h 2011-10-27 18:42:51.463283288 +0200
+@@ -1,7 +1,6 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <math.h>
+-#include <string.h>
+
+ #define AAs "A_CDEFGHI_KLMN_PQRST_VW_Y_"
+ #define PI 3.1415
+Index: coils-2002/read_matrix.c
+===================================================================
+--- coils-2002.orig/read_matrix.c 2002-08-22 18:47:34.000000000 +0200
++++ coils-2002/read_matrix.c 2011-10-27 18:42:59.403284487 +0200
+@@ -1,4 +1,5 @@
+ #include <ncoils.h>
++#include <string.h>
+
+ /* Copyright (c) 2002 Robert B. Russell
+ * EMBL, Meyerhofstrasse 1, 69917 Heidelberg, Germany
Modified: trunk/packages/coils/trunk/debian/patches/series
===================================================================
--- trunk/packages/coils/trunk/debian/patches/series 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/patches/series 2011-10-27 16:47:34 UTC (rev 8319)
@@ -1 +1,2 @@
strcpy.patch
+coils-wrap
Deleted: trunk/packages/coils/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/coils/trunk/debian/patches/xyz.diff 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/patches/xyz.diff 2011-10-27 16:47:34 UTC (rev 8319)
@@ -1,68 +0,0 @@
---- coils-2002.orig/ncoils.h
-+++ coils-2002/ncoils.h
-@@ -1,5 +1,6 @@
- #include <stdio.h>
- #include <stdlib.h>
-+#include <string.h>
- #include <math.h>
-
- #define AAs "A_CDEFGHI_KLMN_PQRST_VW_Y_"
---- coils-2002.orig/ncoils.c
-+++ coils-2002/ncoils.c
-@@ -23,7 +23,7 @@
-
- /* Rob Russell's attempt to make a COILS program */
-
--main(int argc, char *argv[]) {
-+int main(int argc, char *argv[]) {
-
- int i,j,k,l;
- int verb;
-@@ -31,14 +31,16 @@
- int which,weighted;
- int nseq;
- int t,tc;
-- int seqlen;
-+ int seqlen=0;
- int mode;
- int min_seg;
-
- char heptfile[1000];
- char *buff;
- static char *env;
-- char *seq,*title,*ident;
-+ char *seq =(char *) NULL,
-+ *title=(char *) NULL,
-+ *ident=(char *) NULL;
-
- float min_P;
-
-@@ -55,13 +57,13 @@
- min_P = 0.5;
-
- if((env=getenv("COILSDIR"))==NULL) {
-- fprintf(stderr,"error: environment variable COILSDIR must be set\n");
-- exit(-1);
-+ fprintf(stderr,"warning: environment variable COILSDIR not set, assuming /usr/share/ncoils/\n");
-+ strcpy(heptfile,"/usr/share/ncoils/new.mat");
-+ } else {
-+ strncpy(&heptfile[0],env,990);
-+ strcpy(&heptfile[strlen(heptfile)],"/new.mat");
- }
-
-- strcpy(&heptfile[0],env);
-- strcpy(&heptfile[strlen(heptfile)],"/new.mat");
--
-
- for(i=1; i<argc; ++i) {
- if(argv[i][0]!='-') exit_error();
-@@ -171,8 +173,7 @@
- fprintf(stderr,"%8d sequences %8d aas %8d in coil\n",nseq,t,tc);
- free(title); free(ident);
-
-- exit(0);
--
-+ return(0);
- }
-
- void exit_error() {
Modified: trunk/packages/coils/trunk/debian/rules
===================================================================
--- trunk/packages/coils/trunk/debian/rules 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/rules 2011-10-27 16:47:34 UTC (rev 8319)
@@ -20,13 +20,22 @@
CFLAGS += -O2
endif
-build: build-stamp
+VERSION=2002
-build-stamp:
+build: build-arch build-indep
+
+build-indep:
+
+build-arch: build-stamp
+
+%.1 : %.pod
+ pod2man -c 'User Commands' -r "$(VERSION)" $< $@
+
+build-stamp: ncoils.1 coils-wrap.1
dh_testdir
# Add here commands to compile the package.
- $(CC) $(CFLAGS) -I. -o ncoils ncoils.c read_matrix.c -lm
+ $(CC) $(CFLAGS) -I. -o ncoils ncoils.c read_matrix.c -lm -D__PKGDATADIR__=\"/usr/share/ncoils\"
touch build-stamp
@@ -36,7 +45,7 @@
rm -f build-stamp configure-stamp
# Add here commands to clean up after the build process.
- dh_clean ncoils
+ dh_clean ncoils ncoils.1 coils-wrap.1
install: build
dh_testdir
@@ -46,6 +55,7 @@
# Add here commands to install the package into debian/ncoils.
cp ncoils $(CURDIR)/debian/ncoils/usr/bin/
+ cp coils-wrap.pl $(CURDIR)/debian/ncoils/usr/bin/coils-wrap && sed -i -e 's|__pkgdatadir__|/usr/share/ncoils|g' $(CURDIR)/debian/ncoils/usr/bin/coils-wrap
cp *.mat $(CURDIR)/debian/ncoils/usr/share/ncoils/
# Build architecture-independent files here.
@@ -57,8 +67,8 @@
dh_testdir
dh_testroot
dh_installchangelogs
- dh_installdocs 1srya.fa *.pl
- dh_installman debian/ncoils.1
+ dh_installdocs 1srya.fa
+ dh_installman ncoils.1 coils-wrap.1
dh_link
dh_strip
dh_compress
@@ -69,15 +79,14 @@
dh_md5sums
dh_builddeb
-version=2002
d="../coils.upstream.tar.gz"
get-orig-source:
echo "Downloading to $(d)." ; \
- wget -O "$(d)" http://www.russell.embl-heidelberg.de/coils/coils.tar.gz ; \
+ wget -O "$(d)" http://www.russelllab.org/coils/coils.tar.gz ; \
cd `dirname $(d)` ; tar --exclude ncoils-linux -xzf `basename $(d)`
- cd `dirname $(d)` ; mv coils coils-$(version)
- cd `dirname $(d)` ; tar --exclude ncoils-linux -czvf coils_$(version).orig.tar.gz coils-$(version)
+ cd `dirname $(d)` ; mv coils coils-$(VERSION)
+ cd `dirname $(d)` ; tar --exclude ncoils-linux -czvf coils_$(VERSION).orig.tar.gz coils-$(VERSION)
binary: binary-indep binary-arch
.PHONY: build clean binary-indep binary-arch binary install configure
Modified: trunk/packages/coils/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/coils/trunk/debian/upstream-metadata.yaml 2011-10-27 15:38:14 UTC (rev 8318)
+++ trunk/packages/coils/trunk/debian/upstream-metadata.yaml 2011-10-27 16:47:34 UTC (rev 8319)
@@ -1,9 +1,9 @@
-Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
+Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl
Name: Coils
PMID: 2031185
Reference:
Author: A. Lupas, M. Van Dyke, and J. Stock
- Title: Predicting coiled coils from protein sequences Science
+ Title: Predicting coiled coils from protein sequences
Journal: Science
Volume: 252
Pages: 1162-1164
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