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 <[email protected]> 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 <[email protected]> DM-Upload-Allowed: yes Uploaders: Steffen Moeller <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7) -Standards-Version: 3.9.1 + Andreas Tille <[email protected]>, + Laszlo Kajan <[email protected]> +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 ) { ++ $weighted = " -w "; + } + + sub exit_error { +- print STDERR "coils-wrap.pl [options] [fasta file]\n"; ++ print STDERR "coils-wrap.pl [options] [fasta file] [output file]\n"; + print STDERR " -m [matrix type] set matrix (MTK or MTIDK)\n"; + print STDERR " -w weight a&d = b,c,e,f&g\n"; + exit; + } + +-@data = read_align($fastafile,$type); ++@data = read_align($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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
