Mercurial > repos > yufei-luo > s_mart
diff SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl @ 31:0ab839023fe4
Uploaded
author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl Tue Apr 30 14:33:21 2013 -0400 @@ -0,0 +1,71 @@ +#!/usr/bin/perl -w +### +# But : ajout ou modif de couleur d'un gff +# +# Entrees : fichier gff +# +# Sortie : gff affiche a l'ecran +# +###------------------------------------------------------ +use vars qw($USAGE); +use strict; + +=head1 NAME + +colorGff.pl - add or change color of a gff file + +=head1 SYNOPSIS + +% colorGff.pl -i file.gff -c color [-h] + +=head1 DESCRIPTION +This script will parse DOOR repport file and write information in gff3 format. + + -i|--input fileName gff input file name + -c|--color RGBcode RGB code for color + -o|--output fileName gff3 output file name + [-h|--help] help mode then die + +=head1 AUTHOR - Claire Toffano-Nioche - jan.11 + +=cut +#----------------------- +my ($fileName, $colourGff, $outFileName) = ("", "", "colorOut.gff3") ; + # command line check + foreach my $num (0 .. $#ARGV) { + SWITCH: for ($ARGV[$num]) { + /--input|-i/ && do { + $fileName=$ARGV[$num+1]; + open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ; + last }; + /--color|-c/ && do { + $colourGff =$ARGV[$num+1]." ".$ARGV[$num+2]." ".$ARGV[$num+3]; + last }; +# /--output|-o/ && do { +# $outFileName=$ARGV[$num+1]; +# last }; + /--help|-h/ && do { exec("pod2text $0\n") ; die }; + } + } +# open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n"; + # informations retrieval + my @lines = <fichierGff> ; + close fichierGff ; + # treatment + #print "gff file read ; number of lines : $#lines\n"; + for (my $i=0 ; $i <= $#lines ; $i++) { + if ($lines[$i] =~ /;/) { + if ($lines[$i] =~ /color=/) { + $lines[$i] =~ s/color=.*;/color=$colourGff;/ ; + } else { # add colour + $lines[$i] =~ s/;/;color=$colourGff;/ ; + } + } else { # (no = gff bug if col9 begin with semi-coma ?) or only one tag : add color tag + chomp($lines[$i]) ; + $lines[$i] .= "; color=".$colourGff.";\n"; + } +# print OUT $lines[$i] ; + print $lines[$i]; + } +# close OUT ; +exit(0);