annotate detrprok_scripts/colorGff.pl @ 0:a53eb951b164 draft

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#!/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 add or replace the 'color' tag of a gff formated file.

    -i|--input fileName  gff input file name
    -c|--color RGBcode   RGB code for color
   [-h|--help]           help mode then die                              

=head1 AUTHOR - Claire Toffano-Nioche - jan.11

=cut
#-----------------------
my ($fileName, $colorGff) = ("", "") ;
   # 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 {
		$colorGff =$ARGV[$num+1]." ".$ARGV[$num+2]." ".$ARGV[$num+3];
		last };
        /--help|-h/ && do { exec("pod2text $0\n") ; die };
        }
    }

    # informations retrieval
    my @lines = <fichierGff> ; 
    close fichierGff ;
    # treatment
	#print "gff file read ; number of lines : $#lines\n";
    for (my $i=0 ; $i <= $#lines ; $i++) {
	if (defined ($lines[$i])) {
	    if (!($lines[$i] =~ m/^\s*$|^#/)) { # skip both null and comment lines
		if ($lines[$i] =~ /;/) {
		   if ($lines[$i] =~ /color=/) { # replace value
	    		$lines[$i] =~ s/color=.*;*/color=$colorGff;/ ;
		   } else { # add color tag and value
	    		$lines[$i] =~ s/;/;color=$colorGff;/ ;
	    	   } 
	        } else { # only one tag so no coma: add color tag
	    	   chomp($lines[$i]) ;
	    	   $lines[$i] .= "; color=".$colorGff.";\n";
	        }
	    }
            print $lines[$i];
        }
    }
exit(0);