annotate SMART/bacteriaRegulatoryRegion_Detection/colorGff.pl @ 31:0ab839023fe4

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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 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);