diff detrprok_scripts/colorGff.pl @ 0:a53eb951b164 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/detrprok_scripts/colorGff.pl	Mon Mar 25 05:39:29 2013 -0400
@@ -0,0 +1,69 @@
+#!/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);