--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyGTF2bedGraph.pl	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+
+my %opt;
+
+
+GetOptions(\%opt, "gtf=s","po=s","version","mo=s","count=i","chromfile=s","t=s","iCLIP","track","name=s","description=s","color=s","s=s","id=s");
+
+my $cmnd;
+my $prefix = "gb_$opt{id}";
+$prefix =~ s/\s/_/g;
+
+
+if (exists $opt{version}){
+	$cmnd = "python /usr/local/bin/pyGTF2bedGraph.py --version";
+}
+else{
+	$cmnd = "python /usr/local/bin/pyGTF2bedGraph.py --gtf $opt{gtf} --chromfile $opt{chromfile} -t $opt{t} --count $opt{count} -o $prefix";
+
+	if(exists $opt{iCLIP}){
+
+	    $cmnd .= " --iCLIP";
+	}
+
+	if(exists $opt{track}){
+	    $cmnd .= " --track --name \"$opt{name}\" --description \"$opt{description}\"";
+	    
+	    if(exists $opt{color}){$cmnd .= " --color $opt{color}";}
+            if(exists $opt{s}){$cmnd .= " -s \"$opt{s}\"";}
+	}
+}
+
+system $cmnd;
+
+system "mv $prefix"."_plus_strand.bedgraph $opt{po}";
+system "mv $prefix"."_minus_strand.bedgraph $opt{mo}";
+