--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyBinCollector.pl	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,47 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+
+my %opt=(s=>"genomic",numberofbins=>20);
+
+
+GetOptions(\%opt, "f=s","version","gtf=s","range=i","annotation=s", "numberofbins=i","min_length=i","max_length=i","s=s","o=s","ignorestrand","outputall","sd=s","ssub=s","sdel=s","asd=s","assub=s","asdel=s","out=s","options","bins1=i","bins2=i","id=s");
+
+my $cmnd;
+
+my $prefix = "bc_$opt{id}";
+
+if (exists $opt{version}){
+	$cmnd = "python /usr/local/bin/pyBinCollector.py --version";
+}
+else{
+	$cmnd = "python /usr/local/bin/pyBinCollector.py -f $opt{f} --gtf $opt{gtf} --annotation $opt{annotation} -o $prefix";
+
+	if(exists $opt{outputall})
+	{
+	    $cmnd .= " --outputall";
+	}
+
+	if(exists $opt{options}){
+
+	    $cmnd .= " --range=$opt{range} --numberofbins $opt{numberofbins} --min_length $opt{min_length} --max_length $opt{max_length} -s $opt{s}";
+
+            if(exists $opt{ignorestrand}){ $cmnd .= " --ignorestrand";}
+	    if(exists $opt{bins1}){ $cmnd .= " --binselect $opt{bins1} $opt{bins2}";}
+	}
+}
+
+
+system $cmnd;
+if(exists $opt{outputall}){
+
+    system "mv sense_data_$prefix.txt $opt{sd}";
+    system "mv sense_subs_$prefix.txt $opt{ssub}";
+    system "mv sense_dels_$prefix.txt $opt{sdel}";
+    system "mv anti_sense_data_$prefix.txt $opt{asd}";
+    system "mv anti_sense_subs_$prefix.txt $opt{assub}";
+    system "mv anti_sense_dels_$prefix.txt $opt{asdel}";
+}
+else{
+    system "mv $prefix"."_cumulative_densities_$opt{annotation}"."_$opt{s}_"."$opt{numberofbins}_bins.pileup $opt{out}";
+}