--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyReadCounters.pl	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,60 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+
+my %opt;
+
+
+GetOptions(\%opt, "f=s","file_type=s","version","gtf=s","align_quality=i","align_score=i","range=i","length=i","max=i","distance=i","ignorestrand","overlap=i","unique","blocks","mutations=s","countoutput=s","stats=s","hittable=s","intronUTRoverlap=s","discarded=s","options","alignOpt","id=s");
+
+my $cmnd;
+my $prefix = "rc_$opt{id}";
+
+
+if (exists $opt{version}){
+	$cmnd = "python /usr/local/bin/pyReadCounters.py --version";
+}
+else{
+	$cmnd = "python /usr/local/bin/pyReadCounters.py -f $opt{f} --file_type $opt{file_type} --gtf $opt{gtf} -o $prefix";
+
+	if(exists $opt{options}){
+
+	    $cmnd .= " --range=$opt{range} --overlap=$opt{overlap}";
+
+	    if(exists $opt{ignorestrand}){ $cmnd .= " --ignorestrand";}
+	}
+
+	if(exists $opt{alignOpt}){
+	    $cmnd .= " --align_quality=$opt{align_quality} --align_score=$opt{align_score} --length=$opt{length} --distance=$opt{distance}";
+            if(exists $opt{max}){$cmnd .= " --max=$opt{max}";}
+	    if(exists $opt{unique}){$cmnd .= " --unique";}
+            if(exists $opt{blocks}){$cmnd .= " --blocks";}
+            if(exists $opt{mutations}){$cmnd .= " --mutations=$opt{mutations}";}
+            if(exists $opt{discarded}){$cmnd .= " --discarded=$opt{discarded}";}
+
+	}
+}
+
+
+system $cmnd;
+print STDOUT $cmnd;
+
+
+if(exists $opt{blocks}){
+    system "mv $prefix"."_hittable_cDNAs.txt $opt{hittable}";
+    system "mv $prefix"."_file_statistics_cDNAs.txt $opt{stats}";
+    system "mv $prefix"."_intron_and_UTR_overlap_cDNAs.gtf $opt{intronUTRoverlap}";
+    
+    if($opt{file_type} ne "gtf"){
+	system "mv $prefix"."_count_output_cDNAs.gtf $opt{countoutput}";
+    }
+}
+else{
+    system "mv $prefix"."_hittable_reads.txt $opt{hittable}";
+    system "mv $prefix"."_file_statistics_reads.txt $opt{stats}";
+    system "mv $prefix"."_intron_and_UTR_overlap_reads.gtf $opt{intronUTRoverlap}";
+
+    if($opt{file_type} ne "gtf"){
+        system "mv $prefix"."_count_output_reads.gtf $opt{countoutput}";
+    }
+}