--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyMotif.pl	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,41 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+
+my %opt;
+
+
+GetOptions(\%opt, "f=s","version","gtf=s","range=i","overlap=i","--annotation=s", "--tab=s","--k_min=i","--k_max=i","--numberofkmers=i","--count=s","--features=s","--zscores=s","--random=s","options","o=s","id=s");
+
+my $cmnd;
+
+my $prefix = "m_$opt{id}";
+
+
+if (exists $opt{version}){
+	$cmnd = "python /usr/local/bin/pyMotif.py --version";
+}
+else{
+	$cmnd = "python /usr/local/bin/pyMotif.py -f $opt{f} --gtf $opt{gtf} --tab $opt{tab} --annotation $opt{annotation} -o $prefix";
+
+	if(exists $opt{options}){
+
+	    $cmnd .= " --range=$opt{range} --overlap=$opt{overlap} --k_min=$opt{k_min} --k_max=$opt{k_max} --numberofkmers=$opt{numberofkmers}";
+	}
+}
+
+#testing
+#open (COUNT, ">$opt{count}") || die "";
+#print COUNT "$cmnd";
+
+system $cmnd;
+
+
+system "mv $prefix"."_$opt{annotation}_data_k-mers_count.txt $opt{count}";
+system "mv $prefix"."_$opt{annotation}_top_k-mers_in_features.gtf $opt{features}";
+system "mv $prefix"."_$opt{annotation}_k-mer_Z_scores.txt $opt{zscores}";
+system "mv $prefix"."_$opt{annotation}_random_k-mers_count.txt $opt{random}";
+    
+
+
+