--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Tools/CREF/Extract_motif_codes_galaxy.pl	Mon Sep 05 05:53:08 2016 -0400
@@ -0,0 +1,54 @@
+#!/usr/bin/perl -w
+
+# The lines that start with # are comment lines that are not executed
+
+
+$|=1;
+use strict; 
+use warnings;
+
+
+#Script to take output from AME (part of memesuite-org) and extract a
+#list of the overrepresented motifs and print them to a new file
+#called ame-motif-id.list
+
+
+#Checking to see if the user has provided 1 argument - which is the
+#name of the AME results file
+
+if(@ARGV < 2){
+print "\nUsage: Extract_motif_codes.pl ame.txt ame-shorted.txt\n\n";
+exit(0);
+}
+
+#Declaring variables
+my @cols; #an array variable
+my $line; # a scalar varaible
+
+#Using a FIELHANDLE to open the input file
+open (INPUT, "<$ARGV[0]") || 
+   die "File '$ARGV[0]' not found\n" ;
+   
+open (OUTPUT, ">$ARGV[1]") || 
+  die "File '>$ARGV[1]' not found\n" ;
+
+#looping through each line of the file
+ while (<INPUT>){
+   #assigning line to variable $line 
+   #$_ is a special default variable that here holds the line contents
+   $line = $_;
+   #match lines that have Ranksum 
+   if ($line =~ /Ranksum/){
+    printf OUTPUT "%s\n", $line; 
+    #split the lines on white space, so each part of the line gets
+    #stored as an array element
+    @cols=split;
+    #Testing to see what line elements are stored in the array
+    #print "cols [0] is $cols[0] \n";
+    #print "cols [2] is $cols[2] \n\n";
+    
+    #Now see if you can print out the array elemnent that stores the
+    #motif ID to a new file called ame-motif-id.list.
+  }
+ }
+