amadeo: Tools/CREF/Extract_motif_codes

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+:229d36377838
+#!/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.
+}
+}

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