--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hcluster_sg_parser.pl	Mon Dec 12 07:12:23 2016 -0500
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+#
+use strict;
+use warnings;
+# A simple perl parser to convert hcluster_sg 3-column output into list of ids in separate files
+# hcluster_sg_parser.pl <file>
+
+my $file1 = $ARGV[0];
+open my $fh1, '<', $file1;
+
+while (my $line = <$fh1>) {
+    chomp $line;
+    my @row = split(/\t/, $line);
+
+    my $cluster_id = $row[0];
+    my $id_list = $row[2];
+    # Change commas to newlines
+    $id_list =~ s/\,/\n/g;
+
+    my $outfile = $cluster_id."_output.txt";
+    open(my $fh, '>', $outfile) or die "Could not open file '$outfile' for writing: $!";
+    print $fh $id_list;
+    close $fh;
+}
+close $fh1;