--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hcluster_sg_parser.py	Fri Jan 20 06:13:23 2017 -0500
@@ -0,0 +1,36 @@
+"""
+A simple parser to convert the hcluster_sg 3-column output into lists of IDs, one list for each cluster.
+
+When a minimum and/or maximum number of cluster elements are specified, the IDs contained in the filtered-out clusters are collected in the "discarded IDS" output dataset.
+
+Usage:
+
+python hcluster_sg_parser.py [-m <N>] [-M <N>] <file> <discarded_out>
+"""
+import optparse
+import sys
+
+
+def main():
+    parser = optparse.OptionParser()
+    parser.add_option('-m', '--min', type='int', default=0, help='Minimum number of cluster elements')
+    parser.add_option('-M', '--max', type='int', default=sys.maxsize, help='Maximum number of cluster elements')
+    options, args = parser.parse_args()
+
+    with open(args[1], 'w') as discarded_out:
+        with open(args[0]) as fh:
+            for line in fh:
+                line = line.rstrip()
+                (cluster_id, n_ids, id_list) = line.split('\t')
+                n_ids = int(n_ids)
+                id_list = id_list.replace(',', '\n')
+                if n_ids >= options.min and n_ids <= options.max:
+                    outfile = cluster_id + '_output.txt'
+                    with open(outfile, 'w') as f:
+                        f.write(id_list)
+                else:
+                    discarded_out.write(id_list)
+
+
+if __name__ == "__main__":
+    main()