--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repmatch_gff3.py	Wed Dec 23 09:25:42 2015 -0500
@@ -0,0 +1,49 @@
+# repmatch.py
+#
+# Replicate matching - matches paired peaks from two or more replicates
+#
+# Input: one or more gff files (matched_peak output from cwpair2, each a list of paired peaks from a replicate
+#
+# Output: list of matched groups and list of unmatched peaks
+# Files: statistics_table.tabular (file to replicate ID), matched_paired_peaks.tabular, detail.tabular, unmatched_peaks.tabular
+
+import argparse
+import repmatch_gff3_util
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets")
+    parser.add_argument('--method', dest='method', default='closest', help='Method of finding match')
+    parser.add_argument('--distance', dest='distance', type=int, default=50, help='Maximum distance between peaks in different replicates to allow merging')
+    parser.add_argument('--step', dest='step', type=int, default=0, help='Step size of distance for each iteration')
+    parser.add_argument('--replicates', dest='replicates', type=int, default=2, help='Minimum number of replicates that must be matched for merging to occur')
+    parser.add_argument('--low_limit', dest='low_limit', type=int, default=-1000, help='Lower limit for c-w distance filter')
+    parser.add_argument('--up_limit', dest='up_limit', type=int, default=1000, help='Upper limit for c-w distance filter')
+    parser.add_argument('--output_files', dest='output_files', default='all', help='Restrict output dataset collections.')
+    parser.add_argument('--output_matched_peaks', dest='output_matched_peaks', help='Matched groups in gff format')
+    parser.add_argument('--output_unmatched_peaks', dest='output_unmatched_peaks', default=None, help='Unmatched paired peaks in tabular format')
+    parser.add_argument('--output_detail', dest='output_detail', default=None, help='Details in tabular format')
+    parser.add_argument('--output_statistics_table', dest='output_statistics_table', default=None, help='Keys in tabular format')
+    parser.add_argument('--output_statistics_histogram', dest='output_statistics_histogram', default=None, help='Histogram')
+
+    args = parser.parse_args()
+
+    dataset_paths = []
+    hids = []
+    for (dataset_path, hid) in args.inputs:
+        dataset_paths.append(dataset_path)
+        hids.append(hid)
+    repmatch_gff3_util.process_files(dataset_paths,
+                                     hids,
+                                     args.method,
+                                     args.distance,
+                                     args.step,
+                                     args.replicates,
+                                     args.up_limit,
+                                     args.low_limit,
+                                     args.output_files,
+                                     args.output_matched_peaks,
+                                     args.output_unmatched_peaks,
+                                     args.output_detail,
+                                     args.output_statistics_table,
+                                     args.output_statistics_histogram)