--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cwpair2.py	Tue Dec 22 17:03:46 2015 -0500
@@ -0,0 +1,68 @@
+"""
+cwpair2.py
+
+Takes a list of called peaks on both strands and produces a list of matched pairs and a list
+of unmatched orphans using a specified method for finding matched pairs.  Methods for finding
+matched pairs are mode, closest, largest or all, where the analysis is run for each method
+
+Input: list of one or more gff format files
+
+Output: files produced for each input/mode combination:
+MP (matched_pair), D (details), O (orphans), P (frequency preview plot), F (frequency final plot),
+C (statistics graph), statistics.tabular
+"""
+
+import argparse
+import csv
+import cwpair2_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='mode', help='Method of finding match.')
+    parser.add_argument('--up_distance', dest='up_distance', type=int, default=50, help='Distance upstream from a pair.')
+    parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.')
+    parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.')
+    parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
+    parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
+    parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
+    parser.add_argument('--output_files', dest='output_files', default='matched_pair', help='Restrict output dataset collections.')
+    parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
+    args = parser.parse_args()
+
+    cwpair2_util.create_directories()
+
+    statistics = []
+    if args.absolute_threshold > 0:
+        threshold = args.absolute_threshold
+    elif args.relative_threshold > 0:
+        threshold = args.relative_threshold / 100.0
+    else:
+        threshold = 0
+    for (dataset_path, hid) in args.inputs:
+        stats = cwpair2_util.process_file(dataset_path,
+                                          hid,
+                                          args.method,
+                                          threshold,
+                                          args.up_distance,
+                                          args.down_distance,
+                                          args.binsize,
+                                          args.output_files)
+        statistics.extend(stats)
+    # Accumulate statistics.
+    by_file = {}
+    for stats in statistics:
+        # Skip "None" statistics from failed files
+        if not stats:
+            continue
+        path = stats['stats_path']
+        if path not in by_file:
+            by_file[path] = []
+        by_file[path].append(stats)
+    # Write tabular statistics file.
+    keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans']
+    statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t')
+    statistics_out.writerow(keys)
+    for file_path, statistics in by_file.items():
+        for stats in statistics:
+            statistics_out.writerow([stats[key] for key in keys])