diff repmatch_gff3.py @ 9:39cb3eeacdbd draft

Uploaded

--- a/repmatch_gff3.py	Wed Dec 02 16:15:35 2015 -0500
+++ b/repmatch_gff3.py	Wed Dec 02 16:15:42 2015 -0500
@@ -2,10 +2,10 @@
 #
 # Replicate matching - matches paired peaks from two or more replicates
 #
-# Input: one or more gff files (simple output from cwpair2, each a list of paired peaks from a replicate
+# 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 orphans
-# Files: key.tabular (file to replicate IDsummary.tabular, detail.tabular, orphans.tabular
+# 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
@@ -19,12 +19,12 @@
     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='simple', help='Restrict output dataset collections.')
-    parser.add_argument('--output_summary', dest='output_summary', help='Matched groups in gff format')
-    parser.add_argument('--output_orphan', dest='output_orphan', default=None, help='Orphans in tabular format')
+    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_key', dest='output_key', default=None, help='Keys in tabular format')
-    parser.add_argument('--output_histogram', dest='output_histogram', default=None, help='Histogram')
+    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()
 
@@ -42,8 +42,8 @@
                                      args.up_limit,
                                      args.low_limit,
                                      args.output_files,
-                                     args.output_summary,
-                                     args.output_orphan,
+                                     args.output_matched_peaks,
+                                     args.output_unmatched_peaks,
                                      args.output_detail,
-                                     args.output_key,
-                                     args.output_histogram)
+                                     args.output_statistics_table,
+                                     args.output_statistics_histogram)