Mercurial > repos > greg > repmatch_gff3

comparison repmatch_gff3.py @ 9:39cb3eeacdbd draft

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author greg
date Wed, 02 Dec 2015 16:15:42 -0500
parents 6df81aade62c
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8:d10ae3aeebc8 9:39cb3eeacdbd
1 # repmatch.py 1 # repmatch.py
2 # 2 #
3 # Replicate matching - matches paired peaks from two or more replicates 3 # Replicate matching - matches paired peaks from two or more replicates
4 # 4 #
5 # Input: one or more gff files (simple output from cwpair2, each a list of paired peaks from a replicate 5 # Input: one or more gff files (matched_peak output from cwpair2, each a list of paired peaks from a replicate
6 # 6 #
7 # Output: list of matched groups and list of unmatched orphans 7 # Output: list of matched groups and list of unmatched peaks
8 # Files: key.tabular (file to replicate IDsummary.tabular, detail.tabular, orphans.tabular 8 # Files: statistics_table.tabular (file to replicate ID), matched_paired_peaks.tabular, detail.tabular, unmatched_peaks.tabular
9 9
10 import argparse 10 import argparse
11 import repmatch_gff3_util 11 import repmatch_gff3_util
12 12
13 if __name__ == '__main__': 13 if __name__ == '__main__':
17 parser.add_argument('--distance', dest='distance', type=int, default=50, help='Maximum distance between peaks in different replicates to allow merging') 17 parser.add_argument('--distance', dest='distance', type=int, default=50, help='Maximum distance between peaks in different replicates to allow merging')
18 parser.add_argument('--step', dest='step', type=int, default=0, help='Step size of distance for each iteration') 18 parser.add_argument('--step', dest='step', type=int, default=0, help='Step size of distance for each iteration')
19 parser.add_argument('--replicates', dest='replicates', type=int, default=2, help='Minimum number of replicates that must be matched for merging to occur') 19 parser.add_argument('--replicates', dest='replicates', type=int, default=2, help='Minimum number of replicates that must be matched for merging to occur')
20 parser.add_argument('--low_limit', dest='low_limit', type=int, default=-1000, help='Lower limit for c-w distance filter') 20 parser.add_argument('--low_limit', dest='low_limit', type=int, default=-1000, help='Lower limit for c-w distance filter')
21 parser.add_argument('--up_limit', dest='up_limit', type=int, default=1000, help='Upper limit for c-w distance filter') 21 parser.add_argument('--up_limit', dest='up_limit', type=int, default=1000, help='Upper limit for c-w distance filter')
22 parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.') 22 parser.add_argument('--output_files', dest='output_files', default='all', help='Restrict output dataset collections.')
23 parser.add_argument('--output_summary', dest='output_summary', help='Matched groups in gff format') 23 parser.add_argument('--output_matched_peaks', dest='output_matched_peaks', help='Matched groups in gff format')
24 parser.add_argument('--output_orphan', dest='output_orphan', default=None, help='Orphans in tabular format') 24 parser.add_argument('--output_unmatched_peaks', dest='output_unmatched_peaks', default=None, help='Unmatched paired peaks in tabular format')
25 parser.add_argument('--output_detail', dest='output_detail', default=None, help='Details in tabular format') 25 parser.add_argument('--output_detail', dest='output_detail', default=None, help='Details in tabular format')
26 parser.add_argument('--output_key', dest='output_key', default=None, help='Keys in tabular format') 26 parser.add_argument('--output_statistics_table', dest='output_statistics_table', default=None, help='Keys in tabular format')
27 parser.add_argument('--output_histogram', dest='output_histogram', default=None, help='Histogram') 27 parser.add_argument('--output_statistics_histogram', dest='output_statistics_histogram', default=None, help='Histogram')
28 28
29 args = parser.parse_args() 29 args = parser.parse_args()
30 30
31 dataset_paths = [] 31 dataset_paths = []
32 hids = [] 32 hids = []
40 args.step, 40 args.step,
41 args.replicates, 41 args.replicates,
42 args.up_limit, 42 args.up_limit,
43 args.low_limit, 43 args.low_limit,
44 args.output_files, 44 args.output_files,
45 args.output_summary, 45 args.output_matched_peaks,
46 args.output_orphan, 46 args.output_unmatched_peaks,
47 args.output_detail, 47 args.output_detail,
48 args.output_key, 48 args.output_statistics_table,
49 args.output_histogram) 49 args.output_statistics_histogram)