Mercurial > repos > iuc > repmatch_gff3
view repmatch_gff3.py @ 2:d7f1312b3455 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 4eb5632ca7b54134911d40ae94eaf155dc673a71
author | iuc |
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date | Fri, 13 Jan 2017 10:27:44 -0500 |
parents | a072f0f30ea3 |
children | 6acaa2c93f47 |
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# 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)