Mercurial > repos > iuc > repmatch_gff3

annotate repmatch_gff3.py @ 4:6acaa2c93f47 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9
author iuc
date Wed, 12 Jul 2017 10:11:53 -0400
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a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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1 # repmatch.py
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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2 #
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3 # Replicate matching - matches paired peaks from two or more replicates
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4 #
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5 # Input: one or more gff files (matched_peak output from cwpair2, each a list of paired peaks from a replicate
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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6 #
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7 # Output: list of matched groups and list of unmatched peaks
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8 # Files: statistics_table.tabular (file to replicate ID), matched_paired_peaks.tabular, detail.tabular, unmatched_peaks.tabular
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a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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10 import argparse
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6acaa2c93f47 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9
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12 import repmatch_gff3_util
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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14 if __name__ == '__main__':
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15 parser = argparse.ArgumentParser()
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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16 parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets")
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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17 parser.add_argument('--method', dest='method', default='closest', help='Method of finding match')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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18 parser.add_argument('--distance', dest='distance', type=int, default=50, help='Maximum distance between peaks in different replicates to allow merging')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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19 parser.add_argument('--step', dest='step', type=int, default=0, help='Step size of distance for each iteration')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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20 parser.add_argument('--replicates', dest='replicates', type=int, default=2, help='Minimum number of replicates that must be matched for merging to occur')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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21 parser.add_argument('--low_limit', dest='low_limit', type=int, default=-1000, help='Lower limit for c-w distance filter')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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22 parser.add_argument('--up_limit', dest='up_limit', type=int, default=1000, help='Upper limit for c-w distance filter')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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23 parser.add_argument('--output_files', dest='output_files', default='all', help='Restrict output dataset collections.')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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24 parser.add_argument('--output_matched_peaks', dest='output_matched_peaks', help='Matched groups in gff format')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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25 parser.add_argument('--output_unmatched_peaks', dest='output_unmatched_peaks', default=None, help='Unmatched paired peaks in tabular format')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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26 parser.add_argument('--output_detail', dest='output_detail', default=None, help='Details in tabular format')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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27 parser.add_argument('--output_statistics_table', dest='output_statistics_table', default=None, help='Keys in tabular format')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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28 parser.add_argument('--output_statistics_histogram', dest='output_statistics_histogram', default=None, help='Histogram')
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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30 args = parser.parse_args()
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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32 dataset_paths = []
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33 hids = []
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34 for (dataset_path, hid) in args.inputs:
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35 dataset_paths.append(dataset_path)
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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36 hids.append(hid)
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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37 repmatch_gff3_util.process_files(dataset_paths,
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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38 hids,
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39 args.method,
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40 args.distance,
a072f0f30ea3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9
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41 args.step,
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42 args.replicates,
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43 args.up_limit,
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44 args.low_limit,
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45 args.output_files,
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46 args.output_matched_peaks,
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47 args.output_unmatched_peaks,
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48 args.output_detail,
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49 args.output_statistics_table,
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50 args.output_statistics_histogram)