Mercurial > repos > iuc > cwpair2
annotate cwpair2.py @ 6:c4b926c9831c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit ca66053a0d915edba3d7f1d4ce014718e7f4f0f2
author | iuc |
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date | Thu, 02 May 2019 08:30:22 -0400 |
parents | d843468aeb8f |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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1 """ |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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2 cwpair2.py |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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3 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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4 Takes a list of called peaks on both strands and produces a list of matched pairs and a list |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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5 of unmatched orphans using a specified method for finding matched pairs. Methods for finding |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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6 matched pairs are mode, closest, largest or all, where the analysis is run for each method |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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7 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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8 Input: list of one or more gff format files |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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9 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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10 Output: files produced for each input/mode combination: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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11 MP (matched_pair), D (details), O (orphans), P (frequency preview plot), F (frequency final plot), |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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12 C (statistics graph), statistics.tabular |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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13 """ |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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14 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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15 import argparse |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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16 import csv |
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d843468aeb8f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
iuc
parents:
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17 |
0
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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18 import cwpair2_util |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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19 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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20 if __name__ == '__main__': |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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21 parser = argparse.ArgumentParser() |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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22 parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets") |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
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23 parser.add_argument('--method', dest='method', default='mode', help='Method of finding match.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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24 parser.add_argument('--up_distance', dest='up_distance', type=int, default=50, help='Distance upstream from a pair.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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25 parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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26 parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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27 parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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28 parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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29 parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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30 parser.add_argument('--output_files', dest='output_files', default='matched_pair', help='Restrict output dataset collections.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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31 parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.') |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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32 args = parser.parse_args() |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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33 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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34 cwpair2_util.create_directories() |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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35 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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36 statistics = [] |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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37 if args.absolute_threshold > 0: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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38 threshold = args.absolute_threshold |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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39 elif args.relative_threshold > 0: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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40 threshold = args.relative_threshold / 100.0 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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41 else: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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42 threshold = 0 |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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43 for (dataset_path, hid) in args.inputs: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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44 stats = cwpair2_util.process_file(dataset_path, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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45 hid, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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46 args.method, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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47 threshold, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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48 args.up_distance, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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49 args.down_distance, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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50 args.binsize, |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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51 args.output_files) |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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52 statistics.extend(stats) |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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53 # Accumulate statistics. |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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54 by_file = {} |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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55 for stats in statistics: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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56 # Skip "None" statistics from failed files |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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57 if not stats: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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58 continue |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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59 path = stats['stats_path'] |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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60 if path not in by_file: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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61 by_file[path] = [] |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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62 by_file[path].append(stats) |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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63 # Write tabular statistics file. |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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64 keys = ['fname', 'final_mode', 'preview_mode', 'perc95', 'paired', 'orphans'] |
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c4b926c9831c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit ca66053a0d915edba3d7f1d4ce014718e7f4f0f2
iuc
parents:
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65 statistics_out = csv.writer(open(args.statistics_output, 'wt'), delimiter='\t', lineterminator="\n") |
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8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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66 statistics_out.writerow(keys) |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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67 for file_path, statistics in by_file.items(): |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
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68 for stats in statistics: |
8600bfe7ed52
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
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69 statistics_out.writerow([stats[key] for key in keys]) |