Mercurial > repos > earlhaminst > replace_chromosome_names

comparison replace_chromosome_names.py @ 1:6c0373cc070f draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ commit c8418d1d7657dacae7f81fe4aa0aba051873d4ad
author earlhaminst
date Tue, 13 Jun 2017 14:43:07 -0400
parents 97c11d04cd4c
children
comparison
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0:97c11d04cd4c 1:6c0373cc070f
30 print(line, file=args.output) 30 print(line, file=args.output)
31 else: 31 else:
32 line_cols = line.split('\t') 32 line_cols = line.split('\t')
33 for col_to_map in cols_to_map: 33 for col_to_map in cols_to_map:
34 old_value = line_cols[col_to_map] 34 old_value = line_cols[col_to_map]
35 line_cols[col_to_map] = map_dict.get(old_value, old_value) 35 new_value = map_dict.get(old_value, '')
36 mapped_line = '\t'.join(line_cols) 36 if not new_value:
37 print(mapped_line, file=args.output) 37 print('%s has no valid mapping, skipping line: %s' % (old_value, line), file=sys.stderr)
38 break
39 line_cols[col_to_map] = new_value
40 else:
41 mapped_line = '\t'.join(line_cols)
42 print(mapped_line, file=args.output)
38 43
39 44
40 if __name__ == "__main__": 45 if __name__ == "__main__":
41 main() 46 main()