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

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ commit c8418d1d7657dacae7f81fe4aa0aba051873d4ad

0:97c11d04cd4c

            print(line, file=args.output)
        else:
            line_cols = line.split('\t')
            for col_to_map in cols_to_map:
                old_value = line_cols[col_to_map]
                line_cols[col_to_map] = map_dict.get(old_value, old_value)
            mapped_line = '\t'.join(line_cols)
            print(mapped_line, file=args.output)


if __name__ == "__main__":
    main()

1:6c0373cc070f

            print(line, file=args.output)
        else:
            line_cols = line.split('\t')
            for col_to_map in cols_to_map:
                old_value = line_cols[col_to_map]
                new_value = map_dict.get(old_value, '')
                if not new_value:
                    print('%s has no valid mapping, skipping line: %s' % (old_value, line), file=sys.stderr)
                    break
                line_cols[col_to_map] = new_value
            else:
                mapped_line = '\t'.join(line_cols)
                print(mapped_line, file=args.output)


if __name__ == "__main__":
    main()