comparison bed_to_protein_map.py @ 1:a7c58b43cbaa draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"

0:024ed7b0ad93

    output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout

    try:
        for linenum, line in enumerate(input_rdr):
            if args.debug:
                print >> sys.stderr, "%d: %s\n" % (linenum, line)
            if line.startswith('#'):
                continue
            if line.strip() == '':
                continue
            fields = line.rstrip('\r\n').split('\t')
            if len(fields) < 12:
                print >> sys.stderr, "%d: %s\n" % (linenum, line)
                continue
            (chrom, _chromStart, _chromEnd, name, score, strand,
             _thickStart, _thickEnd, itemRgb,
             _blockCount, blockSizes, blockStarts) = fields[0:12]
            chromStart = int(_chromStart)

                    output_wtr.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n'
                                     % (name, chrom, start, end,
                                        strand, cds_start, cds_end))
                    cds_start = cds_end
                pass
    except Exception, e:
        print >> sys.stderr, "failed: %s" % e
        exit(1)


if __name__ == "__main__":
    __main__()

1:a7c58b43cbaa

    output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout

    try:
        for linenum, line in enumerate(input_rdr):
            if args.debug:
                sys.stderr.write("%d: %s\n" % (linenum, line))
            if line.startswith('#'):
                continue
            if line.strip() == '':
                continue
            fields = line.rstrip('\r\n').split('\t')
            if len(fields) < 12:
                sys.stderr.write("%d: %s\n" % (linenum, line))
                continue
            (chrom, _chromStart, _chromEnd, name, score, strand,
             _thickStart, _thickEnd, itemRgb,
             _blockCount, blockSizes, blockStarts) = fields[0:12]
            chromStart = int(_chromStart)

                    output_wtr.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n'
                                     % (name, chrom, start, end,
                                        strand, cds_start, cds_end))
                    cds_start = cds_end
                pass
    except Exception as e:
        sys.stderr.write("failed: %s\n" % e)
        exit(1)


if __name__ == "__main__":
    __main__()