group.py 文件源码

def add_arguments(parser):
    arg = parser.add_argument
    group = parser.add_mutually_exclusive_group()
    group.add_argument('--real-cdr3', action='store_true', default=False,
        help='In addition to barcode, group sequences by real CDR3 (detected with regex).')
    group.add_argument('--pseudo-cdr3', nargs='?', default=None,
        type=slice_arg, const=slice(-80, -60), metavar='START:END',
        help='In addition to barcode, group sequences by pseudo CDR3. '
            'If START:END is omitted, use -80:-60.')
    arg('--groups-output', metavar='FILE', default=None,
        help='Write tab-separated table with groups to FILE')
    arg('--plot-sizes', metavar='FILE', default=None,
        help='Plot group sizes to FILE (.png or .pdf)')
    arg('--limit', default=None, type=int, metavar='N',
        help='Limit processing to the first N reads')
    arg('--trim-g', action='store_true', default=False,
        help="Trim 'G' nucleotides at 5' end")
    arg('--minimum-length', '-l', type=int, default=0,
        help='Minimum sequence length')
    arg('--barcode-length', '-b', type=int, default=12,
        help="Length of barcode. Positive for 5' barcode, negative for 3' barcode. Default: %(default)s")
    arg('fastx', metavar='FASTA/FASTQ',
        help='FASTA or FASTQ file (can be gzip-compressed) with sequences')