core.py 文件源码

def getArgs():
    """
    Parses command line arguments and returns them to the caller
    """
    __version__ = 'v0.2.5'
    parser = argparse.ArgumentParser()
    parser._action_groups.pop()
    required = parser.add_argument_group('Required arguments')
    required.add_argument('-i', '--input', required=True, metavar='<FILE>', help='Input file in FASTA format')
    optional = parser.add_argument_group('Optional arguments')
    optional.add_argument('-o', '--output', type=argparse.FileType('w'), metavar='<FILE>', default=sys.stdout, help='Output file name. Default: Input file name + _perf.tsv')
    optional.add_argument('-a', '--analyse', action='store_true', default=False, help='Generate a summary HTML report.')
    cutoff_group = optional.add_mutually_exclusive_group()
    cutoff_group.add_argument('-l', '--min-length', type=int, metavar='<INT>', help='Minimum length cutoff of repeat')
    cutoff_group.add_argument('-u', '--min-units', metavar='INT or FILE', help="Minimum number of repeating units to be considered. Can be an integer or a file specifying cutoffs for different motif sizes.")
    optional.add_argument('-rep', '--repeats', type=argparse.FileType('r'), metavar='<FILE>', help='File with list of repeats (Not allowed with -m and/or -M)')
    optional.add_argument('-m', '--min-motif-size', type=int, metavar='<INT>', help='Minimum size of a repeat motif in bp (Not allowed with -rep)')
    optional.add_argument('-M', '--max-motif-size', type=int, metavar='<INT>', help='Maximum size of a repeat motif in bp (Not allowed with -rep)')
    optional.add_argument('-s', '--min-seq-length', type=int, metavar = '<INT>', default=0, help='Minimum size of sequence length for consideration (in bp)')
    optional.add_argument('-S', '--max-seq-length', type=float, metavar='<FLOAT>', default=inf, help='Maximum size of sequence length for consideration (in bp)')
    seqid_group = optional.add_mutually_exclusive_group()
    seqid_group.add_argument('-f', '--filter-seq-ids', metavar='<FILE>')
    seqid_group.add_argument('-F', '--target-seq-ids', metavar='<FILE>')
    optional.add_argument('--version', action='version', version='PERF ' + __version__)

    args = parser.parse_args()
    if args.repeats and (args.min_motif_size or args.max_motif_size):
        parser.error("-rep is not allowed with -m/-M")
    if args.repeats is None:
        if args.min_motif_size is None:
            args.min_motif_size = 1
        if args.max_motif_size is None:
            args.max_motif_size = 6
    if args.output.name == "<stdout>":
        args.output = open(splitext(args.input)[0] + '_perf.tsv', 'w')

    return args