INNER CODE UNIT · Python
parse_args
BirolLab/straglr · straglr.py:10
def parse_args():
trf_args_meta = ('Match', 'Mismatch', 'Delta', 'PM', 'PI', 'Minscore', 'MaxPeriod')
parser = argparse.ArgumentParser()
parser.add_argument("bam", type=str, help="bam file")
parser.add_argument("genome_fasta", type=str, help="genome_fasta")
parser.add_argument("out_prefix", type=str, help="output prefix")
scan = parser.add_argument_group('genome scan')
scan.add_argument("--min_ins_size", type=int, default=100, help="minimum insertion size. Default:100")
scan.add_argument("--min_str_len", type=int, help="minimum STR length. Default:2", default=2)
scan.add_argument("--max_str_len", type=int, help="maximum STR length. Default:50", default=50)
scan.add_argument("--min_support", type=int, help="minimum number of supporting reads for detecting expansion. Default:2", default=2)
scan.add_argument("--trf_args", type=int, nargs=7, help="tandem repeat finder arguments. Default:2 5 5 80 10 10 500", metavar=trf_args_meta, default=[2,5,5,80,10,10,500])
scan.add_argument("--chroms", type=str, nargs="+", help="chromosomes")
scan.add_argument("--regions", type=str, help="bed file for scanning only specific regions")
scan.add_argument("--exclude", type=str, help="bed file to exclude regions")
scan.add_argument("--include_alt_chroms", action='store_true', help="include alternate chromosomes. By default, only chroms 1-22,X,Y are considered in genome scan")
scan.add_argument("--max_cov", type=int, help="maximum allowed coverage for ins inspection. Default:100", default=100)