benchmarking.py 文件源码

def parse_args():
    dstring = "Prototype implementation of ARG tracking and regular garbage collection."
    parser = argparse.ArgumentParser(description=dstring,
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument('--popsize', '-N', type=int,
                        help="Diploid population size")
    parser.add_argument('--theta', '-T', type=float,  help="4Nu")
    parser.add_argument('--rho', '-R', type=float,  help="4Nr")
    parser.add_argument('--pdel',  default=0.0, type=float,
                        help="Ratio of deleterious mutations to neutral mutations.")

    parser.add_argument('--nsam', '-n', type=int,
                        help="Sample size (in chromosomes).")
    parser.add_argument('--seed', '-S', type=int,  help="RNG seed")
    parser.add_argument('--gc', '-G', type=int,
                        help="GC interval")
    parser.add_argument('--neutral', action='store_true',
                        help="Simulate no selection")
    parser.add_argument('--neutral_mutations',
                        action='store_true',
                        help="Simulate neutral mutations.  If False, ARG is tracked instead and neutral mutations dropped down on the sample afterwards.")
    return parser