diff --git a/build_pop.py b/build_pop.py index eae3f35ccddb624a849f900242a2c8902b4549e8..8f30c202d2ee0dbed441c299795c0d11584eb0cb 100755 --- a/build_pop.py +++ b/build_pop.py @@ -21,16 +21,16 @@ def parse_args(): """ parser = argparse.ArgumentParser(description='Generate simulated populations with SV', formatter_class=argparse.ArgumentDefaultsHelpFormatter) - parser.add_argument("--nb-inds", help="Number of individuals to generate", required=True, type=int) - parser.add_argument("--reference", help="Reference genome", required=True) - parser.add_argument("--sv-list", help="File containing the SVs", required=False) - parser.add_argument("--coverage", help="Coverage of reads", default=15, type=int) - parser.add_argument("--output-directory", help="Output directory", default="res") - parser.add_argument("--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True, + parser.add_argument("-n", "--nb-inds", help="Number of individuals to generate", required=True, type=int) + parser.add_argument("-r", "--reference", help="Reference genome", required=True) + parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False) + parser.add_argument("-c", "--coverage", help="Coverage of reads", default=15, type=int) + parser.add_argument("-o", "--output-directory", help="Output directory", default="res") + parser.add_argument("-f", "--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True, default=False) - parser.add_argument("--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", const=True, + parser.add_argument("-a", "--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", const=True, default=False) - parser.add_argument("--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001) + parser.add_argument("-p", "--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001) parser.add_argument("-l", "--read-len", help="Generate reads having a length of LEN", type=int, default=100) parser.add_argument("-m", "--insert-len-mean", help="Generate inserts (fragments) having an average length of LEN", type=int, default=300)