gseapy/__main__.py
def add_prerank_parser(subparsers):
    """Add function 'prerank' argument parsers."""

    argparser_prerank = subparsers.add_parser("prerank", help="Run GSEApy Prerank tool on preranked gene list.")

    # group for input files
    prerank_input = argparser_prerank.add_argument_group("Input files arguments")
    prerank_input.add_argument("-r", "--rnk", dest="rnk", action="store", type=str, required=True,
                             help="Ranking metric file in .rnk format. Same with GSEA.")
    prerank_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
                             help="Gene set database in GMT format. Same with GSEA.")
    prerank_input.add_argument("-l", "--label", action='store', nargs=2, dest='label',
                             metavar=('pos', 'neg'), type=str, default=('Pos','Neg'),
                             help="The phenotype label argument need two parameters to define. Default: ('Pos','Neg')")

    # group for output files
    prerank_output = argparser_prerank.add_argument_group("Output arguments")
    add_output_option(prerank_output)

    # group for General options.
    prerank_opt = argparser_prerank.add_argument_group("GSEA advanced arguments")
    prerank_opt.add_argument("-n", "--permu-num", dest = "n", action="store", type=int, default=1000, metavar='nperm',
                             help="Number of random permutations. For calculating esnulls. Default: 1000")
    prerank_opt.add_argument("--min-size",  dest="mins", action="store", type=int, default=15, metavar='int',
                             help="Min size of input genes presented in Gene Sets. Default: 15")
    prerank_opt.add_argument("--max-size", dest = "maxs", action="store", type=int, default=500, metavar='int',
                             help="Max size of input genes presented in Gene Sets. Default: 500")
    prerank_opt.add_argument("-w", "--weight", action='store', dest='weight', default=1.0, type=float, metavar='float',
                             help='Weighted_score of rank_metrics. For weighting input genes. Choose from {0, 1, 1.5, 2}. Default: 1',)
    prerank_opt.add_argument("-a", "--ascending", action='store_true', dest='ascending', default=False,
                             help='Rank metric sorting order. If the -a flag was chosen, then ascending equals to True. Default: False.')
    prerank_opt.add_argument("-s", "--seed", dest = "seed", action="store", type=int, default=None, metavar='',
                             help="Number of random seed. Default: None")
    prerank_opt.add_argument("-p", "--threads", dest = "threads", action="store", type=int, default=1, metavar='procs',
                           help="Number of Processes you are going to use. Default: 1")

    return
def add_prerank_parser(subparsers):
    """Add function 'prerank' argument parsers."""

    argparser_prerank = subparsers.add_parser("prerank", help="Run GSEApy Prerank tool on preranked gene list.")

    # group for input files
    prerank_input = argparser_prerank.add_argument_group("Input files arguments")
    prerank_input.add_argument("-r", "--rnk", dest="rnk", action="store", type=str, required=True,
                             help="Ranking metric file in .rnk format. Same with GSEA.")
    prerank_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
                             help="Gene set database in GMT format. Same with GSEA.")
    prerank_input.add_argument("-l", "--label", action='store', nargs=2, dest='label',
                             metavar=('pos', 'neg'), type=str, default=('Pos','Neg'),
                             help="The phenotype label argument need two parameters to define. Default: ('Pos','Neg')")

    # group for output files
    prerank_output = argparser_prerank.add_argument_group("Output arguments")
    add_output_option(prerank_output)

    # group for General options.
    prerank_opt = argparser_prerank.add_argument_group("GSEA advanced arguments")
    prerank_opt.add_argument("-n", "--permu-num", dest = "n", action="store", type=int, default=1000, metavar='nperm',
                             help="Number of random permutations. For calculating esnulls. Default: 1000")
    prerank_opt.add_argument("--min-size",  dest="mins", action="store", type=int, default=15, metavar='int',
                             help="Min size of input genes presented in Gene Sets. Default: 15")
    prerank_opt.add_argument("--max-size", dest = "maxs", action="store", type=int, default=500, metavar='int',
                             help="Max size of input genes presented in Gene Sets. Default: 500")
    prerank_opt.add_argument("-w", "--weight", action='store', dest='weight', default=1.0, type=float, metavar='float',
                             help='Weighted_score of rank_metrics. For weighting input genes. Choose from {0, 1, 1.5, 2}. Default: 1',)
    prerank_opt.add_argument("-a", "--ascending", action='store_true', dest='ascending', default=False,
                             help='Rank metric sorting order. If the -a flag was chosen, then ascending equals to True. Default: False.')
    prerank_opt.add_argument("-s", "--seed", dest = "seed", action="store", type=int, default=None, metavar='',
                             help="Number of random seed. Default: None")
    prerank_opt.add_argument("-p", "--threads", dest = "threads", action="store", type=int, default=1, metavar='procs',
                           help="Number of Processes you are going to use. Default: 1")

    return
Add function 'prerank' argument parsers.