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