gseapy/__main__.py
def add_gsea_parser(subparsers):
    """Add main function 'gsea' argument parsers."""

    argparser_gsea = subparsers.add_parser("gsea", help="Main GSEApy Function: run GSEApy instead of GSEA.")

    # group for input files
    group_input = argparser_gsea.add_argument_group("Input files arguments")
    group_input.add_argument("-d", "--data", dest="data", action="store", type=str, required=True,
                             help="Input gene expression dataset file in txt format.Same with GSEA.")
    group_input.add_argument("-c", "--cls", dest="cls", action="store", type=str, required=True,
                             help="Input class vector (phenotype) file in CLS format. Same with GSEA.")
    group_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
                             help="Gene set database in GMT format. Same with GSEA.")
    group_input.add_argument("-t", "--permu-type", action="store", dest="type", type=str, metavar='perType',
                             choices=("gene_set", "phenotype"), default="gene_set",
                             help="Permutation type. Same with GSEA, choose from {'gene_set', 'phenotype'}")

    # group for output files
    group_output = argparser_gsea.add_argument_group("Output arguments")
    add_output_option(group_output)

    # group for General options.
    group_opt = argparser_gsea.add_argument_group("GSEA advanced arguments")
    group_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")
    group_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")
    group_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")
    group_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',)
    group_opt.add_argument("-m", "--method", action="store", dest="method", type=str, metavar='',
                           choices=("signal_to_noise", "t_test", "ratio_of_classes", "diff_of_classes", "log2_ratio_of_classes"),
                           default="log2_ratio_of_classes",
                           help="Methods to calculate correlations of ranking metrics. \
                           Choose from {'signal_to_noise', 't_test', 'ratio_of_classes', 'diff_of_classes','log2_ratio_of_classes'}.\
                           Default: 'log2_ratio_of_classes'")
    group_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.')
    group_opt.add_argument("-s", "--seed", dest = "seed", action="store", type=int, default=None, metavar='',
                           help="Number of random seed. Default: None")
    group_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_gsea_parser(subparsers):
    """Add main function 'gsea' argument parsers."""

    argparser_gsea = subparsers.add_parser("gsea", help="Main GSEApy Function: run GSEApy instead of GSEA.")

    # group for input files
    group_input = argparser_gsea.add_argument_group("Input files arguments")
    group_input.add_argument("-d", "--data", dest="data", action="store", type=str, required=True,
                             help="Input gene expression dataset file in txt format.Same with GSEA.")
    group_input.add_argument("-c", "--cls", dest="cls", action="store", type=str, required=True,
                             help="Input class vector (phenotype) file in CLS format. Same with GSEA.")
    group_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
                             help="Gene set database in GMT format. Same with GSEA.")
    group_input.add_argument("-t", "--permu-type", action="store", dest="type", type=str, metavar='perType',
                             choices=("gene_set", "phenotype"), default="gene_set",
                             help="Permutation type. Same with GSEA, choose from {'gene_set', 'phenotype'}")

    # group for output files
    group_output = argparser_gsea.add_argument_group("Output arguments")
    add_output_option(group_output)

    # group for General options.
    group_opt = argparser_gsea.add_argument_group("GSEA advanced arguments")
    group_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")
    group_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")
    group_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")
    group_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',)
    group_opt.add_argument("-m", "--method", action="store", dest="method", type=str, metavar='',
                           choices=("signal_to_noise", "t_test", "ratio_of_classes", "diff_of_classes", "log2_ratio_of_classes"),
                           default="log2_ratio_of_classes",
                           help="Methods to calculate correlations of ranking metrics. \
                           Choose from {'signal_to_noise', 't_test', 'ratio_of_classes', 'diff_of_classes','log2_ratio_of_classes'}.\
                           Default: 'log2_ratio_of_classes'")
    group_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.')
    group_opt.add_argument("-s", "--seed", dest = "seed", action="store", type=int, default=None, metavar='',
                           help="Number of random seed. Default: None")
    group_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_gsea_parser ( subparsers ) : argparser_gsea = subparsers . add_parser ( "gsea" , help = "Main GSEApy Function: run GSEApy instead of GSEA." ) # group for input files group_input = argparser_gsea . add_argument_group ( "Input files arguments" ) group_input . add_argument ( "-d" , "--data" , dest = "data" , action = "store" , type = str , required = True , help = "Input gene expression dataset file in txt format.Same with GSEA." ) group_input . add_argument ( "-c" , "--cls" , dest = "cls" , action = "store" , type = str , required = True , help = "Input class vector (phenotype) file in CLS format. Same with GSEA." ) group_input . add_argument ( "-g" , "--gmt" , dest = "gmt" , action = "store" , type = str , required = True , help = "Gene set database in GMT format. Same with GSEA." ) group_input . add_argument ( "-t" , "--permu-type" , action = "store" , dest = "type" , type = str , metavar = 'perType' , choices = ( "gene_set" , "phenotype" ) , default = "gene_set" , help = "Permutation type. Same with GSEA, choose from {'gene_set', 'phenotype'}" ) # group for output files group_output = argparser_gsea . add_argument_group ( "Output arguments" ) add_output_option ( group_output ) # group for General options. group_opt = argparser_gsea . add_argument_group ( "GSEA advanced arguments" ) group_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" ) group_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" ) group_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" ) group_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' , ) group_opt . add_argument ( "-m" , "--method" , action = "store" , dest = "method" , type = str , metavar = '' , choices = ( "signal_to_noise" , "t_test" , "ratio_of_classes" , "diff_of_classes" , "log2_ratio_of_classes" ) , default = "log2_ratio_of_classes" , help = "Methods to calculate correlations of ranking metrics. \
                           Choose from {'signal_to_noise', 't_test', 'ratio_of_classes', 'diff_of_classes','log2_ratio_of_classes'}.\
                           Default: 'log2_ratio_of_classes'" ) group_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.' ) group_opt . add_argument ( "-s" , "--seed" , dest = "seed" , action = "store" , type = int , default = None , metavar = '' , help = "Number of random seed. Default: None" ) group_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 main function 'gsea' argument parsers.
Add main function gsea argument parsers .