humann/tools/build_custom_database.py
def parse_arguments(args):
    """ 
    Parse the arguments from the user
    """
    
    parser = argparse.ArgumentParser(
        description= "Create a custom database file\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "-i","--input",
        help="the fasta input file\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the output folder\n",
        required=True)
    parser.add_argument(
        "--id-mapping",
        help="the file mapping fasta ids to taxonomy")
    parser.add_argument(
        "--taxonomic-profile",
        help="the file containing the taxonomic profile")
    parser.add_argument(
        "--format",
        help="the final database format",
        default="fasta",
        choices=["fasta","diamond"])
    parser.add_argument(
        "--genus-abundance-threshold",
        help="the minimum abundance for a genus to be included in the database",
        type=float,
        default=config.prescreen_threshold)

    return parser.parse_args()
 
    Parse the arguments from the user
    
Parse the arguments from the user
Parse the arguments from the user
def parse_arguments(args):
    parser = argparse.ArgumentParser(
        description= "Create a custom database file\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "-i","--input",
        help="the fasta input file\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the output folder\n",
        required=True)
    parser.add_argument(
        "--id-mapping",
        help="the file mapping fasta ids to taxonomy")
    parser.add_argument(
        "--taxonomic-profile",
        help="the file containing the taxonomic profile")
    parser.add_argument(
        "--format",
        help="the final database format",
        default="fasta",
        choices=["fasta","diamond"])
    parser.add_argument(
        "--genus-abundance-threshold",
        help="the minimum abundance for a genus to be included in the database",
        type=float,
        default=config.prescreen_threshold)
    return parser.parse_args()
def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Create a custom database file\n" , formatter_class = argparse . RawTextHelpFormatter ) parser . add_argument ( "-i" , "--input" , help = "the fasta input file\n" , required = True ) parser . add_argument ( "-o" , "--output" , help = "the output folder\n" , required = True ) parser . add_argument ( "--id-mapping" , help = "the file mapping fasta ids to taxonomy" ) parser . add_argument ( "--taxonomic-profile" , help = "the file containing the taxonomic profile" ) parser . add_argument ( "--format" , help = "the final database format" , default = "fasta" , choices = [ "fasta" , "diamond" ] ) parser . add_argument ( "--genus-abundance-threshold" , help = "the minimum abundance for a genus to be included in the database" , type = float , default = config . prescreen_threshold ) return parser . parse_args ( )
Parse the arguments from the user
Parse the arguments from the user
""" 
    Parse the arguments from the user
    """
args