scripts/support/fasta2rfamseq.py
def parse_arguments():
    """
    Basic argument parsing using Python's argparse

    return: An argparse parser object
    """
    
    parser = argparse.ArgumentParser(description='Rfam family Auro-Builder')
    # group required arguments together

    req_args = parser.add_argument_group("required arguments")

    mutually_exclusive_args = parser.add_mutually_exclusive_group(required=False)
    mutually_exclusive_args.add_argument('--dest-dir', help='destination directory where create new \
                family directories', type=str, required=True)
    mutually_exclusive_args.add_argument('--project', help='generates rfamseq metadata for all genomes \
        in the project directory', type=str, required=True)
    mutually_exclusive_args.add_argument('--input', help='a directory with multiple SEEDs or a single SEED',
                type=str, required=True)

    req_args.add_argument('--upid-list', help='a list of upids to generate rfamseq metadata for',
                type=str, action='strore_true')
    req_args.add_argument('--upid-gca-taxids', help='a list of upid/gca/taxid mappings',
                type=str, action='strore_true')

    req_args.add_argument('--multi', help='specifies that fasta contains sequences from multiple species',
                type=str, action='strore_true')

    # source

    return parser

    Basic argument parsing using Python's argparse

    return: An argparse parser object
    
Basic argument parsing using Python's argparse
return: An argparse parser object
Basic argument parsing using Python ' s argparse return : An argparse parser object
def parse_arguments():
    parser = argparse.ArgumentParser(description='Rfam family Auro-Builder')
    req_args = parser.add_argument_group("required arguments")
    mutually_exclusive_args = parser.add_mutually_exclusive_group(required=False)
    mutually_exclusive_args.add_argument('--dest-dir', help='destination directory where create new \
                family directories', type=str, required=True)
    mutually_exclusive_args.add_argument('--project', help='generates rfamseq metadata for all genomes \
        in the project directory', type=str, required=True)
    mutually_exclusive_args.add_argument('--input', help='a directory with multiple SEEDs or a single SEED',
                type=str, required=True)
    req_args.add_argument('--upid-list', help='a list of upids to generate rfamseq metadata for',
                type=str, action='strore_true')
    req_args.add_argument('--upid-gca-taxids', help='a list of upid/gca/taxid mappings',
                type=str, action='strore_true')
    req_args.add_argument('--multi', help='specifies that fasta contains sequences from multiple species',
                type=str, action='strore_true')
    return parser
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = 'Rfam family Auro-Builder' ) req_args = parser . add_argument_group ( "required arguments" ) mutually_exclusive_args = parser . add_mutually_exclusive_group ( required = False ) mutually_exclusive_args . add_argument ( '--dest-dir' , help = 'destination directory where create new \
                family directories' , type = str , required = True ) mutually_exclusive_args . add_argument ( '--project' , help = 'generates rfamseq metadata for all genomes \
        in the project directory' , type = str , required = True ) mutually_exclusive_args . add_argument ( '--input' , help = 'a directory with multiple SEEDs or a single SEED' , type = str , required = True ) req_args . add_argument ( '--upid-list' , help = 'a list of upids to generate rfamseq metadata for' , type = str , action = 'strore_true' ) req_args . add_argument ( '--upid-gca-taxids' , help = 'a list of upid/gca/taxid mappings' , type = str , action = 'strore_true' ) req_args . add_argument ( '--multi' , help = 'specifies that fasta contains sequences from multiple species' , type = str , action = 'strore_true' ) return parser
Basic argument parsing using Python's argparse
return: An argparse parser object
Basic argument parsing using Python ' s argparse return : An argparse parser object
"""
    Basic argument parsing using Python's argparse

    return: An argparse parser object
    """ # group required arguments together # source