bin/kraken_parse.py
def _get_args():
    '''This function parses and return arguments passed in'''
    parser = argparse.ArgumentParser(
        prog='kraken_parse',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description='Parsing kraken')
    parser.add_argument('krakenReport', help="path to kraken report file")
    parser.add_argument(
        '-c',
        dest="count",
        default=50,
        help="Minimum number of hits on clade to report it. Default = 50")
    parser.add_argument(
        '-or',
        dest="readout",
        default=None,
        help="Read count output file. Default = <basename>.read_kraken_parsed.csv")
    parser.add_argument(
        '-ok',
        dest="kmerout",
        default=None,
        help="Kmer Output file. Default = <basename>.kmer_kraken_parsed.csv")

    args = parser.parse_args()

    infile = args.krakenReport
    countlim = int(args.count)
    readout = args.readout
    kmerout = args.kmerout

    return(infile, countlim, readout, kmerout)
This function parses and return arguments passed in
This function parses and return arguments passed in
This function parses and return arguments passed in
def _get_args():
    parser = argparse.ArgumentParser(
        prog='kraken_parse',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description='Parsing kraken')
    parser.add_argument('krakenReport', help="path to kraken report file")
    parser.add_argument(
        '-c',
        dest="count",
        default=50,
        help="Minimum number of hits on clade to report it. Default = 50")
    parser.add_argument(
        '-or',
        dest="readout",
        default=None,
        help="Read count output file. Default = <basename>.read_kraken_parsed.csv")
    parser.add_argument(
        '-ok',
        dest="kmerout",
        default=None,
        help="Kmer Output file. Default = <basename>.kmer_kraken_parsed.csv")
    args = parser.parse_args()
    infile = args.krakenReport
    countlim = int(args.count)
    readout = args.readout
    kmerout = args.kmerout
    return(infile, countlim, readout, kmerout)
def _get_args ( ) : parser = argparse . ArgumentParser ( prog = 'kraken_parse' , formatter_class = argparse . RawDescriptionHelpFormatter , description = 'Parsing kraken' ) parser . add_argument ( 'krakenReport' , help = "path to kraken report file" ) parser . add_argument ( '-c' , dest = "count" , default = 50 , help = "Minimum number of hits on clade to report it. Default = 50" ) parser . add_argument ( '-or' , dest = "readout" , default = None , help = "Read count output file. Default = <basename>.read_kraken_parsed.csv" ) parser . add_argument ( '-ok' , dest = "kmerout" , default = None , help = "Kmer Output file. Default = <basename>.kmer_kraken_parsed.csv" ) args = parser . parse_args ( ) infile = args . krakenReport countlim = int ( args . count ) readout = args . readout kmerout = args . kmerout return ( infile , countlim , readout , kmerout )
This function parses and return arguments passed in
This function parses and return arguments passed in
'''This function parses and return arguments passed in'''