INNER CODE UNIT · Python

_get_basename

nf-core/eager · bin/kraken_parse.py:42

def _get_basename(file_name):
    if ("/") in file_name:
        basename = file_name.split("/")[-1].split(".")[0]
    else:
        basename = file_name.split(".")[0]
    return(basename)


def parse_kraken(infile, countlim):
    '''
    INPUT:
        infile (str): path to kraken report file
        countlim (int): lowest count threshold to report hit
    OUTPUT:
        resdict (dict): key=taxid, value=readCount

    '''
    with open(infile, 'r') as f:

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