INNER CODE UNIT · Python

parse_kraken

nf-core/eager · bin/kraken_parse.py:50

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:
        read_dict = {}
        kmer_dict = {}
        csvreader = csv.reader(f, delimiter='\t')
        for line in csvreader:
            reads = int(line[1])
            if reads >= countlim:
                taxid = line[6]
                kmer = line[3]

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