kevlar-call-table.py

import argparse
import khmer
import pandas

parser = argparse.ArgumentParser()
parser.add_argument('--counts', nargs='+')
parser.add_argument('--samples', nargs='+')
parser.add_argument('window', nargs='+')
args = parser.parse_args()

counts = [khmer.Counttable.load(cfile) for cfile in args.counts]
if not args.samples:
    labels = ['Sample{:d}Abund'.format(i) for i in range(len(counts))]
else:
    labels = ['{:s}Abund'.format(sample) for sample in args.samples]
assert len(labels) == len(counts)
for window in args.window:
    data = pandas.DataFrame(
        [[k] + [c.get(k) for c in counts] for k in counts[0].get_kmers(window)],
        columns=['K-mer'] + labels,
    )
    print(data.to_string(index=False))