bloom-count.py

#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
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#       notice, this list of conditions and the following disclaimer.
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#     * Redistributions in binary form must reproduce the above
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#       with the distribution.
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring,no-member

import khmer
import sys
import screed
from screed.fasta import fasta_iter


def main():
    filename = sys.argv[1]
    K = int(sys.argv[2])  # size of kmer
    HT_SIZE = int(sys.argv[3])  # size of hashtable
    N_HT = int(sys.argv[4])  # number of hashtables

    ht = khmer.Nodegraph(K, HT_SIZE, N_HT)

    n_unique = 0
    for n, record in enumerate(fasta_iter(open(filename))):
        sequence = record['sequence']
        seq_len = len(sequence)
        for n in range(0, seq_len + 1 - K):
            kmer = sequence[n:n + K]
            if (not ht.get(kmer)):
                n_unique += 1
            ht.count(kmer)

    print(n_unique)
    print(ht.n_occupied())
    print(ht.n_unique_kmers())


if __name__ == '__main__':
    main()