count-kmers.py

#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2015, The Regents of the University of California.
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# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring,invalid-name
"""
Produce k-mer counts for all the k-mers in the given sequence file,
using the given countgraph.

% python sandbox/count-kmers.py <ct> <fasta/fastq> [ <fasta/fastq> ... ]

Use '-h' for parameter help.
"""

import sys
import khmer
import argparse
import screed
import csv
from khmer import Countgraph
from khmer.khmer_args import info


def get_parser():
    parser = argparse.ArgumentParser(
        description="Output abundances of the k-mers in "
        "the sequence files using a pre-made k-mer countgraph.",
        formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    parser.add_argument('input_count_graph_filename', help='The name of the'
                        ' input k-mer countgraph file.')
    parser.add_argument('input_sequence_filenames', help='The input'
                        ' FAST[AQ] sequence file(s).', nargs='+')

    parser.add_argument('-o', '--out', metavar="output_file",
                        dest='output_file',
                        type=argparse.FileType('w'),
                        default=None, help='output counts to this file')

    return parser


def main():
    info('count-kmers.py', ['counting'])
    args = get_parser().parse_args()

    print ('hashtable from', args.input_count_graph_filename,
           file=sys.stderr)
    countgraph = Countgraph.load(
        args.input_count_graph_filename)

    kmer_size = countgraph.ksize()
    hashsizes = countgraph.hashsizes()
    tracking = khmer.Nodegraph(  # pylint: disable=protected-access
        kmer_size, 1, 1, primes=hashsizes)

    if args.output_file is None:
        args.output_file = sys.stdout
    writer = csv.writer(args.output_file)

    for filename in args.input_sequence_filenames:
        for record in screed.open(filename):
            seq = record.sequence.replace('N', 'A')
            for i in range(len(seq) - kmer_size + 1):
                kmer = seq[i:i+kmer_size]
                if not tracking.get(kmer):
                    tracking.count(kmer)
                    writer.writerow([kmer, str(countgraph.get(kmer))])

    print ('Total number of unique k-mers: {0}'.format(
        countgraph.n_unique_kmers()), file=sys.stderr)


if __name__ == '__main__':
    main()

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