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graph-size.py
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graph-size.py
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#! /usr/bin/env python2
#
# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project@idyll.org
#
import khmer
import sys
import screed
import os.path
from khmer.thread_utils import ThreadedSequenceProcessor, verbose_fasta_iter
K = 32
HASHTABLE_SIZE = int(4e6)
THRESHOLD = 500
N_HT = 4
WORKER_THREADS = 5
###
GROUPSIZE = 100
###
def main():
infile = sys.argv[1]
outfile = os.path.basename(infile) + '.graphsize'
if len(sys.argv) == 3:
outfile = sys.argv[2]
print 'input file to graphsize filter: %s' % infile
print 'filtering to output:', outfile
print '-- settings:'
print 'K', K
print 'HASHTABLE SIZE %g' % HASHTABLE_SIZE
print 'N HASHTABLES %d' % N_HT
print 'THRESHOLD', THRESHOLD
print 'N THREADS', WORKER_THREADS
print '--'
print 'creating ht'
ht = khmer.new_hashbits(K, HASHTABLE_SIZE, N_HT)
print 'eating fa', infile
total_reads, n_consumed = ht.consume_fasta(infile)
outfp = open(outfile, 'w')
###
def process_fn(record, ht=ht):
kmer = record['sequence'][:K]
size = ht.calc_connected_graph_size(kmer, THRESHOLD)
if size >= THRESHOLD:
return record['name'], record['sequence']
return None, None
tsp = ThreadedSequenceProcessor(process_fn, WORKER_THREADS, GROUPSIZE)
###
tsp.start(verbose_fasta_iter(infile), outfp)
if __name__ == '__main__':
main()