/
slice-reads-by-coverage.py
executable file
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/
slice-reads-by-coverage.py
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#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2014-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
import argparse
import screed
import sys
import khmer
def output_single(read):
if hasattr(read, 'quality'):
return "@%s\n%s\n+\n%s\n" % (read.name, read.sequence, read.quality)
else:
return ">%s\n%s\n" % (read.name, read.sequence)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-m', '--min-coverage', type=int, default=None)
parser.add_argument('-M', '--max-coverage', type=int, default=None)
parser.add_argument('input_count_graph')
parser.add_argument('input_readfile')
parser.add_argument('output_readfile')
args = parser.parse_args()
print('min_coverage: %s' % args.min_coverage, file=sys.stderr)
print('max_coverage: %s' % args.max_coverage, file=sys.stderr)
if not (args.min_coverage or args.max_coverage):
print("neither min nor max coverage specified!? exiting!", file=sys.stderr)
sys.exit(1)
if args.min_coverage and args.max_coverage and \
args.max_coverage < args.min_coverage:
print("min_coverage > max_coverage!? exiting!", file=sys.stderr)
sys.exit(1)
htable = khmer.load_countgraph(args.input_count_graph)
output_file = args.output_readfile
output_fp = open(output_file, 'w')
n_kept = 0
n = 0
for n, record in enumerate(screed.open(args.input_readfile)):
if n % 100000 == 0:
print('...', n, n_kept, file=sys.stderr)
seq = record.sequence.upper()
seq = seq.replace('N', 'A')
try:
med, _, _ = htable.get_median_count(seq)
except ValueError:
continue
keep = True
if args.min_coverage and med < args.min_coverage:
keep = False
if args.max_coverage and med > args.max_coverage:
keep = False
if keep:
n_kept += 1
output_fp.write(output_single(record))
print('consumed %d reads; kept %d' % (n, n_kept), file=sys.stderr)
if __name__ == '__main__':
main()