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collect-reads.py
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collect-reads.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) 2011-2015, 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
# pylint: disable=missing-docstring,invalid-name
"""
Build a counting Bloom filter from the given sequences, save in <htname>.
Stop collecting reads when the average coverage gets above -C (default 50).
Place reads into -o output_file.
% collect-reads.py <htname> <data1> [ <data2> <...> ]
Use '-h' for parameter help.
"""
import sys
import textwrap
import khmer
from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, report_on_config, info,
calculate_graphsize, sanitize_help)
from khmer.kfile import check_input_files, check_space
from khmer.kfile import check_space_for_graph
import argparse
import screed
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 get_parser():
epilog = """
The memory usage of this script with :option:`-b` will be about
1.15x the product of the :option:`-x` and :option:`-N` numbers.
Example::
collect-reads.py -k 20 -x 5e7 out.ct data/100k-filtered.fa
"""
parser = build_counting_args("Collect reads until a given avg coverage.",
epilog=textwrap.dedent(epilog))
parser.add_argument('output_countgraph_filename', help="The name of the"
" file to write the k-mer countgraph to.")
parser.add_argument('input_sequence_filename', nargs='+',
help="The names of one or more FAST[AQ] input "
"sequence files.")
parser.add_argument('--report-total-kmers', '-t', action='store_true',
help="Prints the total number of k-mers to stderr")
parser.add_argument('-C', '--coverage', type=int, default=50,
help='Collect reads until this coverage, then exit.')
parser.add_argument('-o', '--output', type=argparse.FileType('w'),
help='Write collect reads into this file.')
parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
action='store_false',
help='Do not count k-mers past 255')
return parser
def main():
info('collect-reads.py', ['counting'])
args = sanitize_help(get_parser()).parse_args()
report_on_config(args)
base = args.output_countgraph_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, False)
check_space(args.input_sequence_filename, False)
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.output_countgraph_filename, tablesize,
False)
print('Saving k-mer countgraph to %s' % base)
print('Loading sequences from %s' % repr(filenames))
if args.output:
print('Outputting sequences to', args.output)
print('making countgraph', file=sys.stderr)
htable = khmer_args.create_countgraph(args)
htable.set_use_bigcount(args.bigcount)
total_coverage = 0.
n = 0
for index, filename in enumerate(filenames):
for record in screed.open(filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'A')
try:
med, _, _ = htable.get_median_count(seq)
except ValueError:
continue
total_coverage += med
n += 1
if total_coverage / float(n) > args.coverage:
print('reached target average coverage:', \
total_coverage / float(n))
break
htable.consume(seq)
if args.output:
args.output.write(output_single(record))
if n % 100000 == 0:
print('...', index, filename, n, total_coverage / float(n))
if total_coverage / float(n) > args.coverage:
break
print('Collected %d reads' % (n,))
if args.report_total_kmers:
print('Total number of k-mers: {0}'.format(
htable.n_occupied()), file=sys.stderr)
print('saving', base)
htable.save(base)
info_fp = open(base + '.info', 'w')
info_fp.write('through end: %s\n' % filenames[-1])
# Change 0.2 only if you really grok it. HINT: You don't.
fp_rate = khmer.calc_expected_collisions(htable, False,
max_false_pos=.2)
print('fp rate estimated to be %1.3f' % fp_rate)
print('fp rate estimated to be %1.3f' % fp_rate, file=info_fp)
print('DONE.')
if __name__ == '__main__':
main()
# vim: set filetype=python tabstop=4 softtabstop=4 shiftwidth=4 expandtab:
# vim: set textwidth=79: