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#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, 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=invalid-name,missing-docstring
"""
De-interleave a file.
Take an interleaved set of reads (/1 and /2), and extract them into separate
files (.1 and .2).
% scripts/split-paired-reads.py <infile>
Reads FASTQ and FASTA input, retains format for output.
"""
from __future__ import print_function
import screed
import sys
import os
import textwrap
import argparse
from khmer import __version__
from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
_VersionStdErrAction)
from khmer.utils import (write_record, broken_paired_reader,
UnpairedReadsError)
from khmer.kfile import (check_input_files, check_space,
add_output_compression_type,
get_file_writer, is_block, describe_file_handle)
def get_parser():
epilog = """\
Some programs want paired-end read input in the One True Format, which is
interleaved; other programs want input in the Insanely Bad Format, with
left- and right- reads separated. This reformats the former to the latter.
The directory into which the left- and right- reads are output may be
specified using :option:`-d`/:option:`--output-dir`. This directory will be
created if it does not already exist.
Alternatively, you can specify the filenames directly with
:option:`-1`/:option:`--output-first` and
:option:`-2`/:option:`--output-second`, which will override the
:option:`-d`/:option:`--output-dir` setting on a file-specific basis.
:option:`-0`/:option:'--output-orphans` will allow broken-paired format,
and orphaned reads will be saved separately, to the specified file.
Example::
split-paired-reads.py tests/test-data/paired.fq
Example::
split-paired-reads.py -0 reads-output-file tests/test-data/paired.fq
Example::
split-paired-reads.py -1 reads.1 -2 reads.2 tests/test-data/paired.fq
"""
parser = argparse.ArgumentParser(
description='Split interleaved reads into two files, left and right.',
epilog=textwrap.dedent(epilog),
formatter_class=ComboFormatter)
parser.add_argument('infile', nargs='?', default='/dev/stdin')
parser.add_argument('-d', '--output-dir', metavar="output_directory",
dest='output_directory', default='', help='Output '
'split reads to specified directory. Creates '
'directory if necessary')
parser.add_argument('-0', '--output-orphaned', metavar='output_orphaned',
help='Allow "orphaned" reads and extract them to ' +
'this file',
type=argparse.FileType('wb'))
parser.add_argument('-1', '--output-first', metavar='output_first',
default=None, help='Output "left" reads to this '
'file', type=argparse.FileType('wb'))
parser.add_argument('-2', '--output-second', metavar='output_second',
default=None, help='Output "right" reads to this '
'file', type=argparse.FileType('wb'))
parser.add_argument('--version', action=_VersionStdErrAction,
version='khmer {v}'.format(v=__version__))
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
add_output_compression_type(parser)
return parser
def main():
info('split-paired-reads.py')
args = sanitize_help(get_parser()).parse_args()
infile = args.infile
filenames = [infile]
check_input_files(infile, args.force)
check_space(filenames, args.force)
basename = os.path.basename(infile)
# decide where to put output files - specific directory? or just default?
if infile in ('/dev/stdin', '-'):
if not (args.output_first and args.output_second):
print("Accepting input from stdin; "
"output filenames must be provided.", file=sys.stderr)
sys.exit(1)
elif args.output_directory:
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
out1 = os.path.join(args.output_directory, basename + '.1')
out2 = os.path.join(args.output_directory, basename + '.2')
else:
out1 = basename + '.1'
out2 = basename + '.2'
# OVERRIDE output file locations with -1, -2
if args.output_first:
fp_out1 = get_file_writer(args.output_first, args.gzip, args.bzip)
out1 = fp_out1.name
else:
# Use default filename created above
fp_out1 = get_file_writer(open(out1, 'wb'), args.gzip, args.bzip)
if args.output_second:
fp_out2 = get_file_writer(args.output_second, args.gzip, args.bzip)
out2 = fp_out2.name
else:
# Use default filename created above
fp_out2 = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
# put orphaned reads here, if -0!
if args.output_orphaned:
fp_out0 = get_file_writer(args.output_orphaned, args.gzip, args.bzip)
out0 = describe_file_handle(args.output_orphaned)
counter1 = 0
counter2 = 0
counter3 = 0
index = None
screed_iter = screed.open(infile)
# walk through all the reads in broken-paired mode.
paired_iter = broken_paired_reader(screed_iter,
require_paired=not args.output_orphaned)
try:
for index, is_pair, record1, record2 in paired_iter:
if index % 10000 == 0:
print('...', index, file=sys.stderr)
if is_pair:
write_record(record1, fp_out1)
counter1 += 1
write_record(record2, fp_out2)
counter2 += 1
elif args.output_orphaned:
write_record(record1, fp_out0)
counter3 += 1
except UnpairedReadsError as e:
print("Unpaired reads found starting at {name}; exiting".format(
name=e.r1.name), file=sys.stderr)
sys.exit(1)
print("DONE; split %d sequences (%d left, %d right, %d orphans)" %
(counter1 + counter2, counter1, counter2, counter3), file=sys.stderr)
print("/1 reads in %s" % out1, file=sys.stderr)
print("/2 reads in %s" % out2, file=sys.stderr)
if args.output_orphaned:
print("orphans in %s" % out0, file=sys.stderr)
if __name__ == '__main__':
main()
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