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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=invalid-name,missing-docstring
"""
Interleave left and right reads.
Take two files containing left & right reads from a paired-end sequencing run,
and interleave them.
% scripts/interleave-reads.py <R1> <R2> [ -o <outputfile> ]
By default, output is sent to stdout; or use -o. Use '-h' for parameter help.
"""
from __future__ import print_function
import screed
import sys
import textwrap
from khmer import __version__
from khmer.kfile import check_input_files, check_space
from khmer.khmer_args import sanitize_help, KhmerArgumentParser
from khmer.khmer_args import FileType as khFileType
from khmer.kfile import (add_output_compression_type, get_file_writer,
describe_file_handle)
from khmer.utils import (write_record_pair, check_is_left, check_is_right,
check_is_pair)
try:
from itertools import zip_longest
except ImportError:
from itertools import izip_longest as zip_longest
def get_parser():
epilog = """\
The output is an interleaved set of reads, with each read in <R1> paired
with a read in <R2>. By default, the output goes to stdout unless
:option:`-o`/:option:`--output` is specified.
As a "bonus", this file ensures that if read names are not already
formatted properly, they are reformatted consistently, such that
they look like the pre-1.8 Casava format (`@name/1`, `@name/2`).
This reformatting can be switched off with the
:option:`--no-reformat` flag.
Example::
interleave-reads.py tests/test-data/paired.fq.1 \\
tests/test-data/paired.fq.2 -o paired.fq"""
parser = KhmerArgumentParser(
description='Produce interleaved files from R1/R2 paired files',
epilog=textwrap.dedent(epilog))
parser.add_argument('left')
parser.add_argument('right')
parser.add_argument('-o', '--output', metavar="filename",
type=khFileType('wb'),
default=sys.stdout)
parser.add_argument('--no-reformat', default=False, action='store_true',
help='Do not reformat read names or enforce\
consistency')
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():
args = sanitize_help(get_parser()).parse_args()
check_input_files(args.left, args.force)
check_input_files(args.right, args.force)
check_space([args.left, args.right], args.force)
s1_file = args.left
s2_file = args.right
print("Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file), file=sys.stderr)
outfp = get_file_writer(args.output, args.gzip, args.bzip)
counter = 0
screed_iter_1 = screed.open(s1_file)
screed_iter_2 = screed.open(s2_file)
for read1, read2 in zip_longest(screed_iter_1, screed_iter_2):
if read1 is None or read2 is None:
print(("ERROR: Input files contain different number"
" of records."), file=sys.stderr)
sys.exit(1)
if counter % 100000 == 0:
print('...', counter, 'pairs', file=sys.stderr)
counter += 1
name1 = read1.name
name2 = read2.name
if not args.no_reformat:
if not check_is_left(name1):
name1 += '/1'
if not check_is_right(name2):
name2 += '/2'
read1.name = name1
read2.name = name2
if not check_is_pair(read1, read2):
print("ERROR: This doesn't look like paired data! "
"%s %s" % (read1.name, read2.name), file=sys.stderr)
sys.exit(1)
write_record_pair(read1, read2, outfp)
print('final: interleaved %d pairs' % counter, file=sys.stderr)
print('output written to', describe_file_handle(outfp), file=sys.stderr)
if __name__ == '__main__':
main()
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