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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) 2015-2016, 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
"""
Split up pairs and singletons.
Take a file containing a mixture of interleaved and orphaned reads, and
extract them into separate files (.pe and .se).
% scripts/extract-paired-reads.py <infile>
Reads FASTQ and FASTA input, retains format for output.
"""
from __future__ import print_function
import sys
import os.path
import textwrap
from khmer import ReadParser
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
from khmer.kfile import get_file_writer
from khmer.utils import broken_paired_reader, write_record, write_record_pair
def get_parser():
epilog = """\
Many read-handling programs (assemblers, mappers, etc.) require
that you give them either perfectly interleaved files, or files
containing only single reads. This script takes files that were
originally interleaved but where reads may have been orphaned (via
error filtering, application of abundance filtering, digital
normalization in non-paired mode, or partitioning) and separates
the interleaved reads from the orphaned reads.
The default output is two files, `<input file>.pe` and `<input
file>.se`, placed in the current directory. The .pe file contains
interleaved and properly paired sequences, while the .se file
contains orphan sequences.
The directory into which the interleaved and orphaned 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:`-p`/:option:`--output-paired` and
:option:`-s`/:option:`--output-single`, which will override the
:option:`-d`/:option:`--output-dir` option.
Example::
extract-paired-reads.py tests/test-data/paired.fq
"""
parser = KhmerArgumentParser(
description='Take a mixture of reads and split into pairs and '
'orphans.', epilog=textwrap.dedent(epilog))
parser.add_argument('infile', nargs='?', default='/dev/stdin')
parser.add_argument('-d', '--output-dir', default='', help='Output '
'split reads to specified directory. Creates '
'directory if necessary')
parser.add_argument('-p', '--output-paired', metavar="filename",
type=khFileType('wb'),
default=None, help='Output paired reads to this '
'file')
parser.add_argument('-s', '--output-single', metavar="filename",
type=khFileType('wb'), default=None,
help='Output orphaned reads to this file')
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()
infile = args.infile
check_input_files(infile, args.force)
check_space([infile], args.force)
# decide where to put output files - specific directory? or just default?
if infile in ('/dev/stdin', '-'):
# seqan only treats '-' as "read from stdin"
infile = '-'
if not (args.output_paired and args.output_single):
print("Accepting input from stdin; output filenames must be "
"provided.", file=sys.stderr)
sys.exit(1)
elif args.output_dir:
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
out1 = args.output_dir + '/' + os.path.basename(infile) + '.se'
out2 = args.output_dir + '/' + os.path.basename(infile) + '.pe'
else:
out1 = os.path.basename(infile) + '.se'
out2 = os.path.basename(infile) + '.pe'
# OVERRIDE default output file locations with -p, -s
if args.output_paired:
paired_fp = get_file_writer(args.output_paired, args.gzip, args.bzip)
out2 = paired_fp.name
else:
# Don't override, just open the default filename from above
paired_fp = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
if args.output_single:
single_fp = get_file_writer(args.output_single, args.gzip, args.bzip)
out1 = args.output_single.name
else:
# Don't override, just open the default filename from above
single_fp = get_file_writer(open(out1, 'wb'), args.gzip, args.bzip)
print('reading file "%s"' % infile, file=sys.stderr)
print('outputting interleaved pairs to "%s"' % out2, file=sys.stderr)
print('outputting orphans to "%s"' % out1, file=sys.stderr)
n_pe = 0
n_se = 0
reads = ReadParser(infile)
for index, is_pair, read1, read2 in broken_paired_reader(reads):
if index % 100000 == 0 and index > 0:
print('...', index, file=sys.stderr)
if is_pair:
write_record_pair(read1, read2, paired_fp)
n_pe += 1
else:
write_record(read1, single_fp)
n_se += 1
single_fp.close()
paired_fp.close()
if n_pe == 0:
raise TypeError("no paired reads!? check file formats...")
print('DONE; read %d sequences,'
' %d pairs and %d singletons' %
(n_pe * 2 + n_se, n_pe, n_se), file=sys.stderr)
print('wrote to: %s and %s' % (out2, out1),
file=sys.stderr)
if __name__ == '__main__':
main()
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