#!/Users/runner/bioconda/conda-bld/khmer_1597109715336/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/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
"""
Deinterleave 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.
"""
import sys
import os
import textwrap

from khmer import __version__
from khmer import ReadParser
from khmer.khmer_args import sanitize_help, KhmerArgumentParser
from khmer.khmer_args import FileType as khFileType
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, 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 = KhmerArgumentParser(
        description='Split interleaved reads into two files, left and right.',
        epilog=textwrap.dedent(epilog))

    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=khFileType('wb'))
    parser.add_argument('-1', '--output-first', metavar='output_first',
                        default=None, help='Output "left" reads to this '
                        'file', type=khFileType('wb'))
    parser.add_argument('-2', '--output-second', metavar='output_second',
                        default=None, help='Output "right" reads to this '
                        'file', type=khFileType('wb'))
    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

    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', '-'):
        # seqan only treats '-' as "read from stdin"
        infile = '-'
        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

    # walk through all the reads in broken-paired mode.
    paired_iter = broken_paired_reader(ReadParser(infile),
                                       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.read1.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()
