#!/home/chelseaju/TahcoRoll/TahcoRoll/khmer/khmerEnv/bin/python2.7
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# 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()
