#!/opt/mambaforge/envs/bioconda/conda-bld/khmer_1737589152632/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/python
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# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring,invalid-name
"""
Sequence trimming by abundance using countgraph.

Trim sequences at k-mers of the given abundance, based on the given countgraph.
Output sequences will be placed in 'infile.abundfilt'.

% python scripts/filter-abund.py <coungraph> <data1> [ <data2> <...> ]

Use '-h' for parameter help.
"""
import sys
import os
import textwrap
import khmer

from khmer import __version__
from khmer import ReadParser, Countgraph
from khmer.utils import (broken_paired_reader, write_record)
from khmer.khmer_args import (add_threading_args, KhmerArgumentParser,
                              sanitize_help, check_argument_range)
from khmer.khmer_args import FileType as khFileType
from khmer.kfile import (check_input_files, check_space,
                         add_output_compression_type, get_file_writer)
from khmer.khmer_logger import (configure_logging, log_info, log_error,
                                log_warn)
from khmer.trimming import (trim_record)

DEFAULT_NORMALIZE_LIMIT = 20
DEFAULT_CUTOFF = 2


def get_parser():
    epilog = """\
    Trimmed sequences will be placed in
    ``${input_sequence_filename}.abundfilt`` for each input sequence file. If
    the input sequences are from RNAseq or metagenome sequencing then
    :option:`--variable-coverage` should be used.

    Example::

        load-into-counting.py -k 20 -x 5e7 countgraph data/100k-filtered.fa
        filter-abund.py -C 2 countgraph data/100k-filtered.fa
    """
    parser = KhmerArgumentParser(
        description='Trim sequences at a minimum k-mer abundance.',
        epilog=textwrap.dedent(epilog),
        citations=['counting'])
    parser.add_argument('input_graph', metavar='input_count_graph_filename',
                        help='The input k-mer countgraph filename')
    parser.add_argument('input_filename', metavar='input_sequence_filename',
                        help='Input FAST[AQ] sequence filename', nargs='+')
    add_threading_args(parser)
    parser.add_argument('-C', '--cutoff', dest='cutoff',
                        default=DEFAULT_CUTOFF,
                        type=check_argument_range(0, 256, 'cutoff'),
                        help="Trim at k-mers below this abundance.")
    parser.add_argument('-V', '--variable-coverage', action='store_true',
                        dest='variable_coverage', default=False,
                        help='Only trim low-abundance k-mers from sequences '
                        'that have high coverage.')
    parser.add_argument('-Z', '--normalize-to', type=int, dest='normalize_to',
                        help='Base the variable-coverage cutoff on this median'
                        ' k-mer abundance.',
                        default=DEFAULT_NORMALIZE_LIMIT)
    parser.add_argument('-o', '--output', dest='single_output_file',
                        type=khFileType('wb'),
                        metavar="optional_output_filename",
                        help='Output the trimmed sequences into a single file '
                        'with the given filename instead of creating a new '
                        'file for each input file.')
    parser.add_argument('-f', '--force', default=False, action='store_true',
                        help='Overwrite output file if it exists')
    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
                        action='store_true')
    add_output_compression_type(parser)
    return parser


def main():
    args = sanitize_help(get_parser()).parse_args()

    configure_logging(args.quiet)

    infiles = args.input_filename
    if ('-' in infiles or '/dev/stdin' in infiles) and not \
       args.single_output_file:
        log_error("Accepting input from stdin; output filename must "
                  "be provided with -o.")
        sys.exit(1)

    for filename in infiles:
        check_input_files(filename, args.force)

    check_space(infiles, args.force)

    log_info('loading countgraph: {graph}', graph=args.input_graph)
    countgraph = Countgraph.load(args.input_graph)
    ksize = countgraph.ksize()

    log_info("K: {ksize}", ksize=ksize)

    if args.single_output_file:
        outfile = args.single_output_file.name
        outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)

    # the filtering loop
    for infile in infiles:
        log_info('filtering {infile}', infile=infile)
        if not args.single_output_file:
            outfile = os.path.basename(infile) + '.abundfilt'
            outfp = open(outfile, 'wb')
            outfp = get_file_writer(outfp, args.gzip, args.bzip)

        paired_iter = broken_paired_reader(ReadParser(infile),
                                           min_length=ksize,
                                           force_single=True)

        for n, is_pair, read1, read2 in paired_iter:
            assert not is_pair
            assert read2 is None

            trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
                                            args.variable_coverage,
                                            args.normalize_to)
            if trimmed_record:
                write_record(trimmed_record, outfp)

        log_info('output in {outfile}', outfile=outfile)


if __name__ == '__main__':
    main()
