#!/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
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
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# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring
"""
Produce the k-mer abundance distribution for the given file.

% python scripts/abundance-dist.py [ -z -s ] <countgraph> <data> <histout>

Use '-h' for parameter help.
"""

import sys
import csv
import khmer
import textwrap
import os
from khmer import Countgraph
from khmer.kfile import check_input_files
from khmer.khmer_args import (sanitize_help, KhmerArgumentParser)
from khmer.khmer_logger import (configure_logging, log_info, log_error,
                                log_warn)


def get_parser():
    epilog = """\
    Example::

        load-into-counting.py -x 1e7 -N 2 -k 17 counts \\
                tests/test-data/test-abund-read-2.fa
        abundance-dist.py counts tests/test-data/test-abund-read-2.fa test-dist
    """
    parser = KhmerArgumentParser(
        description="Calculate abundance distribution of the k-mers in "
        "the sequence file using a pre-made k-mer countgraph.",
        epilog=textwrap.dedent(epilog), citations=['counting'])

    parser.add_argument('input_count_graph_filename', help='The name of the'
                        ' input k-mer countgraph file.')
    parser.add_argument('input_sequence_filename', help='The name of the input'
                        ' FAST[AQ] sequence file.')
    parser.add_argument('output_histogram_filename', help='The columns are: '
                        '(1) k-mer abundance, (2) k-mer count, (3) cumulative '
                        'count, (4) fraction of total distinct k-mers.')
    parser.add_argument('-z', '--no-zero', dest='output_zero', default=True,
                        action='store_false',
                        help='Do not output zero-count bins')
    parser.add_argument('-s', '--squash', dest='squash_output', default=False,
                        action='store_true',
                        help='Overwrite existing output_histogram_filename')
    parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
                        action='store_false',
                        help='Do not count k-mers past 255')
    parser.add_argument('-f', '--force', default=False, action='store_true',
                        help='Continue even if specified input files '
                        'do not exist or are empty.')
    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
                        action='store_true')
    return parser


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

    configure_logging(args.quiet)

    infiles = [args.input_count_graph_filename,
               args.input_sequence_filename]
    for infile in infiles:
        check_input_files(infile, False)

    log_info('Loading counting graph from {graph}',
             graph=args.input_count_graph_filename)
    countgraph = Countgraph.load(args.input_count_graph_filename)

    if not countgraph.get_use_bigcount() and args.bigcount:
        log_warn("WARNING: The loaded graph has bigcount DISABLED while "
                 "bigcount reporting is ENABLED--counts higher than 255 will "
                 "not be reported.")

    countgraph.set_use_bigcount(args.bigcount)

    kmer_size = countgraph.ksize()
    hashsizes = countgraph.hashsizes()
    tracking = khmer.Nodegraph(  # pylint: disable=protected-access
        kmer_size, 1, 1, primes=hashsizes)

    log_info('K: {ksize}', ksize=kmer_size)
    log_info('outputting to {output}', output=args.output_histogram_filename)

    if args.output_histogram_filename in ('-', '/dev/stdout'):
        pass
    elif os.path.exists(args.output_histogram_filename):
        if not args.squash_output:
            log_error('ERROR: {output} exists; not squashing.',
                      output=args.output_histogram_filename)
            sys.exit(1)

        log_info('** squashing existing file {output}',
                 output=args.output_histogram_filename)

    log_info('preparing hist...')
    abundances = countgraph.abundance_distribution(
        args.input_sequence_filename, tracking)
    total = sum(abundances)

    if 0 == total:
        log_error("ERROR: abundance distribution is uniformly zero; "
                  "nothing to report.")
        log_error("\tPlease verify that the input files are valid.")
        sys.exit(1)

    if args.output_histogram_filename in ('-', '/dev/stdout'):
        countgraph_fp = sys.stdout
    else:
        countgraph_fp = open(args.output_histogram_filename, 'w')
    countgraph_fp_csv = csv.writer(countgraph_fp)
    # write headers:
    countgraph_fp_csv.writerow(['abundance', 'count', 'cumulative',
                                'cumulative_fraction'])

    sofar = 0
    for _, i in enumerate(abundances):
        if i == 0 and not args.output_zero:
            continue

        sofar += i
        frac = sofar / float(total)

        countgraph_fp_csv.writerow([_, i, sofar, round(frac, 3)])

        if sofar == total:
            break


if __name__ == '__main__':
    main()

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