remock

#!/usr/bin/env python3
#
#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
#
#     This program is free software: you can redistribute it and/or modify
#     it under the terms of the GNU Affero General Public License as
#     published by the Free Software Foundation, either version 3 of the
#     License, or (at your option) any later version.
#
#     This program is distributed in the hope that it will be useful,
#     but WITHOUT ANY WARRANTY; without even the implied warranty of
#     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#     GNU Affero General Public License for more details.
#
#     You should have received a copy of the GNU Affero General Public License
#     along with this program. If not, see <https://www.gnu.org/licenses/>.
#
"""
Generate mock samples for Recentrifuge
"""

import argparse
import os
import sys

from recentrifuge import __version__, __author__, __date__
from recentrifuge.mock import generate_mock
from recentrifuge.config import Filename, gray, blue
from recentrifuge.config import LICENSE, NODES_FILE, NAMES_FILE, TAXDUMP_PATH
from recentrifuge.taxonomy import Taxonomy

# optional package pandas (to read Excel with mock layout)
_USE_PANDAS = True
try:
    import pandas as pd
except ImportError:
    pd = None
    _USE_PANDAS = False


def main():
    """Main entry point to script."""

    def configure_parser():
        """Argument Parser Configuration"""
        parser = argparse.ArgumentParser(
            description='Generate mock samples for Recentrifuge',
            epilog=f'%(prog)s  - Release {__version__} - {__date__}' + LICENSE,
            formatter_class=argparse.RawDescriptionHelpFormatter
        )
        parser_mode = parser.add_mutually_exclusive_group(required=True)
        parser_mode.add_argument(
            '-f', '--file',
            action='store',
            metavar='FILE',
            type=Filename,
            help='Explicit source: Centrifuge output file as source'
        )
        parser_mode.add_argument(
            '-r', '--random',
            action='store',
            metavar='MHL',
            type=int,
            default=15,
            help=('Random score generated. Please provide the minimum hit '
                  'length (mhl) of the classification; 15 by default')
        )
        parser.add_argument(
            '-d', '--debug',
            action='store_true',
            help='increase output verbosity and perform additional checks'
        )
        parser_input = parser.add_mutually_exclusive_group(required=True)
        parser_input.add_argument(
            '-m', '--mock',
            action='append',
            metavar='FILE',
            type=Filename,
            help=('Mock files to be read for mock Centrifuge sequences layout.'
                  ' If a single directory is entered, every .mck file inside '
                  'will be taken as a different sample. '
                  'Multiple -f is available to include several samples.')
        )
        if _USE_PANDAS:
            parser_input.add_argument(
                '-x', '--xcel',
                action='store',
                metavar='FILE',
                type=Filename,
                help='Excel file with the mock layout.'
            )
            # Test mode really characterized by None in mock and xcel arguments
            parser_input.add_argument(
                '-t', '--test',
                action='store_true',
                help='generate mock data ready for testing Recentrifuge'
            )
        parser.add_argument(
            '-n', '--nodespath',
            action='store',
            metavar='PATH',
            default=TAXDUMP_PATH,
            help=('path for the nodes information files '
                  '(nodes.dmp and names.dmp from NCBI)')
        )
        parser.add_argument(
            '-c', '--compress',
            action='store_true',
            help='Any generated FASTQ file will be gzipped'
        )
        parser.add_argument(
            '-V', '--version',
            action='version',
            version=f'%(prog)s release {__version__} ({__date__})'
        )
        return parser

    def check_debug():
        """Check debugging mode"""
        if args.debug:
            print(blue('INFO:'), gray('Debugging mode activated'))
            print(blue('INFO:'), gray('Active parameters:'))
            for key, value in vars(args).items():
                if value:
                    print(gray(f'\t{key} ='), f'{value}')

    # Program header
    print(f'\n=-= {sys.argv[0]} =-= v{__version__} - {__date__}'
          f' =-= by {__author__} =-=\n')
    sys.stdout.flush()

    # Parse arguments
    argparser = configure_parser()
    args = argparser.parse_args()
    nodesfile: Filename = Filename(os.path.join(args.nodespath, NODES_FILE))
    namesfile: Filename = Filename(os.path.join(args.nodespath, NAMES_FILE))

    check_debug()

    # Load NCBI nodes, names and build children
    ncbi: Taxonomy = Taxonomy(nodesfile, namesfile, None, False)

    generate_mock(ncbi,
                  args.file, args.random,
                  args.mock, args.xcel,
                  args.debug, gzipped=args.compress)


if __name__ == '__main__':
    main()