runclinicalfiltering.py

"""
Copyright (c) 2021 Genome Research Limited
Author: Ruth Eberhardt <re3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

import logging
from datetime import datetime

from utils.parse_args import get_options
from file_loading.ped_files import create_ped, openped
from filtering.filter import Filter
from output.print_results import create_output


def main():
    """
    Run the clinical filtering analyses
    """
    args = get_options()
    timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")

    if args.ped is None:
        logfile = args.outdir + "/clinical_filter." + timestamp + ".log"
    else:
        logfile = args.ped + "." + timestamp + ".log"
    logging.basicConfig(filename=logfile, level=logging.DEBUG)

    if args.ped is None:
        # create ped file from family members on command line
        args.ped = args.outdir + "/ped." + timestamp + ".ped"
        create_ped(args.ped, args.child, args.mother, args.father, args.sex,
                   args.mum_aff, args.dad_aff)

    families = openped(args.ped, args.proband_list)

    variants_per_family = {}
    inheritance_reports_per_family = {}
    for family in families.keys():
        varfilter = Filter(families[family], args.known_genes,
                           args.known_regions, args.trusted_variants,
                           args.outdir)
        filtered_variants, inheritance_report = varfilter.filter_trio()

        variants_per_family[family] = filtered_variants
        inheritance_reports_per_family[family] = inheritance_report

    create_output(families, variants_per_family, inheritance_reports_per_family,
                  args.outdir)


if __name__ == "__main__":
    main()