#!/usr/bin/env python
import argparse
import logging
from typing import Optional
from dae.gpf_instance.gpf_instance import GPFInstance
from dae.utils.verbosity_configuration import VerbosityConfiguration
[docs]def main(
gpf_instance: Optional[GPFInstance] = None,
argv: Optional[list[str]] = None,
) -> None:
"""Generate denovo gene sets CLI."""
description = "Generate genovo gene sets tool"
parser = argparse.ArgumentParser(description=description)
VerbosityConfiguration.set_arguments(parser)
parser.add_argument(
"--show-studies",
help="This option will print available "
"genotype studies and groups names",
default=False,
action="store_true",
)
parser.add_argument(
"--studies",
help="Specify genotype studies and groups "
"names for generating denovo gene sets. Default to all.",
default=None,
action="store",
)
args = parser.parse_args(argv)
VerbosityConfiguration.set(args)
logging.getLogger("impala").setLevel(logging.WARNING)
if gpf_instance is None:
gpf_instance = GPFInstance.build()
denovo_gene_sets_db = gpf_instance.denovo_gene_sets_db
if args.show_studies:
for study_id in denovo_gene_sets_db.get_genotype_data_ids():
print(study_id)
else:
if args.studies:
filter_studies_ids = None
studies = args.studies.split(",")
else:
studies = gpf_instance.get_genotype_data_ids()
print("generating de Novo gene sets for studies:", studies)
filter_studies_ids = [
study_id
for study_id in denovo_gene_sets_db.get_genotype_data_ids()
if study_id in studies
]
# pylint: disable=protected-access
denovo_gene_sets_db._build_cache(filter_studies_ids)
if __name__ == "__main__":
main()