def main():
""" run the clinical filtering analyses
"""
args = get_options()
# set the level of logging to generate
numeric_level = getattr(logging, args.loglevel.upper(), None)
log_filename = "clinical-filter.log"
if args.ped is not None:
log_filename = args.ped + ".log"
logging.basicConfig(level=numeric_level, filename=log_filename)
families = get_families(args)
count = sum([y.is_affected() for x in families for y in x.children])
finder = Filter(args.populations, count, args.known_genes, args.genes_date,
args.regions, args.lof_sites, args.pp_filter,
args.sum_x_lr2_file, args.output, args.export_vcf,
args.debug_chrom, args.debug_pos)
for family in families:
finder.filter_trio(family)
def setUp(self):
""" create a default Filter object to test
"""
count = 1
regions = None
known_genes, genes_date = None, None
output_path, export_vcf = None, None
debug_chrom, debug_pos = None, None
pp_filter = 0.9
lof_sites = None
population_tags = [
"AFR_AF", "AMR_AF", "ASN_AF", "DDD_AF", "EAS_AF", "ESP_AF",
"EUR_AF", "MAX_AF", "SAS_AF", "UK10K_cohort_AF"
]
sum_x_lr2 = None #
self.finder = Filter(population_tags, count, known_genes, genes_date,
regions, lof_sites, pp_filter, sum_x_lr2,
output_path, export_vcf, debug_chrom, debug_pos)
