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 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)