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
"""
options = get_options()
# set the level of logging to generate
numeric_level = getattr(logging, options.loglevel.upper(), None)
log_filename = "clinical-filter.log"
if options.ped is not None:
log_filename = options.ped + ".log"
logging.basicConfig(level=numeric_level, filename=log_filename)
finder = ClinicalFilter(options)
finder.filter_trios()
def main():
""" run the clinical filtering analyses
"""
options = get_options()
# set the level of logging to generate
numeric_level = getattr(logging, options.loglevel.upper(), None)
log_filename = "clinical-filter.log"
if options.ped is not None:
log_filename = options.ped + ".log"
logging.basicConfig(level=numeric_level, filename=log_filename)
finder = ClinicalFilter(options)
finder.filter_trios()
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)
