def reload(self):
# drop the whole database
self._db.connection.drop_database(self._db.name)
for cohort in self.cohorts:
self._annotator.add_vcf_file_to_annotator(cohort['vcf'])
indiv_ids = vcf_stuff.get_ids_from_vcf_path(cohort['vcf'])
self.add_family(cohort['slug'], 'control_cohort', indiv_ids)
self.load_family_set(cohort['vcf'], [(cohort['slug'], 'control_cohort')])
def indivs_missing_from_vcf(family, vcf_file):
"""
Return list of indiv_ids in family that are not in vcf_file
Empty list if all individuals are in vcf
"""
in_vcf = set(vcf_stuff.get_ids_from_vcf_path(vcf_file))
not_in_vcf = []
for indiv_id in family['individuals'].keys():
if not indiv_id in in_vcf:
not_in_vcf.append(indiv_id)
return not_in_vcf
def indivs_missing_from_vcf(family, vcf_file):
"""
Return list of indiv_ids in family that are not in vcf_file
Empty list if all individuals are in vcf
"""
in_vcf = set(vcf_stuff.get_ids_from_vcf_path(vcf_file))
not_in_vcf = []
for indiv_id in family['individuals'].keys():
if not indiv_id in in_vcf:
not_in_vcf.append(indiv_id)
return not_in_vcf
def sample_id_list(self):
return vcf_stuff.get_ids_from_vcf_path(self.path())
