def missing_from_vcf(family_set, vcf_file):
"""
Get indiv_ids in the VCF file that are not accounted for by the individuals in family_set
Can be extra indivs in families
"""
not_seen = set()
for family in family_set:
for indiv_id in family['individuals']:
not_seen.add(indiv_id)
for indiv_id in set(vcf_stuff.get_ids_from_vcf_path(vcf_file)):
not_seen.discard(indiv_id)
return list(not_seen)
def extra_indivs_in_vcf(family_set, vcf_file):
"""
Get indiv_ids in the VCF file that are not accounted for by the individuals in family_set
Can be extra indivs in families
"""
ids_in_vcf = vcf_stuff.get_ids_from_vcf_path(vcf_file)
seen = {indiv_id: False for indiv_id in ids_in_vcf}
for family in family_set:
for indiv_id in family['individuals']:
if indiv_id in seen:
seen[indiv_id] = True
return [i for i in seen if seen[i] == False]
def sample_id_list(self):
return vcf_stuff.get_ids_from_vcf_path(self.path())
def sample_id_list(self):
return vcf_stuff.get_ids_from_vcf_path(self.path())
