def _remove_variant_set(self, variant_set_name):
vs = VariantSet.objects.get(name=variant_set_name,
reference_set=self.reference_set)
for call_set in VariantCallSet.objects(variant_sets=vs):
call_set.variant_sets.remove(vs)
call_set.save()
# Remove calls from callsets that only have this variantset
if len(call_set.variant_sets) < 2:
VariantCall.objects(call_set=call_set).delete()
call_set.delete()
# Remove variants that are ONLY from this variant set
Variant.objects(variant_sets=vs, variant_sets__size=2).delete()
VariantSetMetadata.objects(variant_set=vs).delete()
vs.delete()
def test_add_add_variants_and_calls(self):
vcf = VCF(f="tests/vcf_tests/test.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantCall.objects().count() == 21
assert Variant.objects().count() == 21
def test_add_second_vcf_variant_set(self):
# This VCF only has one Variant which is not in the first VCF
vcf = VCF(f="tests/vcf_tests/test2.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantSet.objects().count() == 3
assert VariantCallSet.objects().count() == 2
assert VariantCall.objects().count() == 42
assert Variant.objects().count() == 22
assert len(Variant.objects()[0].variant_sets) == 3
assert len(
Variant.objects.get(
names="UNION_BC_k31_var_147").variant_sets) == 3
def test_add_second_vcf_variant_set(self):
# This VCF only has one Variant which is not in the first VCF
vcf = VCF(f="tests/vcf_tests/test3.vcf",
reference_set_id=self.reference_set.id,
method="CORTEX")
vcf.add_to_database()
assert VariantSet.objects().count() == 2
assert VariantCallSet.objects().count() == 1
assert VariantCall.objects().count() == 106
assert Variant.objects().count() == 106
assert Variant.snps().count() == 89
assert Variant.indels().count() == 17
assert Variant.insertions().count() == 8
assert Variant.deletions().count() == 8
assert Variant.ph_snps.count() == 1