def test_add_new_vcf_variant_set(self): vcf = VCF(f="tests/vcf_tests/test.vcf", reference_set_id=self.reference_set.id, method="CORTEX") vcf.add_to_database() # We create a global variant set as well as one for the individual VCF assert VariantSet.objects().count() == 2 vs = VariantSet.objects()[0] assert len(Variant.objects()[0].variant_sets) == 2 assert vs.name == "test.vcf"
def _create_new_variant_set(self): variant_set_name = os.path.basename(self.f) if VariantSet.objects(name=variant_set_name, reference_set=self.reference_set): if not self.force: raise NotUniqueError( "VariantSet %s already exists. Rerun with -f to recreate." % variant_set_name) else: self._remove_variant_set(variant_set_name) self.vcf_variant_set = VariantSet.create_and_save( name=variant_set_name, reference_set=self.reference_set)
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