def test___nanopolish_third_record(self): nanopolish_variant_record = retrieve_nanopolish_entry_from_test_vcf(2) nanopolish_vcf = VCFFactory.create_Nanopolish_VCF_from_VariantRecord_and_Sample(nanopolish_variant_record, "SAMPLE") assert nanopolish_vcf.genotype == 1 assert math.isclose(nanopolish_vcf.genotype_confidence, 560.2, abs_tol=0.0001) assert nanopolish_vcf.svtype == "NA" assert nanopolish_vcf.coverage == 81
def test___samtools_third_real_record(self): samtools_variant_record = retrieve_samtools_entry_from_test_vcf(2) samtools_vcf = VCFFactory.create_Samtools_VCF_from_VariantRecord_and_Sample(samtools_variant_record, "sample_name") assert samtools_vcf.genotype == 1 assert math.isclose(samtools_vcf.genotype_confidence, 0.0, abs_tol=0.0001) assert samtools_vcf.svtype == "SNP" assert samtools_vcf.coverage == 82
def test___from_VariantRecord_and_Sample___valid_PandoraVCF(self, *mocks): variant_mock = Mock() sample_mock = Mock() vcf = VCFFactory.create_Pandora_VCF_from_VariantRecord_and_Sample( variant_mock, sample_mock) assert vcf.variant == variant_mock assert vcf.sample == sample_mock
def test___medaka_third_record(self): medaka_variant_record = retrieve_medaka_entry_from_test_vcf(2) medaka_vcf = VCFFactory.create_Medaka_VCF_from_VariantRecord_and_Sample( medaka_variant_record, "SAMPLE") assert medaka_vcf.genotype == 1 assert math.isclose(medaka_vcf.genotype_confidence, 53.109, abs_tol=0.0001) assert medaka_vcf.svtype == "NA" assert medaka_vcf.coverage == 1000
def test___snippy_third_real_record(self): snippy_variant_record = retrieve_snippy_entry_from_test_vcf(2) snippy_vcf = VCFFactory.create_Snippy_VCF_from_VariantRecord_and_Sample( snippy_variant_record, "H131800734") assert snippy_vcf.genotype == 1 assert math.isclose(snippy_vcf.genotype_confidence, 1957.94, abs_tol=0.0001) assert snippy_vcf.svtype == "complex" assert snippy_vcf.coverage == 1000
def test___medaka_fifth_record___gt_2___fails(self): medaka_variant_record = retrieve_medaka_entry_from_test_vcf(4) medaka_vcf = VCFFactory.create_Medaka_VCF_from_VariantRecord_and_Sample( medaka_variant_record, "SAMPLE")
def test___samtools_fails_with_genotype_2(self): samtools_variant_record = retrieve_samtools_entry_from_test_vcf(4) samtools_vcf = VCFFactory.create_Samtools_VCF_from_VariantRecord_and_Sample(samtools_variant_record, "sample_name")
def test___nanopolish_fifth_record___gt_2___fails(self): nanopolish_variant_record = retrieve_nanopolish_entry_from_test_vcf(4) nanopolish_vcf = VCFFactory.create_Nanopolish_VCF_from_VariantRecord_and_Sample(nanopolish_variant_record, "SAMPLE")
def test___from_VariantRecord_and_Sample___null_PandoraVCF_raises_NullVCFError( self, *mocks): with pytest.raises(NullVCFError): VCFFactory.create_Pandora_VCF_from_VariantRecord_and_Sample(1, 2)
def test___snippy_fails_with_genotype_0_0(self): snippy_variant_record = retrieve_snippy_entry_from_test_vcf(5) snippy_vcf = VCFFactory.create_Snippy_VCF_from_VariantRecord_and_Sample( snippy_variant_record, "H131800734")