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")
