def testDuplicateAnnotationMetaData(self): """ Tests that the metadata is populated correctly in cases where duplicate annotations are present in the input VCF file. """ inputFilename = os.path.join(*["testdata", "vcf", "example.duplicate_annotation.vcf"]) creator = VcfInputMutationCreator(inputFilename) md = creator.getMetadata() self.assertTrue("variant_status" in md, "variant_status field is missing in metadata.") self.assertTrue("sample_variant_status" in md, "sample_variant_status is missing in metadata.")
def testGetMetaDataWithNoSampleNameExampleVcf(self): """ Tests to ensure that the metadata can be retrieved even before createMutations has been called. """ inputFilename = os.path.join(*["testdata", "vcf", "example.sampleName.removed.vcf"]) creator = VcfInputMutationCreator(inputFilename) gtKeys = {'genotype', 'read_depth', 'genotype_quality', 'haplotype_quality', 'q10', 's50', 'samples_number', 'depth_across_samples', 'allele_frequency', 'ancestral_allele', 'dbSNP_membership', 'id', 'qual', 'hapmap2_membership'} md = creator.getMetadata() ks = set(md.keys()) diff = gtKeys.symmetric_difference(ks) self.assertTrue(len(diff) == 0, "Missing keys that should have been seen in the metadata: " + str(diff))