def testCreateDatabase(self):
dsFile = os.path.join(*["testdata", "vcf", "example.vcf"])
destDir = "out"
datasourceBuilder = TabixIndexedVcfDatasourceCreator()
datasourceFilename = datasourceBuilder._createDatabase(destDir=destDir, ds_file=dsFile)
tabixIndexedFilename = string.join([destDir, os.sep, datasourceFilename], "")
self.assertTrue(os.path.exists(tabixIndexedFilename), "No index file was generated.")
vcfReader = vcf.Reader(filename=tabixIndexedFilename, compressed=True, strict_whitespace=True)
vcfRecords = vcfReader.fetch(chrom=20, start=1230237, end=1230237)
for vcfRecord in vcfRecords:
self.assertEqual(vcfRecord.INFO["NS"], 3, "Expected %s but got %s." % (3, vcfRecord.INFO["NS"]))
self.assertEqual(vcfRecord.INFO["DP"], 13, "Expected %s but got %s." % (13, vcfRecord.INFO["DP"]))
