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"]))
def testCreateDatasourceFromGZFile(self):
dsFile = os.path.join("testdata", "example.vcf.gz")
destDir = "out"
configFilename = os.path.join("out", "esp.config")
datasourceFilename = "example.vcf.gz"
dataSourceType = "indexed_vcf"
datasourceMatchMode = "avg"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
datasourceBuilder = TabixIndexedVcfDatasourceCreator()
datasourceBuilder.createDatasource(destDir, dsFile, configFilename, dataSourceType, dataSourceName,
dataSourceVersion, datasourceMatchMode)
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "match_mode"),
"match_mode option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "match_mode"), datasourceMatchMode,
"Expected data source match mode is %s but was %s."
% (datasourceMatchMode, configParser.get("general", "match_mode")))