def test_tabix_database(self): #init self.init_test('test_tabix_database') self.init_ljb_controller_instance() test_file = os.path.join(self.data_dir, 'test_tabix_database.txt') working_file = os.path.join(self.working_dir, 'test_tabix_database.txt') out_file = os.path.join(self.working_dir, 'test_tabix_database.txt.gz') self.copy_file(test_file, working_file) #test if the 'tabix' files are produced self.__ljb_controller.tabix_database(working_file) self.assertTrue(os.path.exists(out_file), "Tabix doesn't work correctly") self.assertTrue(os.path.exists(out_file+'.tbi'), "Tabix doesn't work correctly") #test if it is readable ljb_reader = LjbReader() ljb_reader.read(out_file) readable = False for rec in ljb_reader.fetch_array_snps('3', 108549516, 108549517): #to be tested again readable = True self.assertEqual(rec[combivep_settings.LJB_PARSED_0_INDEX_POS], '108549517', "Database tabixing doesn't work correctly") break self.assertTrue(readable, "Tabixed ljb database is not readable")