def app_combivep_reference_updater():
#update LJB reference database
ljb_controller = LjbController()
ljb_controller.update()
#update UCSC reference database
ucsc_controller = UcscController()
ucsc_controller.update()
def init_ljb_controller_instance(self):
self.__ljb_controller = LjbController()
class TestLjbController(SafeRefDBTester):
def __init__(self, test_name):
SafeRefDBTester.__init__(self, test_name)
def setUp(self):
self.test_class = 'ljb_controller'
def init_ljb_controller_instance(self):
self.__ljb_controller = LjbController()
def test_clean_raw_database(self):
#initialize variables
# self.individual_debug = True
self.init_test('test_clean_raw_database')
self.init_ljb_controller_instance()
test_file = os.path.join(self.data_dir, 'test_clean_raw_database.txt')
out_file = os.path.join(self.working_dir, 'clean_database.txt')
expected_out_file = os.path.join(self.data_dir, 'expected_clean_database.txt')
#call function
# self.__ljb_controller.raw_db_file = test_file
# self.__ljb_controller.clean_db_file = out_file
self.__ljb_controller.clean_raw_database(test_file, out_file)
self.assertTrue(filecmp.cmp(out_file, expected_out_file), "Raw LJB database haven't been clean properly");
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")
def test_concat_chromosone_files(self):
#init
self.individual_debug = True
self.init_test('test_concat_chromosome_files')
self.init_ljb_controller_instance()
file_prefix = os.path.join(self.data_dir, 'dummy_dbNSFP_light1.3')
file_suffix = '.txt'
out_file = os.path.join(self.working_dir, 'out_concat.txt')
expected_out_file = os.path.join(self.data_dir, 'expected_concat_file.txt')
#runtest
self.__ljb_controller.concat_chromosome_files(file_prefix, file_suffix, out_file)
self.assertTrue(filecmp.cmp(out_file, expected_out_file), "chromosome files concatenation doesn't work properly");
def test_not_update(self):
#init
self.init_test('test_not_update')
self.init_ljb_controller_instance()
self.__ljb_controller.config_file = os.path.join(self.data_dir, 'test_not_update_config_file.txt')
#run test
self.assertFalse(self.__ljb_controller.update(), "LJB controller cannot identify correct update status")
def tearDown(self):
self.remove_working_dir()