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")
