diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 23 |
1 files changed, 12 insertions, 11 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index bcc5dab9..a44ccb00 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -168,28 +168,29 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.json") - def test_parse_loco_output_file_found(self,mock_json,mock_os): + def test_parse_loco_output_file_found(self, mock_json, mock_os): """add tests for parse loco output file found""" - mock_json.load.return_value={ - "files":[["file_name","user","~/file1"], - ["file_name","user","~/file2"]] + mock_json.load.return_value = { + "files": [["file_name", "user", "~/file1"], + ["file_name", "user", "~/file2"]] } - return_file_1="""X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 + return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" - return_file_2="""chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" + return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" with mock.patch("builtins.open") as mock_open: - handles=(mock.mock_open(read_data="gwas").return_value,mock.mock_open(read_data=return_file_1).return_value,mock.mock_open(read_data=return_file_2).return_value) - mock_open.side_effect=handles + handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( + read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) + mock_open.side_effect = handles results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") - expected_results= [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] - - self.assertEqual(expected_results,results) + expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { + 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + self.assertEqual(expected_results, results) @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") |