add test for parse gemma output in marker_regression/gemma_mapping.py

1 files changed, 20 insertions, 2 deletions

diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py
index e47c8335..bcc5dab9 100644
--- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py
@@ -167,11 +167,29 @@ 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")
-    def test_parse_loco_output_file_found(self, mock_os):
+    @mock.patch("wqflask.marker_regression.gemma_mapping.json")
+    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"]]
+        }
+        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"""
         mock_os.path.isfile.return_value = True
         file_to_write = """{"files":["file_1","file_2"]}"""
-        pass
+        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
+            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)
+
 
     @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
     @mock.patch("wqflask.marker_regression.gemma_mapping.os")