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authorAlexanderlacuna2020-11-12 21:11:28 +0300
committerAlexanderlacuna2020-11-12 21:11:28 +0300
commita48e8d5e652551eb2d57953304ea0ec3587217ce (patch)
tree249423498e13fe2866ab3529cb92a452f67f61fd
parentf4dbdc51102d942079c7159ac48071282ec995ea (diff)
downloadgenenetwork2-a48e8d5e652551eb2d57953304ea0ec3587217ce.tar.gz
add test for parse gemma output in marker_regression/gemma_mapping.py
-rw-r--r--wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py22
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")