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authorAlexanderlacuna2020-11-12 21:12:48 +0300
committerAlexanderlacuna2020-11-12 21:12:48 +0300
commitda794df7cf9094fc81edbcf007149db86bf68d01 (patch)
tree39daadbd4b03665f9e6f7d3c78a4496f46c15ffe /wqflask/tests
parenta48e8d5e652551eb2d57953304ea0ec3587217ce (diff)
downloadgenenetwork2-da794df7cf9094fc81edbcf007149db86bf68d01.tar.gz
add pep8 fixes in marker_regression/gemma_mapping.py
Diffstat (limited to 'wqflask/tests')
-rw-r--r--wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py23
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")