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| author | Alexanderlacuna | 2020-11-09 21:15:24 +0300 |
|---|---|---|
| committer | Alexanderlacuna | 2020-11-09 21:15:24 +0300 |
| commit | 3ccc964fc466467c1c65f000fa7b43a38e10987a (patch) | |
| tree | f9e4e7c233ddf82a108c35f91a736d1f862e48b0 /wqflask | |
| parent | bf22cc3fbb37147b5e6c3012658fe5e43b696637 (diff) | |
| download | genenetwork2-3ccc964fc466467c1c65f000fa7b43a38e10987a.tar.gz | |
refactor test_run_gemma function
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 963c131f..bc0cb4e0 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -46,11 +46,10 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.logger") @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") - @mock.patch("wqflask.marker_regression.gemma_mapping.string.ascii_uppercase", "R") - @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os,mock_choice,mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): chromosomes = [] for i in range(1, 5): @@ -70,6 +69,7 @@ class TestGemmaMapping(unittest.TestCase): mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True mock_gen_covar.return_value = None + mock_choice.return_value="R" mock_flat_files.return_value = "/home/genotype/bimbam" mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ @@ -177,7 +177,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 def test_parse_loco_output_file_found(self, mock_os): mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" - #incomplete + # incomplete @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") |