diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 43 |
1 files changed, 9 insertions, 34 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index fd45fd65..963c131f 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -21,13 +21,6 @@ class MockDatasetGroup(AttributeSetter): class TestGemmaMapping(unittest.TestCase): - # def test_fail(self): - # self.assertEqual(2,3) - - def setUp(self): - pass - - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): @@ -36,7 +29,6 @@ class TestGemmaMapping(unittest.TestCase): output_files = "file1" use_loco = False - mock_parse_loco.side_effect = None mock_parse_loco.return_value = [] this_trait = AttributeSetter({"name": "t1"}) @@ -46,7 +38,6 @@ class TestGemmaMapping(unittest.TestCase): expected_results = ([], "file1") self.assertEqual(expected_results, result) - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") @@ -59,7 +50,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") @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_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): chromosomes = [] for i in range(1, 5): @@ -75,35 +66,28 @@ class TestGemmaMapping(unittest.TestCase): trait = AttributeSetter({"name": "trait1"}) samples = [] - mock_gen_pheno_txt.side_effect = None + mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True - mock_os.system.return_value = None - mock_os.system.side_effect = None - mock_gen_covar.side_effect = None mock_gen_covar.return_value = None mock_flat_files.return_value = "/home/genotype/bimbam" - mock_parse_loco.side_effect = None mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - # check results self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) mock_gen_pheno_txt.assert_called_once() self.assertEqual(mock_flat_files.call_count, 4) - - system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] mock_os.system.assert_has_calls(system_calls) - mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt')) + mock_os.path.isfile.assert_called_once_with( + ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count,2) - + self.assertEqual(mock_logger.debug.call_count, 2) - mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): @@ -144,7 +128,6 @@ class TestGemmaMapping(unittest.TestCase): with mock.patch("builtins.open", mock.mock_open())as mock_open: gen_covariates_file(this_dataset=this_dataset, covariates=covariates, samples=["x1", "x2", "X3"]) - # test mocked methods create_dataset.assert_has_calls( [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) @@ -157,13 +140,10 @@ class TestGemmaMapping(unittest.TestCase): create_trait.assert_has_calls(mock_calls) - # test writing of covariates.txt - flat_files.assert_called_once_with('mapping') mock_open.assert_called_once_with( 'Home/Genenetwork/group_X_covariates.txt', 'w') filehandler = mock_open() - # expected all-9 filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) @@ -186,23 +166,18 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 self.assertEqual(results, expected) @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_xparse_gemma_output_empty_return(self): + def test_parse_gemma_output_empty_return(self): output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") self.assertEqual(results, []) - @mock.patch("builtins.open", mock.mock_open(read_data="chr\t")) - def test_parse_gemma_output_empty_return(self): - # duplicate - string_read = parse_gemma_output(genofile_name="hdf") - # print(string_read) - @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_os.path.isfile.return_value = False + mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" + #incomplete @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") |