diff options
| -rw-r--r-- | wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 30 |
1 files changed, 7 insertions, 23 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index bc0cb4e0..06ce55d8 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -49,52 +49,41 @@ class TestGemmaMapping(unittest.TestCase): @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_choice,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): chromosomes.append(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": chromosomes}) - dataset_group = MockDatasetGroup( {"name": "GP1", "genofile": "file_geno"}) - dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", "species": AttributeSetter({"chromosomes": chromo})}) - trait = AttributeSetter({"name": "trait1"}) samples = [] - 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_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=[ ], vals=[], covariates="", use_loco=True) - 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_gen_pheno_txt.assert_called_once() + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count, 2) - - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") + self.assertEqual(mock_flat_files.call_count, 4) + self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): with mock.patch("builtins.open", mock.mock_open())as mock_open: gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ "x", "w", "q", "we", "R"], trait_filename="fitr.re") - mock_open.assert_called_once_with( '/home/user/data/gn2/fitr.re.txt', 'w') filehandler = mock_open() @@ -159,26 +148,21 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 results = parse_gemma_output(genofile_name="gema_file") expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] - mock_open.assert_called_once_with( "/home/user/img/gema_file_output.assoc.txt") - self.assertEqual(results, expected) - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") 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("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 = True file_to_write = """{"files":["file_1","file_2"]}""" - # incomplete - + pass @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): |