diff options
Diffstat (limited to 'wqflask/tests')
5 files changed, 38 insertions, 38 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py index d0264b87..bd99838d 100644 --- a/wqflask/tests/unit/wqflask/api/test_correlation.py +++ b/wqflask/tests/unit/wqflask/api/test_correlation.py @@ -127,9 +127,9 @@ class TestCorrelations(unittest.TestCase): expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6] expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6] for i, val in enumerate(expected_pearsonr): - self.assertAlmostEqual(val, results_pearsonr[i],4) + self.assertAlmostEqual(val, results_pearsonr[i], 4) for i, val in enumerate(expected_spearmanr): - self.assertAlmostEqual(val, results_spearmanr[i],4) + self.assertAlmostEqual(val, results_spearmanr[i], 4) self.assertEqual(results_num_overlap, None) @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits") diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index fe2569b8..f194c6c9 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -47,11 +47,11 @@ 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_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco): """add tests for run_gemma where first run is set to true""" - this_chromosomes={} + this_chromosomes = {} for i in range(1, 5): - this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"})) + this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"})) chromosomes = AttributeSetter({"chromosomes": this_chromosomes}) dataset_group = MockGroup( @@ -68,9 +68,9 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - self.assertEqual(mock_os.system.call_count,2) + self.assertEqual(mock_os.system.call_count, 2) mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True) + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True) mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) self.assertEqual(mock_flat_files.call_count, 4) @@ -144,7 +144,7 @@ class TestGemmaMapping(unittest.TestCase): "files": [["file_name", "user", "~/file1"], ["file_name", "user", "~/file2"]] } - return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t + return_file = """X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5 Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7 X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" @@ -159,7 +159,7 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" mock_open.side_effect = handles results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") - expected_results= [ + expected_results = [ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727}, {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812}, {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432}, diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index b47f877a..bbb79f98 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -1,20 +1,20 @@ import unittest -from unittest import mock -from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file +from unittest import mock +from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file -#issues some methods in genofile object are not defined -#modify samples should equal to vals +# issues some methods in genofile object are not defined +# modify samples should equal to vals class TestQtlReaperMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals=["V1","x","V4","V3","x"] - samples=["S1","S2","S3","S4","S5"] - trait_filename="trait_file" + def test_gen_pheno_txt_file(self): + vals = ["V1", "x", "V4", "V3","x"] + samples = ["S1", "S2", "S3", "S4","S5"] + trait_filename = "trait_file" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") - filehandler=mock_open() - write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] + gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") + filehandler = mock_open() + write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index c585f1df..0e617e93 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -8,7 +8,7 @@ from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names class TestRqtlMapping(unittest.TestCase): def setUp(self): - self.app_context=app.app_context() + self.app_context = app.app_context() self.app_context.push() def tearDown(self): @@ -17,28 +17,28 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self,mock_logger,mock_db): + def test_get_trait_data(self, mock_logger, mock_db): """test for getting trait data_type return True""" - query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("traid_id") + query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results = get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(query_value) - self.assertEqual(results,"fer434f") + self.assertEqual(results, "fer434f") def test_sanitize_rqtl_phenotype(self): """test for sanitizing rqtl phenotype""" - vals=['f',"x","r","x","x"] - results=sanitize_rqtl_phenotype(vals) - expected_phenotype_string='c(f,NA,r,NA,NA)' + vals = ['f', "x", "r", "x","x"] + results = sanitize_rqtl_phenotype(vals) + expected_phenotype_string = 'c(f,NA,r,NA,NA)' - self.assertEqual(results,expected_phenotype_string) + self.assertEqual(results, expected_phenotype_string) def test_sanitize_rqtl_names(self): """test for sanitzing rqtl names""" - vals=['f',"x","r","x","x"] - expected_sanitized_name="c('f',NA,'r',NA,NA)" - results=sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name,results) + vals = ['f', "x", "r", "x","x"] + expected_sanitized_name = "c('f',NA,'r',NA,NA)" + results = sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name, results) diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py index 34c51e3e..441a88a7 100644 --- a/wqflask/tests/wqflask/show_trait/testSampleList.py +++ b/wqflask/tests/wqflask/show_trait/testSampleList.py @@ -10,7 +10,7 @@ class TestSampleList(unittest.TestCase): characters_list = ["z", "f", "q", "s", "t", "a", "g"] names_list = ["temp1", "publish", "Sample", "Dataset"] - sorted_list_a=natural_sort(characters_list) - sorted_list_b=natural_sort(names_list) + sorted_list_a = natural_sort(characters_list) + sorted_list_b = natural_sort(names_list) self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"]) - self.assertEqual(sorted_list_b,["Dataset", "Sample", "publish", "temp1"]) + self.assertEqual(sorted_list_b, ["Dataset", "Sample", "publish", "temp1"]) |