diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 45 |
1 files changed, 17 insertions, 28 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 6414c3b..d264738 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -10,9 +10,8 @@ from gn3.computations.correlations import do_bicor from gn3.computations.correlations import compute_sample_r_correlation from gn3.computations.correlations import compute_all_sample_correlation from gn3.computations.correlations import filter_shared_sample_keys -from gn3.computations.correlations import tissue_lit_corr_for_probe_type -from gn3.computations.correlations import tissue_correlation_for_trait_list -from gn3.computations.correlations import lit_correlation_for_trait_list +from gn3.computations.correlations import tissue_correlation_for_trait +from gn3.computations.correlations import lit_correlation_for_trait from gn3.computations.correlations import fetch_lit_correlation_data from gn3.computations.correlations import query_formatter from gn3.computations.correlations import map_to_mouse_gene_id @@ -214,20 +213,8 @@ class TestCorrelation(TestCase): filter_shared_samples.assert_called_once_with( this_trait_data.get("trait_sample_data"), traits_dataset[0].get("trait_sample_data")) - @unittest.skip("not implemented") - def test_tissue_lit_corr_for_probe_type(self): - """Tests for doing tissue and lit correlation for trait list\ - if both the dataset and target dataset are probeset runs\ - on after initial correlation has been done - """ - - results = tissue_lit_corr_for_probe_type( - corr_type="tissue", top_corr_results={}) - - self.assertEqual(results, (None, None)) - @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value") - def test_tissue_correlation_for_trait_list(self, mock_compute_corr_coeff): + def test_tissue_correlation_for_trait(self, mock_compute_corr_coeff): """Test given a primary tissue values for a trait and and a list of\ target tissues for traits do the tissue correlation for them """ @@ -236,8 +223,8 @@ class TestCorrelation(TestCase): target_tissues_values = [1, 2, 3] mock_compute_corr_coeff.side_effect = [(0.4, 0.9), (-0.2, 0.91)] expected_tissue_results = {"1456_at": {"tissue_corr": 0.4, - "p_value": 0.9, "tissue_number": 3}} - tissue_results = tissue_correlation_for_trait_list( + "tissue_p_val": 0.9, "tissue_number": 3}} + tissue_results = tissue_correlation_for_trait( primary_tissue_values, target_tissues_values, corr_method="pearson", trait_id="1456_at", compute_corr_p_value=mock_compute_corr_coeff) @@ -246,7 +233,7 @@ class TestCorrelation(TestCase): @mock.patch("gn3.computations.correlations.fetch_lit_correlation_data") @mock.patch("gn3.computations.correlations.map_to_mouse_gene_id") - def test_lit_correlation_for_trait_list(self, mock_mouse_gene_id, fetch_lit_data): + def test_lit_correlation_for_trait(self, mock_mouse_gene_id, fetch_lit_data): """Fetch results from db call for lit correlation given a trait list\ after doing correlation """ @@ -260,7 +247,7 @@ class TestCorrelation(TestCase): fetch_lit_data.side_effect = [(15, 9), (17, 8), (11, 12)] - lit_results = lit_correlation_for_trait_list( + lit_results = lit_correlation_for_trait( conn=conn, target_trait_lists=target_trait_lists, species="rat", trait_gene_id="12") @@ -289,7 +276,7 @@ class TestCorrelation(TestCase): input trait mouse gene id and mouse gene id """ - expected_db_results = [namedtuple("lit_coeff", "val")(x*0.1) + expected_db_results = [("val", x*0.1) for x in range(1, 4)] conn = DataBase(expected_results=expected_db_results) expected_results = ("1", 0.1) @@ -375,10 +362,10 @@ class TestCorrelation(TestCase): self.assertEqual(results, expected_results) - @mock.patch("gn3.computations.correlations.lit_correlation_for_trait_list") + @mock.patch("gn3.computations.correlations.lit_correlation_for_trait") def test_compute_all_lit_correlation(self, mock_lit_corr): """Test for compute all lit correlation which acts\ - as an abstraction for lit_correlation_for_trait_list + as an abstraction for lit_correlation_for_trait and is used in the api/correlation/lit """ @@ -395,7 +382,7 @@ class TestCorrelation(TestCase): self.assertEqual(lit_correlation_results, expected_mocked_lit_results) - @mock.patch("gn3.computations.correlations.tissue_correlation_for_trait_list") + @mock.patch("gn3.computations.correlations.tissue_correlation_for_trait") @mock.patch("gn3.computations.correlations.process_trait_symbol_dict") def test_compute_all_tissue_correlation(self, process_trait_symbol, mock_tissue_corr): """Test for compute all tissue corelation which abstracts @@ -417,13 +404,15 @@ class TestCorrelation(TestCase): target_tissue_data = {"trait_symbol_dict": target_trait_symbol, "symbol_tissue_vals_dict": target_symbol_tissue_vals} - mock_tissue_corr.side_effect = [{"tissue_corr": -0.5, "p_value": 0.9, "tissue_number": 3}, - {"tissue_corr": 1.11, "p_value": 0.2, "tissue_number": 3}] + mock_tissue_corr.side_effect = [{"tissue_corr": -0.5, "tissue_p_val": 0.9, + "tissue_number": 3}, + {"tissue_corr": 1.11, "tissue_p_val": 0.2, + "tissue_number": 3}] expected_results = [{"1412_at": - {"tissue_corr": 1.11, "p_value": 0.2, "tissue_number": 3}}, + {"tissue_corr": 1.11, "tissue_p_val": 0.2, "tissue_number": 3}}, {"1418702_a_at": - {"tissue_corr": -0.5, "p_value": 0.9, "tissue_number": 3}}] + {"tissue_corr": -0.5, "tissue_p_val": 0.9, "tissue_number": 3}}] results = compute_all_tissue_correlation( primary_tissue_dict=primary_tissue_dict, |