diff options
| author | Muriithi Frederick Muriuki | 2021-11-20 18:06:32 +0300 |
|---|---|---|
| committer | GitHub | 2021-11-20 18:06:32 +0300 |
| commit | 92d5766f5514181cd6aa82fc0d0f225666e892cb (patch) | |
| tree | 74840e8e2118e24e1f49eb780ca0bbf24704e510 /tests/unit | |
| parent | abc0d36f39c691652fee81bce808d625fc368e72 (diff) | |
| parent | 08c81b8892060353bb7fb15555875f03bbdcb46e (diff) | |
| download | genenetwork3-92d5766f5514181cd6aa82fc0d0f225666e892cb.tar.gz | |
Merge pull request #56 from genenetwork/partial-correlations
Partial correlations
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt | 1009 | ||||
| -rw-r--r-- | tests/unit/computations/test_partial_correlations.py | 92 | ||||
| -rw-r--r-- | tests/unit/test_data_helpers.py | 30 | ||||
| -rw-r--r-- | tests/unit/test_heatmaps.py | 4 |
4 files changed, 1068 insertions, 67 deletions
diff --git a/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt b/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt new file mode 100644 index 0000000..6254902 --- /dev/null +++ b/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt @@ -0,0 +1,1009 @@ +------------------------------------------------------------ +function_name: pcor.rec +count: 18 +x: 27.0465861540288, 85.84661539644, 23.6260315869004, -6.64654695428908, 66.0871273837984, -74.3310157675296, -7.09130000323057, -11.6802562493831, 24.9050020240247, -22.3750857636333, 68.0144839920104, 16.7857648339123, -26.3561313506216, 57.9470653086901, -9.12516843527555, -36.0829488374293, 68.283180333674, -83.6802623700351 +y: 12.4649536795914, -20.5139847937971, -33.6048585828394, 19.9723906349391, 35.5448212940246, 31.2940447591245, -14.5105968695134, 79.1401757858694, -13.6585284024477, -57.8275624662638, -81.5757951233536, 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gn3.computations.partial_correlations import ( fix_samples, control_samples, + build_data_frame, dictify_by_samples, tissue_correlation, find_identical_traits, - partial_correlation_matrix, - good_dataset_samples_indexes, - partial_correlation_recursive) + good_dataset_samples_indexes) sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -93,29 +95,6 @@ dictified_control_samples = ( "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}) -def parse_test_data_csv(filename): - """ - Parse test data csv files for R -> Python conversion of some functions. - """ - def __str__to_tuple(line, field): - return tuple(float(s.strip()) for s in line[field].split(",")) - - with open(filename, newline="\n") as csvfile: - reader = csv.DictReader(csvfile, delimiter=",", quotechar='"') - lines = tuple(row for row in reader) - - methods = {"p": "pearson", "s": "spearman", "k": "kendall"} - return tuple({ - **line, - "x": __str__to_tuple(line, "x"), - "y": __str__to_tuple(line, "y"), - "z": __str__to_tuple(line, "z"), - "method": methods[line["method"]], - "rm": line["rm"] == "TRUE", - "result": float(line["result"]) - } for line in lines) - - class TestPartialCorrelations(TestCase): """Class for testing partial correlations computation functions""" @@ -272,7 +251,7 @@ class TestPartialCorrelations(TestCase): with self.assertRaises(error, msg=error_msg): tissue_correlation(primary, target, method) - def test_tissue_correlation(self): + def test_tissue_correlation(self): # pylint: disable=R0201 """ Test that the correct correlation values are computed for the given: - primary trait @@ -281,11 +260,11 @@ class TestPartialCorrelations(TestCase): """ for primary, target, method, expected in ( ((12.34, 18.36, 42.51), (37.25, 46.25, 46.56), "pearson", - (0.6761779253, 0.5272701134)), + (0.6761779252651052, 0.5272701133657985)), ((1, 2, 3, 4, 5), (5, 6, 7, 8, 7), "spearman", - (0.8207826817, 0.0885870053))): + (0.8207826816681233, 0.08858700531354381))): with self.subTest(primary=primary, target=target, method=method): - self.assertEqual( + assert_allclose( tissue_correlation(primary, target, method), expected) def test_good_dataset_samples_indexes(self): @@ -298,38 +277,21 @@ class TestPartialCorrelations(TestCase): ("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l")), (0, 4, 8, 10)) - @skip - def test_partial_correlation_matrix(self): + def test_build_data_frame(self): """ - Test that `partial_correlation_matrix` computes the appropriate - correlation value. + Check that the function builds the correct data frame. """ - for sample in parse_test_data_csv( - ("tests/unit/computations/partial_correlations_test_data/" - "pcor_mat_blackbox_test.csv")): - with self.subTest( - xdata=sample["x"], ydata=sample["y"], zdata=sample["z"], - method=sample["method"], omit_nones=sample["rm"]): - self.assertEqual( - partial_correlation_matrix( - sample["x"], sample["y"], sample["z"], - method=sample["method"], omit_nones=sample["rm"]), - sample["result"]) - - @skip - def test_partial_correlation_recursive(self): - """ - Test that `partial_correlation_recursive` computes the appropriate - correlation value. - """ - for sample in parse_test_data_csv( - ("tests/unit/computations/partial_correlations_test_data/" - "pcor_rec_blackbox_test.csv")): - with self.subTest( - xdata=sample["x"], ydata=sample["y"], zdata=sample["z"], - method=sample["method"], omit_nones=sample["rm"]): - self.assertEqual( - partial_correlation_recursive( - sample["x"], sample["y"], sample["z"], - method=sample["method"], omit_nones=sample["rm"]), - sample["result"]) + for xdata, ydata, zdata, expected in ( + ((0.1, 1.1, 2.1), (2.1, 3.1, 4.1), (5.1, 6.1, 7.1), + pandas.DataFrame({ + "x": (0.1, 1.1, 2.1), "y": (2.1, 3.1, 4.1), + "z": (5.1, 6.1, 7.1)})), + ((0.1, 1.1, 2.1), (2.1, 3.1, 4.1), + ((5.1, 6.1, 7.1), (5.2, 6.2, 7.2), (5.3, 6.3, 7.3)), + pandas.DataFrame({ + "x": (0.1, 1.1, 2.1), "y": (2.1, 3.1, 4.1), + "z0": (5.1, 6.1, 7.1), "z1": (5.2, 6.2, 7.2), + "z2": (5.3, 6.3, 7.3)}))): + with self.subTest(xdata=xdata, ydata=ydata, zdata=zdata): + self.assertTrue( + build_data_frame(xdata, ydata, zdata).equals(expected)) diff --git a/tests/unit/test_data_helpers.py b/tests/unit/test_data_helpers.py index 39aea45..88ea469 100644 --- a/tests/unit/test_data_helpers.py +++ b/tests/unit/test_data_helpers.py @@ -4,7 +4,7 @@ Test functions in gn3.data_helpers from unittest import TestCase -from gn3.data_helpers import partition_all, parse_csv_line +from gn3.data_helpers import partition_by, partition_all, parse_csv_line class TestDataHelpers(TestCase): """ @@ -59,3 +59,31 @@ class TestDataHelpers(TestCase): parse_csv_line( line=line, delimiter=delimiter, quoting=quoting), expected) + + def test_partition_by(self): + """ + Test that `partition_by` groups the data using the given predicate + + Given: + - `part_fn`: a predicate funtion that return boolean True/False + - `items`: a sequence of items + When: + - the partitioning predicate function and the sequence of items are + passed to the `partition_by` function + Then: + - the result is a tuple, with sub-tuples containing the data in the + original sequence. Each sub-tuple is a partition, ending as soon as + the next value in the sequence, when passed to `part_fn`, returns + boolean `True`. + """ + for part_fn, items, expected in ( + (lambda s: s.startswith("----"), + ("------", "a", "b", "-----", "c", "----", "d", "e", "---", + "f"), + (("------", "a", "b"), ("-----", "c"), + ("----", "d", "e", "---", "f"))), + (lambda x: (x % 2) == 0, + (0, 1, 3, 2, 4, 5, 7, 6, 9, 1), + ((0, 1, 3), (2,), (4, 5, 7), (6, 9, 1))),): + with self.subTest(items=items): + self.assertEqual(partition_by(part_fn, items), expected) diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py index e4c929d..a88341b 100644 --- a/tests/unit/test_heatmaps.py +++ b/tests/unit/test_heatmaps.py @@ -1,6 +1,8 @@ """Module contains tests for gn3.heatmaps.heatmaps""" from unittest import TestCase + from numpy.testing import assert_allclose + from gn3.heatmaps import ( cluster_traits, get_loci_names, @@ -25,7 +27,7 @@ slinked = ( class TestHeatmap(TestCase): """Class for testing heatmap computation functions""" - def test_cluster_traits(self): + def test_cluster_traits(self): # pylint: disable=R0201 """ Test that the clustering is working as expected. """ |