diff options
Diffstat (limited to 'tests/unit/computations/test_partial_correlations.py')
| -rw-r--r-- | tests/unit/computations/test_partial_correlations.py | 61 |
1 files changed, 60 insertions, 1 deletions
diff --git a/tests/unit/computations/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py index f7217a9..c5c35d1 100644 --- a/tests/unit/computations/test_partial_correlations.py +++ b/tests/unit/computations/test_partial_correlations.py @@ -1,5 +1,6 @@ """Module contains tests for gn3.partial_correlations""" +import csv from unittest import TestCase from gn3.computations.partial_correlations import ( fix_samples, @@ -7,7 +8,9 @@ from gn3.computations.partial_correlations import ( dictify_by_samples, tissue_correlation, find_identical_traits, - good_dataset_samples_indexes) + partial_correlation_matrix, + good_dataset_samples_indexes, + partial_correlation_recursive) sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -90,6 +93,28 @@ 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""" @@ -271,3 +296,37 @@ class TestPartialCorrelations(TestCase): ("a", "e", "i", "k"), ("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l")), (0, 4, 8, 10)) + + def test_partial_correlation_matrix(self): + """ + Test that `partial_correlation_matrix` computes the appropriate + correlation value. + """ + 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"]) + + 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"]) |