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| author | Frederick Muriuki Muriithi | 2021-10-18 05:47:45 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-10-18 05:59:54 +0300 |
| commit | 27cca4c118cba6a5f8e8b03d152070f83a44a9e5 (patch) | |
| tree | 3c24dc254f0efd29f2fc9f5f7f064e7f31e48f05 /tests | |
| parent | 77099cac68e8f4792bf54d8e1f7ce6f315bedfa7 (diff) | |
| download | genenetwork3-27cca4c118cba6a5f8e8b03d152070f83a44a9e5.tar.gz | |
Migrate `export_informative` function
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: Implement a mostly, bug-compatible
`export_informative` function as part of migrating the partial correlations
feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
work in a similar manner as that one in GN1.
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 92 |
1 files changed, 92 insertions, 0 deletions
diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py new file mode 100644 index 0000000..6eea078 --- /dev/null +++ b/tests/unit/test_partial_correlations.py @@ -0,0 +1,92 @@ +"""Module contains tests for gn3.partial_correlations""" + +from unittest import TestCase +from gn3.partial_correlations import export_informative + +class TestPartialCorrelations(TestCase): + """Class for testing partial correlations computation functions""" + + def test_export_informative(self): + """Test that the function exports appropriate data.""" + for trait_data, inc_var, expected in [ + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": None, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": 7, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, 0, ( + ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6), + (None, None, None, None))], + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": None, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": None, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, 0, ( + ("sample1", "sample2", "sample4"), (9, 8, 6), + (None, None, None))], + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": None, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": 7, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, True, (tuple(), tuple(), tuple())], + [{"data": { + "sample1": { + "sample_name": "sample1", "value": 9, "variance": None, + "ndata": 13 + }, + "sample2": { + "sample_name": "sample2", "value": 8, "variance": 0.657, + "ndata": 13 + }, + "sample3": { + "sample_name": "sample3", "value": 7, "variance": None, + "ndata": 13 + }, + "sample4": { + "sample_name": "sample4", "value": 6, "variance": None, + "ndata": 13 + }, + }}, 0, ( + ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6), + (None, 0.657, None, None))]]: + with self.subTest(trait_data=trait_data): + self.assertEqual( + export_informative(trait_data, inc_var), expected) |