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| author | Muriithi Frederick Muriuki | 2021-08-20 14:10:45 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-20 14:10:45 +0300 |
| commit | 8b2c776771d2a70613a1e31d6e6671b612cfbafc (patch) | |
| tree | ad7ab6dcd4c43b15afdbe74322fbac76db0f34db /tests | |
| parent | ded960e3d32e4d7ebe590deda27fc47175be73d9 (diff) | |
| download | genenetwork3-8b2c776771d2a70613a1e31d6e6671b612cfbafc.tar.gz | |
Retrieve the strains with valid values
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: add function to get strains with values
* tests/unit/computations/test_heatmap.py: new tests
Add function to get the strains whose values are not `None` from the
`trait_data` object passed in.
This migrates
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221
into a separate function that can handle that and be tested independently of
any other code.
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_heatmap.py | 14 |
1 files changed, 13 insertions, 1 deletions
diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/computations/test_heatmap.py index 14807bb..686288d 100644 --- a/tests/unit/computations/test_heatmap.py +++ b/tests/unit/computations/test_heatmap.py @@ -3,7 +3,8 @@ from unittest import TestCase from gn3.computations.heatmap import ( cluster_traits, export_trait_data, - compute_heatmap_order) + compute_heatmap_order, + retrieve_strains_and_values) strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] trait_data = { @@ -164,3 +165,14 @@ class TestHeatmap(TestCase): with self.subTest(xoffset=xoff): self.assertEqual( compute_heatmap_order(slinked, xoffset=xoff), expected) + + def test_retrieve_strains_and_values(self): + """Test retrieval of strains and values.""" + for slist, tdata, expected in [ + [["s1", "s2", "s3", "s4"], [9, None, 5, 4], + (("s1", "s3", "s4"), (9, 5, 4))], + [["s1", "s2", "s3", "s4", "s5"], [6, None, None, 4, None], + (("s1", "s4"), (6, 4))]]: + with self.subTest(strainlist=slist, traitdata=tdata): + self.assertEqual( + retrieve_strains_and_values(slist, tdata), expected) |