diff options
| author | Frederick Muriuki Muriithi | 2021-10-19 10:31:24 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-10-19 16:33:32 +0300 |
| commit | a3d4bc848caa8021e14282bab1a13ca7aadeb82d (patch) | |
| tree | e1b3c6a22a47834a50d6eaaf70544b4dce4a335e /tests/unit | |
| parent | b829bf6f5a26edaa57acde0c4a21e2c24d695e87 (diff) | |
| download | genenetwork3-a3d4bc848caa8021e14282bab1a13ca7aadeb82d.tar.gz | |
Implement remaining `fix_samples` functionality
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/partial_correlations.py: implement `fix_samples` function
* tests/unit/test_partial_correlations.py: implement tests for `fix_samples`
function
Implement the remaining partial migration for the
`web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 52 |
1 files changed, 38 insertions, 14 deletions
diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py index 6302f74..7631a71 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/test_partial_correlations.py @@ -1,7 +1,10 @@ """Module contains tests for gn3.partial_correlations""" from unittest import TestCase -from gn3.partial_correlations import control_samples, dictify_by_samples +from gn3.partial_correlations import ( + fix_samples, + control_samples, + dictify_by_samples) sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -69,6 +72,21 @@ control_traits = ( "sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None}}}) +dictified_control_samples = ( + {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, + "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, + {"BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, + {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}) + class TestPartialCorrelations(TestCase): """Class for testing partial correlations computation functions""" @@ -112,16 +130,22 @@ class TestPartialCorrelations(TestCase): ((None, None, None, None, None, None), (None, None, None, None), (None, None, None)), (6, 4, 3))), - ({"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, - "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, - "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, - "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, - "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, - "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, - {"BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None}, - "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None}, - "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None}, - "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}}, - {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None}, - "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None}, - "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}})) + dictified_control_samples) + + def test_fix_samples(self): + """Test that fix_samples fixes the values""" + self.assertEqual( + fix_samples( + {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, + "variance": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, + "variance": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, + "variance": None}}, + dictified_control_samples), + (("BXD2",), (7.80944,), + (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944, 8.39265, + 8.17443, 8.30401, 7.80944, 7.51879, 7.77141, 7.80944), + (None,), + (None, None, None, None, None, None, None, None, None, None, None, + None, None))) |