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authorFrederick Muriuki Muriithi2021-10-18 14:14:04 +0300
committerFrederick Muriuki Muriithi2021-10-18 14:14:04 +0300
commit1544776b072d7240773cf14d423078841e4c1a07 (patch)
treea08516c851eb6f2f7fd03ead773458e56c0dec12 /tests
parent94ca79045baf978d6aab964c7c70b84911c1124f (diff)
downloadgenenetwork3-1544776b072d7240773cf14d423078841e4c1a07.tar.gz
Implement `control_samples` function as is in GN1
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement `control_samples` function * tests/unit/test_partial_correlations.py: add tests for `control_samples` function Implement the function `control_samples` and make it mostly bug-compatible with the `web/webqtl/correlation/correlationFunction.controlStrain` function in GN1. This implementation in GN3 does not do any calls to the database. It will rely on other functions to provide the data from the database to it.
Diffstat (limited to 'tests')
-rw-r--r--tests/unit/test_partial_correlations.py80
1 files changed, 80 insertions, 0 deletions
diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py
index f204d4f..0083ef7 100644
--- a/tests/unit/test_partial_correlations.py
+++ b/tests/unit/test_partial_correlations.py
@@ -1,7 +1,87 @@
"""Module contains tests for gn3.partial_correlations"""
from unittest import TestCase
+from gn3.partial_correlations import control_samples
+sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
+control_traits = (
+ {
+ "mysqlid": 36688172,
+ "data": {
+ "B6cC3-1": {
+ "sample_name": "B6cC3-1", "value": 7.51879, "variance": None,
+ "ndata": None},
+ "BXD1": {
+ "sample_name": "BXD1", "value": 7.77141, "variance": None,
+ "ndata": None},
+ "BXD12": {
+ "sample_name": "BXD12", "value": 8.39265, "variance": None,
+ "ndata": None},
+ "BXD16": {
+ "sample_name": "BXD16", "value": 8.17443, "variance": None,
+ "ndata": None},
+ "BXD19": {
+ "sample_name": "BXD19", "value": 8.30401, "variance": None,
+ "ndata": None},
+ "BXD2": {
+ "sample_name": "BXD2", "value": 7.80944, "variance": None,
+ "ndata": None}}},
+ {
+ "mysqlid": 36688172,
+ "data": {
+ "B6cC3-21": {
+ "sample_name": "B6cC3-1", "value": 7.51879, "variance": None,
+ "ndata": None},
+ "BXD21": {
+ "sample_name": "BXD1", "value": 7.77141, "variance": None,
+ "ndata": None},
+ "BXD12": {
+ "sample_name": "BXD12", "value": 8.39265, "variance": None,
+ "ndata": None},
+ "BXD16": {
+ "sample_name": "BXD16", "value": 8.17443, "variance": None,
+ "ndata": None},
+ "BXD19": {
+ "sample_name": "BXD19", "value": 8.30401, "variance": None,
+ "ndata": None},
+ "BXD2": {
+ "sample_name": "BXD2", "value": 7.80944, "variance": None,
+ "ndata": None}}},
+ {
+ "mysqlid": 36688172,
+ "data": {
+ "B6cC3-1": {
+ "sample_name": "B6cC3-1", "value": 7.51879, "variance": None,
+ "ndata": None},
+ "BXD1": {
+ "sample_name": "BXD1", "value": 7.77141, "variance": None,
+ "ndata": None},
+ "BXD12": {
+ "sample_name": "BXD12", "value": None, "variance": None,
+ "ndata": None},
+ "BXD16": {
+ "sample_name": "BXD16", "value": None, "variance": None,
+ "ndata": None},
+ "BXD19": {
+ "sample_name": "BXD19", "value": None, "variance": None,
+ "ndata": None},
+ "BXD2": {
+ "sample_name": "BXD2", "value": 7.80944, "variance": None,
+ "ndata": None}}})
class TestPartialCorrelations(TestCase):
"""Class for testing partial correlations computation functions"""
+
+ def test_control_samples(self):
+ """Test that the control_samples works as expected."""
+ self.assertEqual(
+ control_samples(control_traits, sampleslist),
+ ((("B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"),
+ ("BXD12", "BXD16", "BXD19", "BXD2"),
+ ("B6cC3-1", "BXD1", "BXD2")),
+ ((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)),
+ (6, 4, 3)))