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authorFrederick Muriuki Muriithi2021-10-18 14:14:04 +0300
committerBonfaceKilz2021-10-19 16:33:32 +0300
commit38a0b65d234c0019ba14814adf69e09493082298 (patch)
tree49669bf3a2e3a5f11f539c105fdcd0922352e94b
parent42c56d330fdb51820c0fdcbb0b4376ff568ea009 (diff)
downloadgenenetwork3-38a0b65d234c0019ba14814adf69e09493082298.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.
-rw-r--r--gn3/partial_correlations.py38
-rw-r--r--tests/unit/test_partial_correlations.py80
2 files changed, 118 insertions, 0 deletions
diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py
index df390ed..99521c6 100644
--- a/gn3/partial_correlations.py
+++ b/gn3/partial_correlations.py
@@ -5,4 +5,42 @@ It is an attempt to migrate over the partial correlations feature from
GeneNetwork1.
"""
+from typing import Sequence
from functools import reduce
+
+def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]):
+ """
+ Fetches data for the control traits.
+
+ This migrates `web/webqtl/correlation/correlationFunction.controlStrain` in
+ GN1, with a few modifications to the arguments passed in.
+
+ PARAMETERS:
+ controls: A map of sample names to trait data. Equivalent to the `cvals`
+ value in the corresponding source function in GN1.
+ sampleslist: A list of samples. Equivalent to `strainlst` in the
+ corresponding source function in GN1
+ """
+ def __process_control__(trait_data):
+ def __process_sample__(acc, sample):
+ if sample in trait_data["data"].keys():
+ sample_item = trait_data["data"][sample]
+ val = sample_item["value"]
+ if val is not None:
+ return (
+ acc[0] + (sample,),
+ acc[1] + (val,),
+ acc[2] + (sample_item["variance"],))
+ return acc
+ return reduce(
+ __process_sample__, sampleslist, (tuple(), tuple(), tuple()))
+
+ return reduce(
+ lambda acc, item: (
+ acc[0] + (item[0],),
+ acc[1] + (item[1],),
+ acc[2] + (item[2],),
+ acc[3] + (len(item[0]),),
+ ),
+ [__process_control__(trait_data) for trait_data in controls],
+ (tuple(), tuple(), tuple(), tuple()))
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)))