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"""Module contains tests for gn3.partial_correlations"""
from unittest import TestCase
from gn3.partial_correlations import (
fix_samples,
control_samples,
dictify_by_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}}})
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"""
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)))
def test_dictify_by_samples(self):
"""
Given:
a sequence of sequences with sample names, values and variances, as
in the output of `gn3.partial_correlations.control_samples` or
the output of `gn3.db.traits.export_informative`
When:
the sequence is passed as an argument into the
`gn3.partial_correlations.dictify_by_sample`
Then:
return a sequence of dicts with keys being the values of the sample
names, and each of who's values being sub-dicts with the keys
'sample_name', 'value' and 'variance' whose values correspond to the
values passed in.
"""
self.assertEqual(
dictify_by_samples(
((("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))),
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)))
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