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authorMuriithi Frederick Muriuki2021-09-06 08:09:20 +0300
committerMuriithi Frederick Muriuki2021-09-06 08:09:20 +0300
commitd4943f1d01d89a3928c905f80914a23144126c8e (patch)
tree52d9077168fd96634510b6fa0c8af1606f96f0ac /tests/unit/computations/test_qtlreaper.py
parent679a1af832ad9585c7cf72996043edb08e1b0d10 (diff)
downloadgenenetwork3-d4943f1d01d89a3928c905f80914a23144126c8e.tar.gz
Provide function to organise parsed QTLReaper results
* gn3/computations/qtlreaper.py: Provide a function to organise the results by trait for easier use down the line. * tests/unit/computations/test_qtlreaper.py: provide a test to ensure that the organising function works as expected.
Diffstat (limited to 'tests/unit/computations/test_qtlreaper.py')
-rw-r--r--tests/unit/computations/test_qtlreaper.py105
1 files changed, 104 insertions, 1 deletions
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
index fd3434a..1d7347f 100644
--- a/tests/unit/computations/test_qtlreaper.py
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -1,7 +1,9 @@
"""Module contains tests for gn3.computations.qtlreaper"""
from unittest import TestCase
from gn3.computations.qtlreaper import (
- parse_reaper_main_results, parse_reaper_permutation_results)
+ parse_reaper_main_results,
+ organise_reaper_main_results,
+ parse_reaper_permutation_results)
class TestQTLReaper(TestCase):
"""Class for testing qtlreaper interface functions."""
@@ -73,3 +75,104 @@ class TestQTLReaper(TestCase):
5.24619, 5.27961, 5.28228, 5.43903, 5.50188, 5.51694, 5.56830,
5.63874, 5.71346, 5.71936, 5.74275, 5.76764, 5.79815, 5.81671,
5.82775, 5.89659, 5.92117, 5.93396, 5.93396, 5.94957])
+
+ def test_organise_reaper_main_results(self):
+ self.assertEqual(
+ organise_reaper_main_results([
+ {
+ "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+ "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+ "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+ "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+ "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+ "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+ "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+ "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
+ "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+ "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+ "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ }
+ ]),
+ [{"ID": "T1",
+ "chromosomes": [
+ {"Chr": "1",
+ "loci": [
+ {
+ "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ }]},
+ {"Chr": "2",
+ "loci": [
+ {
+ "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ }]}]}])