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-rw-r--r--tests/unit/computations/test_qtlreaper.py135
1 files changed, 135 insertions, 0 deletions
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
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+++ b/tests/unit/computations/test_qtlreaper.py
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+"""Module contains tests for gn3.computations.qtlreaper"""
+from unittest import TestCase
+from gn3.computations.qtlreaper import (
+ parse_reaper_main_results,
+ organise_reaper_main_results,
+ parse_reaper_permutation_results)
+from tests.unit.sample_test_data import organised_trait_1
+
+class TestQTLReaper(TestCase):
+ """Class for testing qtlreaper interface functions."""
+
+ def test_parse_reaper_main_results(self):
+ """Test that the main results file is parsed correctly."""
+ self.assertEqual(
+ parse_reaper_main_results(
+ "tests/unit/computations/data/qtlreaper/main_output_sample.txt"),
+ [
+ {
+ "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": 1, "cM": 2.010,
+ "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs31879829", "Chr": 1, "cM": 2.140,
+ "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs36742481", "Chr": 1, "cM": 2.140,
+ "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ }
+ ])
+
+ def test_parse_reaper_permutation_results(self):
+ """Test that the permutations results file is parsed correctly."""
+ self.assertEqual(
+ parse_reaper_permutation_results(
+ "tests/unit/computations/data/qtlreaper/permu_output_sample.txt"),
+ [4.44174, 5.03825, 5.08167, 5.18119, 5.18578, 5.24563, 5.24619,
+ 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):
+ """Check that results are organised correctly."""
+ self.assertEqual(
+ organise_reaper_main_results([
+ {
+ "ID": "1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+ "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+ "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+ "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+ "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+ "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+ "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+ "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
+ "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+ "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+ "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ }
+ ]),
+ organised_trait_1)