Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/fix_rqtl_covariates

1 files changed, 135 insertions, 0 deletions

diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
new file mode 100644
index 0000000..742d106
--- /dev/null
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -0,0 +1,135 @@
+"""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)