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authorFrederick Muriuki Muriithi2021-09-23 03:45:19 +0300
committerFrederick Muriuki Muriithi2021-09-23 03:45:19 +0300
commit95c5c0e73bffbf0287a17309e703063ee54d25ba (patch)
tree23c3197072d19f4aa9bbb80023ca31780235207b /tests/unit/computations/test_qtlreaper.py
parent56c73324c285d896567268370f3955bbd15754b0 (diff)
downloadgenenetwork3-95c5c0e73bffbf0287a17309e703063ee54d25ba.tar.gz
Refactor: Move common sample data to separate file
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move common sample test data into a separate file where it can be imported from, to prevent pylint error R0801 which proved tricky to silence in any other way.
Diffstat (limited to 'tests/unit/computations/test_qtlreaper.py')
-rw-r--r--tests/unit/computations/test_qtlreaper.py68
1 files changed, 12 insertions, 56 deletions
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
index d420470..742d106 100644
--- a/tests/unit/computations/test_qtlreaper.py
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -4,6 +4,7 @@ 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."""
@@ -81,99 +82,54 @@ class TestQTLReaper(TestCase):
self.assertEqual(
organise_reaper_main_results([
{
- "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "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,
+ "ID": "1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
"Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
"pValue": 1.000
}
]),
- {"T1": {"ID": "T1",
- "chromosomes": {
- 1: {"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
- }]},
- 2: {"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
- }]}}}})
+ organised_trait_1)