1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
"""Module contains tests for gn3.computations.qtlreaper"""
from unittest import TestCase
from gn3.computations.qtlreaper import (
parse_reaper_main_results, parse_reaper_permutation_results)
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])
|
