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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)
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": "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
}
]),
{"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
}]}}}})
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