diff options
Diffstat (limited to 'tests/unit')
3 files changed, 112 insertions, 0 deletions
diff --git a/tests/unit/computations/data/qtlreaper/main_output_sample.txt b/tests/unit/computations/data/qtlreaper/main_output_sample.txt new file mode 100644 index 0000000..12b11b4 --- /dev/null +++ b/tests/unit/computations/data/qtlreaper/main_output_sample.txt @@ -0,0 +1,11 @@ +ID Locus Chr cM Mb LRS Additive pValue +T1 rs31443144 1 1.500 3.010 0.500 -0.074 1.000 +T1 rs6269442 1 1.500 3.492 0.500 -0.074 1.000 +T1 rs32285189 1 1.630 3.511 0.500 -0.074 1.000 +T1 rs258367496 1 1.630 3.660 0.500 -0.074 1.000 +T1 rs32430919 1 1.750 3.777 0.500 -0.074 1.000 +T1 rs36251697 1 1.880 3.812 0.500 -0.074 1.000 +T1 rs30658298 1 2.010 4.431 0.500 -0.074 1.000 +T1 rs51852623 1 2.010 4.447 0.500 -0.074 1.000 +T1 rs31879829 1 2.140 4.519 0.500 -0.074 1.000 +T1 rs36742481 1 2.140 4.776 0.500 -0.074 1.000 diff --git a/tests/unit/computations/data/qtlreaper/permu_output_sample.txt b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt new file mode 100644 index 0000000..64cff07 --- /dev/null +++ b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt @@ -0,0 +1,27 @@ +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 diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py new file mode 100644 index 0000000..ec23664 --- /dev/null +++ b/tests/unit/computations/test_qtlreaper.py @@ -0,0 +1,74 @@ +"""Module contains tests for gn3.computations.qtlreaper""" +import os +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): + 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): + 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]) |