diff options
Diffstat (limited to 'tests/unit/computations/test_qtlreaper.py')
| -rw-r--r-- | tests/unit/computations/test_qtlreaper.py | 68 |
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) |