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-rw-r--r--tests/unit/computations/data/qtlreaper/main_output_sample.txt11
-rw-r--r--tests/unit/computations/data/qtlreaper/permu_output_sample.txt27
-rw-r--r--tests/unit/computations/test_heatmap.py143
-rw-r--r--tests/unit/computations/test_parsers.py4
-rw-r--r--tests/unit/computations/test_qtlreaper.py135
5 files changed, 175 insertions, 145 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_heatmap.py b/tests/unit/computations/test_heatmap.py
deleted file mode 100644
index 650cb45..0000000
--- a/tests/unit/computations/test_heatmap.py
+++ /dev/null
@@ -1,143 +0,0 @@
-"""Module contains tests for gn3.computations.heatmap"""
-from unittest import TestCase
-from gn3.computations.heatmap import cluster_traits, export_trait_data
-
-strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
-trait_data = {
- "mysqlid": 36688172,
- "data": {
- "B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
- "BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
- "BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
- "BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
- "BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
- "BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
- "BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
- "BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
- "BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
- "BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
- "BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
- "BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
- "BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
- "BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
- "BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
- "BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
- "BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
- "BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
- "BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
- "BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
- "BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
- "BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
- "BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
- "BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
- "C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
- "C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
- "DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
-
-class TestHeatmap(TestCase):
- """Class for testing heatmap computation functions"""
-
- def test_export_trait_data_dtype(self):
- """
- Test `export_trait_data` with different values for the `dtype` keyword
- argument
- """
- for dtype, expected in [
- ["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["var", (None, None, None, None, None, None)],
- ["N", (None, None, None, None, None, None)],
- ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
- with self.subTest(dtype=dtype):
- self.assertEqual(
- export_trait_data(trait_data, strainlist, dtype=dtype),
- expected)
-
- def test_export_trait_data_dtype_all_flags(self):
- """
- Test `export_trait_data` with different values for the `dtype` keyword
- argument and the different flags set up
- """
- for dtype, vflag, nflag, expected in [
- ["val", False, False,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["val", False, True,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["val", True, False,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["val", True, True,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["var", False, False, (None, None, None, None, None, None)],
- ["var", False, True, (None, None, None, None, None, None)],
- ["var", True, False, (None, None, None, None, None, None)],
- ["var", True, True, (None, None, None, None, None, None)],
- ["N", False, False, (None, None, None, None, None, None)],
- ["N", False, True, (None, None, None, None, None, None)],
- ["N", True, False, (None, None, None, None, None, None)],
- ["N", True, True, (None, None, None, None, None, None)],
- ["all", False, False,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["all", False, True,
- (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
- 8.30401, None, 7.80944, None)],
- ["all", True, False,
- (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
- 8.30401, None, 7.80944, None)],
- ["all", True, True,
- (7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
- 8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
- ]:
- with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
- self.assertEqual(
- export_trait_data(
- trait_data, strainlist, dtype=dtype, var_exists=vflag,
- n_exists=nflag),
- expected)
-
- def test_cluster_traits(self):
- """
- Test that the clustering is working as expected.
- """
- traits_data_list = [
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944),
- (6.1427, 6.50588, 7.73705, 6.68328, 7.49293, 7.27398),
- (8.4211, 8.30581, 9.24076, 8.51173, 9.18455, 8.36077),
- (10.0904, 10.6509, 9.36716, 9.91202, 8.57444, 10.5731),
- (10.188, 9.76652, 9.54813, 9.05074, 9.52319, 9.10505),
- (6.74676, 7.01029, 7.54169, 6.48574, 7.01427, 7.26815),
- (6.39359, 6.85321, 5.78337, 7.11141, 6.22101, 6.16544),
- (6.84118, 7.08432, 7.59844, 7.08229, 7.26774, 7.24991),
- (9.45215, 10.6943, 8.64719, 10.1592, 7.75044, 8.78615),
- (7.04737, 6.87185, 7.58586, 6.92456, 6.84243, 7.36913)]
- self.assertEqual(
- cluster_traits(traits_data_list),
- ((0.0, 0.20337048635536847, 0.16381088984330505, 1.7388553629398245,
- 1.5025235756329178, 0.6952839500255574, 1.271661230252733,
- 0.2100487290977544, 1.4699690641062024, 0.7934461515867415),
- (0.20337048635536847, 0.0, 0.2198321044997198, 1.5753041735592204,
- 1.4815755944537086, 0.26087293140686374, 1.6939790104301427,
- 0.06024619831474998, 1.7430082449189215, 0.4497104244247795),
- (0.16381088984330505, 0.2198321044997198, 0.0, 1.9073926868549234,
- 1.0396738891139845, 0.5278328671176757, 1.6275069061182947,
- 0.2636503792482082, 1.739617877037615, 0.7127042590637039),
- (1.7388553629398245, 1.5753041735592204, 1.9073926868549234, 0.0,
- 0.9936846292920328, 1.1169999189889366, 0.6007483980555253,
- 1.430209221053372, 0.25879514152086425, 0.9313185954797953),
- (1.5025235756329178, 1.4815755944537086, 1.0396738891139845,
- 0.9936846292920328, 0.0, 1.027827186339337, 1.1441743109173244,
- 1.4122477962364253, 0.8968250491499363, 1.1683723389247052),
- (0.6952839500255574, 0.26087293140686374, 0.5278328671176757,
- 1.1169999189889366, 1.027827186339337, 0.0, 1.8420471110023269,
- 0.19179284676938602, 1.4875072385631605, 0.23451785425383564),
- (1.271661230252733, 1.6939790104301427, 1.6275069061182947,
- 0.6007483980555253, 1.1441743109173244, 1.8420471110023269, 0.0,
- 1.6540234785929928, 0.2140799896286565, 1.7413442197913358),
- (0.2100487290977544, 0.06024619831474998, 0.2636503792482082,
- 1.430209221053372, 1.4122477962364253, 0.19179284676938602,
- 1.6540234785929928, 0.0, 1.5225640692832796, 0.33370067057028485),
- (1.4699690641062024, 1.7430082449189215, 1.739617877037615,
- 0.25879514152086425, 0.8968250491499363, 1.4875072385631605,
- 0.2140799896286565, 1.5225640692832796, 0.0, 1.3256191648260216),
- (0.7934461515867415, 0.4497104244247795, 0.7127042590637039,
- 0.9313185954797953, 1.1683723389247052, 0.23451785425383564,
- 1.7413442197913358, 0.33370067057028485, 1.3256191648260216,
- 0.0)))
diff --git a/tests/unit/computations/test_parsers.py b/tests/unit/computations/test_parsers.py
index 19c3067..b51b0bf 100644
--- a/tests/unit/computations/test_parsers.py
+++ b/tests/unit/computations/test_parsers.py
@@ -15,7 +15,7 @@ class TestParsers(unittest.TestCase):
def test_parse_genofile_with_existing_file(self):
"""Test that a genotype file is parsed correctly"""
- strains = ["bxd1", "bxd2"]
+ samples = ["bxd1", "bxd2"]
genotypes = [
{"chr": "1", "locus": "rs31443144",
"cm": "1.50", "mb": "3.010274",
@@ -51,4 +51,4 @@ class TestParsers(unittest.TestCase):
"../test_data/genotype.txt"
))
self.assertEqual(parse_genofile(
- test_genotype_file), (strains, genotypes))
+ test_genotype_file), (samples, genotypes))
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
new file mode 100644
index 0000000..742d106
--- /dev/null
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -0,0 +1,135 @@
+"""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)
+from tests.unit.sample_test_data import organised_trait_1
+
+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": "1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+ "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+ "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+ "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+ "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+ "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+ "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+ "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
+ "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+ "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+ "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ }
+ ]),
+ organised_trait_1)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 01:31:39 +0000