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Diffstat (limited to 'tests/unit/computations')
| -rw-r--r-- | tests/unit/computations/test_heatmap.py | 187 |
1 files changed, 0 insertions, 187 deletions
diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/computations/test_heatmap.py deleted file mode 100644 index 156af45..0000000 --- a/tests/unit/computations/test_heatmap.py +++ /dev/null @@ -1,187 +0,0 @@ -"""Module contains tests for gn3.computations.heatmap""" -from unittest import TestCase -from gn3.computations.heatmap import ( - cluster_traits, - export_trait_data, - compute_traits_order, - retrieve_strains_and_values) - -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}}} - -slinked = ( - (((0, 2, 0.16381088984330505), - ((1, 7, 0.06024619831474998), 5, 0.19179284676938602), - 0.20337048635536847), - 9, - 0.23451785425383564), - ((3, (6, 8, 0.2140799896286565), 0.25879514152086425), - 4, 0.8968250491499363), - 0.9313185954797953) - -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))) - - def test_compute_heatmap_order(self): - """Test the orders.""" - self.assertEqual( - compute_traits_order(slinked), (0, 2, 1, 7, 5, 9, 3, 6, 8, 4)) - - def test_retrieve_strains_and_values(self): - """Test retrieval of strains and values.""" - for orders, slist, tdata, expected in [ - [ - [2], - ["s1", "s2", "s3", "s4"], - [[2, 9, 6, None, 4], - [7, 5, None, None, 4], - [9, None, 5, 4, 7], - [6, None, None, 4, None]], - [[2, ["s1", "s3", "s4"], [9, 5, 4]]] - ], - [ - [3], - ["s1", "s2", "s3", "s4", "s5"], - [[2, 9, 6, None, 4], - [7, 5, None, None, 4], - [9, None, 5, 4, 7], - [6, None, None, 4, None]], - [[3, ["s1", "s4"], [6, 4]]] - ]]: - with self.subTest(strainlist=slist, traitdata=tdata): - self.assertEqual( - retrieve_strains_and_values(orders, slist, tdata), expected) |