diff options
Diffstat (limited to 'tests/unit/test_heatmaps.py')
| -rw-r--r-- | tests/unit/test_heatmaps.py | 94 |
1 files changed, 5 insertions, 89 deletions
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py index 7b66688..a88341b 100644 --- a/tests/unit/test_heatmaps.py +++ b/tests/unit/test_heatmaps.py @@ -1,46 +1,18 @@ """Module contains tests for gn3.heatmaps.heatmaps""" from unittest import TestCase + +from numpy.testing import assert_allclose + from gn3.heatmaps import ( cluster_traits, get_loci_names, get_lrs_from_chr, - export_trait_data, compute_traits_order, retrieve_samples_and_values, process_traits_data_for_heatmap) from tests.unit.sample_test_data import organised_trait_1, organised_trait_2 samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] -trait_data = { - "mysqlid": 36688172, - "data": { - "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None}, - "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None}, - "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None}, - "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None}, - "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None}, - "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None}, - "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None}, - "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None}, - "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None}, - "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None}, - "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None}, - "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None}, - "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None}, - "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None}, - "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None}, - "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None}, - "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None}, - "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None}, - "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None}, - "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None}, - "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None}, - "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None}, - "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None}, - "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None}, - "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None}, - "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None}, - "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}} slinked = ( (((0, 2, 0.16381088984330505), @@ -55,63 +27,7 @@ slinked = ( 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, samplelist, 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, samplelist, dtype=dtype, var_exists=vflag, - n_exists=nflag), - expected) - - def test_cluster_traits(self): + def test_cluster_traits(self): # pylint: disable=R0201 """ Test that the clustering is working as expected. """ @@ -126,7 +42,7 @@ class TestHeatmap(TestCase): (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( + assert_allclose( cluster_traits(traits_data_list), ((0.0, 0.20337048635536847, 0.16381088984330505, 1.7388553629398245, 1.5025235756329178, 0.6952839500255574, 1.271661230252733, |