diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/test_data_helpers.py | 37 | ||||
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 64 |
2 files changed, 99 insertions, 2 deletions
diff --git a/tests/unit/test_data_helpers.py b/tests/unit/test_data_helpers.py new file mode 100644 index 0000000..1eec3cc --- /dev/null +++ b/tests/unit/test_data_helpers.py @@ -0,0 +1,37 @@ +""" +Test functions in gn3.data_helpers +""" + +from unittest import TestCase + +from gn3.data_helpers import partition_all + +class TestDataHelpers(TestCase): + """ + Test functions in gn3.data_helpers + """ + + def test_partition_all(self): + """ + Test that `gn3.data_helpers.partition_all` partitions sequences as expected. + + Given: + - `num`: The number of items per partition + - `items`: A sequence of items + When: + - The arguments above are passed to the `gn3.data_helpers.partition_all` + Then: + - Return a new sequence with partitions, each of which has `num` + items in the same order as those in `items`, save for the last + partition which might have fewer items than `num`. + """ + for count, items, expected in ( + (1, [0, 1, 2, 3], ((0,), (1,), (2,), (3,))), + (3, (0, 1, 2, 3, 4, 5, 6, 7, 8, 9), + ((0, 1, 2), (3, 4, 5), (6, 7, 8), (9, ))), + (4, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], + ((0, 1, 2, 3), (4, 5, 6, 7), (8, 9))), + (13, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], + ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9), ))): + with self.subTest(n=count, items=items): + self.assertEqual(partition_all(count, items), expected) diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py index 7631a71..60e54c1 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/test_partial_correlations.py @@ -4,7 +4,8 @@ from unittest import TestCase from gn3.partial_correlations import ( fix_samples, control_samples, - dictify_by_samples) + dictify_by_samples, + find_identical_traits) sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -106,6 +107,8 @@ class TestPartialCorrelations(TestCase): def test_dictify_by_samples(self): """ + Test that `dictify_by_samples` generates the appropriate dict + Given: a sequence of sequences with sample names, values and variances, as in the output of `gn3.partial_correlations.control_samples` or @@ -133,7 +136,34 @@ class TestPartialCorrelations(TestCase): dictified_control_samples) def test_fix_samples(self): - """Test that fix_samples fixes the values""" + """ + Test that `fix_samples` returns only the common samples + + Given: + - A primary trait + - A sequence of control samples + When: + - The two arguments are passed to `fix_samples` + Then: + - Only the names of the samples present in the primary trait that + are also present in ALL the control traits are present in the + return value + - Only the values of the samples present in the primary trait that + are also present in ALL the control traits are present in the + return value + - ALL the values for ALL the control traits are present in the + return value + - Only the variances of the samples present in the primary trait + that are also present in ALL the control traits are present in the + return value + - ALL the variances for ALL the control traits are present in the + return value + - The return value is a tuple of the above items, in the following + order: + ((sample_names, ...), (primary_trait_values, ...), + (control_traits_values, ...), (primary_trait_variances, ...) + (control_traits_variances, ...)) + """ self.assertEqual( fix_samples( {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, @@ -149,3 +179,33 @@ class TestPartialCorrelations(TestCase): (None,), (None, None, None, None, None, None, None, None, None, None, None, None, None))) + + def test_find_identical_traits(self): + """ + Test `gn3.partial_correlations.find_identical_traits`. + + Given: + - the name of a primary trait + - the value of a primary trait + - a sequence of names of control traits + - a sequence of values of control traits + When: + - the arguments above are passed to the `find_identical_traits` + function + Then: + - Return ALL trait names that have the same value when up to three + decimal places are considered + """ + for primn, primv, contn, contv, expected in ( + ("pt", 12.98395, ("ct0", "ct1", "ct2"), + (0.1234, 2.3456, 3.4567), tuple()), + ("pt", 12.98395, ("ct0", "ct1", "ct2"), + (12.98354, 2.3456, 3.4567), ("pt", "ct0")), + ("pt", 12.98395, ("ct0", "ct1", "ct2", "ct3"), + (0.1234, 2.3456, 0.1233, 4.5678), ("ct0", "ct2")) + ): + with self.subTest( + primary_name=primn, primary_value=primv, + control_names=contn, control_values=contv): + self.assertEqual( + find_identical_traits(primn, primv, contn, contv), expected) |