diff options
| -rw-r--r-- | gn3/computations/slink.py | 11 | ||||
| -rw-r--r-- | tests/unit/computations/test_slink.py | 5 |
2 files changed, 13 insertions, 3 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py index 928330d..7d13d91 100644 --- a/gn3/computations/slink.py +++ b/gn3/computations/slink.py @@ -46,6 +46,16 @@ If the two distances are different, throw an exception.""" "should be the same in both directions.").format( lists[i][j], lists[j][i])) +def raise_valueerror_on_negative_distances(lists): + """Check that distances between 'somethings' are all positive, otherwise, +raise an exception.""" + def zero_or_positive(val): + return val >= 0; + # flatten lists + flattened = [distance for child in lists for distance in child] + if not all(map(zero_or_positive, flattened)): + raise ValueError("Distances should be positive.") + def nearest(lists, i, j): """Computes some form of distance. This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64. @@ -58,5 +68,6 @@ This description should be updated once the form/type of 'distance' identified." raise_lengtherror_if_child_lists_are_not_same_as_parent(lists) raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists) raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists) + raise_valueerror_on_negative_distances(lists) #### END: Guard Functions #### return None diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py index 207debf..6be3f33 100644 --- a/tests/unit/computations/test_slink.py +++ b/tests/unit/computations/test_slink.py @@ -55,15 +55,14 @@ class TestSlink(TestCase): def test_nearest_expects_zero_or_positive_distances(self): # Based on: # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L87-L89 - for lst in [[[0,1,2,3],[1,0,3,4],[2,3,0,5],[3,4,5,0]], - [[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]], + for lst in [[[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]], [[0,1,-2,3],[1,0,3,4],[-2,3,0,5],[3,4,5,0]], [[0,1,2,3],[1,0,-3,4],[2,-3,0,5],[3,4,5,0]], [[0,1,2,-3],[1,0,3,4],[2,3,0,5],[-3,4,5,0]], [[0,1,2,3],[1,0,3,-4],[2,3,0,5],[3,-4,5,0]], [[0,1,2,3],[1,0,3,4],[2,3,0,-5],[3,4,-5,0]]]: with self.subTest(lst=lst): - with self.assertRaises(ValueError, msg="Got an unexpected negative value!"): + with self.assertRaises(ValueError, msg="Distances should be positive."): nearest(lst, 1, 1) def test_nearest_with_expected(self): |