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-rw-r--r--gn3/computations/slink.py12
-rw-r--r--tests/unit/computations/test_slink.py14
2 files changed, 19 insertions, 7 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index f3a6951..928330d 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -35,6 +35,17 @@ def raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
if not all(map(distance_is_zero, children_distances)):
raise ValueError("Distance of each child list/tuple from itself should be zero!")
+def raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists):
+ """Check that the distance from A to B, is the same as the distance from B to A.
+If the two distances are different, throw an exception."""
+ for i in range(len(lists)):
+ for j in range(len(lists)):
+ if lists[i][j] != lists[j][i]:
+ raise MirrorError(
+ ("Distance from one child({}) to the other ({}) "
+ "should be the same in both directions.").format(
+ lists[i][j], lists[j][i]))
+
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.
@@ -46,5 +57,6 @@ This description should be updated once the form/type of 'distance' identified."
raise_valueerror_if_lists_empty(lists)
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)
#### END: Guard Functions ####
return None
diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py
index 1fb7bbb..207debf 100644
--- a/tests/unit/computations/test_slink.py
+++ b/tests/unit/computations/test_slink.py
@@ -44,7 +44,7 @@ class TestSlink(TestCase):
with self.assertRaises(ValueError):
nearest(lst, 1, 1)
- def test_nearest_expects_exception_if_value_at_index_j_in_list_i_does_not_equals_value_at_index_i_in_list_j(self):
+ def test_nearest_expects_exception_if_distance_from_child_a_to_child_b_is_not_distance_from_child_b_to_child_a(self):
for lst in [[[0,1],[2,0]],
[[0,1,2],[1,0,3],[9,7,0]],
[[0,1,2,3],[7,0,2,3],[2,3,0,1],[8,9,5,0]]]:
@@ -56,12 +56,12 @@ class TestSlink(TestCase):
# 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]],
- [[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]],
+ [[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!"):
nearest(lst, 1, 1)