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authorMuriithi Frederick Muriuki2021-07-22 12:59:46 +0300
committerMuriithi Frederick Muriuki2021-07-22 12:59:46 +0300
commit703fad03660c8f4a5658bd4aecd3a18fad6ce10c (patch)
tree28593c485a54649883324c30c7baa0a58f4329d4 /gn3
parenta826daa77fa56afddb4920ae7ff9dec334f6e646 (diff)
downloadgenenetwork3-703fad03660c8f4a5658bd4aecd3a18fad6ce10c.tar.gz
Check that distance from A to B is same as from B to A
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that the distance from child A to B is the same as distance from child B to A. If not, throw an exception. * tests/unit/computations/test_slink.py: * Change the name of the test to more closely correspond to the business logic being tested. * Update the data in a separate test such that it does not error out due to failing to fulfill the expectations of separate requirement. - pass tests - Rename test - Fix errors: distances same both directions
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/slink.py12
1 files changed, 12 insertions, 0 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