From 70d897fa07cbba3b4ddd1fdf3814bcb9534e6e0f Mon Sep 17 00:00:00 2001
From: Daniel Svensson <daniel.svensson@umu.se>
Date: Thu, 19 Nov 2020 12:51:23 +0100
Subject: [PATCH] fix bug in calculation of kmer distances

---
 krakmeopen/metrics.py | 35 ++---------------------------------
 1 file changed, 2 insertions(+), 33 deletions(-)

diff --git a/krakmeopen/metrics.py b/krakmeopen/metrics.py
index 68eeee0..ae28fab 100644
--- a/krakmeopen/metrics.py
+++ b/krakmeopen/metrics.py
@@ -291,39 +291,8 @@ def tabulate_clade_metrics(self, clade_id):
         distance_dict = {tax_id: None for tax_id in other_kmers if tax_id != 0}  # We can't calculate a distance to 'Unclassified' (tax_id = 0)
         for tax_id in distance_dict:
 
-            # The tax_id is an ancestor of the clade root
-            if tax_id in lineage:
-
-                # The distance between the clade root and the ancestor
-                distance = self.taxonomy_tree.get_distance(tax_id, clade_id)
-
-            # Not an ancestor, must compute two distances and add them together
-            else:
-
-                # Get the lineage of the tax_id
-                tax_id_lineage = self.taxonomy_tree.get_lineage([tax_id])[tax_id]
-                tax_id_lineage.reverse()  # Flip the lineage so that it goes from leaf to root
-
-                # Loop to find the lowest common ancestor (lca) of the clade id and
-                # the tax_id that we are currently getting the distance to
-                lca = None
-                for ancestor in tax_id_lineage:
-                    if ancestor in lineage:
-                        lca = ancestor
-                        break
-
-                # Find the distance between the lca and the clade id
-                clade_lca_distance = self.taxonomy_tree.get_distance(ancestor, clade_id)
-
-                # Find the distance between the lca and the tax_id currently
-                # being investigated
-                tax_id_lca_distance = self.taxonomy_tree.get_distance(ancestor, tax_id)
-
-                # The distance between the clade id and the tax_id is the sum of
-                # the two distances
-                distance = clade_lca_distance + tax_id_lca_distance
-
-            # Save the distance between the clade id and the tax_id
+            # Calc and save the distance between the clade_id and the tax_id
+            distance = self.taxonomy_tree.get_distance(tax_id, clade_id)
             distance_dict[tax_id] = distance
 
         # Multiply the distances with the number of kmers for each tax_id