Merge pull request #216 from BZhao95/BZhao95-patch-1

Update poppunk_iterate.py
bacpop · Sep 12, 2022 · 3b4ab31 · 3b4ab31
2 parents 434408b + 254a47c
commit 3b4ab31
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diff --git a/PopPUNK/__init__.py b/PopPUNK/__init__.py
@@ -3,7 +3,7 @@
 
 '''PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'''
 
-__version__ = '2.5.0'
+__version__ = '2.5.1'
 
 # Minimum sketchlib version
 SKETCHLIB_MAJOR = 2

diff --git a/scripts/poppunk_iterate.py b/scripts/poppunk_iterate.py
@@ -260,17 +260,22 @@ def is_nested(cluster_dict, child_members, node_list):
     for leaf in tree.traverse_leaves():
         parent_node = leaf.get_parent()
         if not parent_node.is_root():
+            if parent_node.get_edge_length() < args.cutoff and parent_node.get_parent().is_root():
+                cut_clusters.add(parent_node)
+            elif parent_node.get_edge_length() < args.cutoff and not parent_node.get_parent().is_root():
             # For each leaf, go back up the tree to find the cluster which
             # crosses the cutoff threshold
-            while not parent_node.is_root() and\
-                parent_node.get_edge_length() < args.cutoff:
-                # Go up a level
-                child_node = parent_node
-                parent_node = child_node.get_parent()
-                if parent_node.is_root() or \
-                    (child_node.get_edge_length() < args.cutoff and \
-                     parent_node.get_edge_length() > args.cutoff):
-                    cut_clusters.add(parent_node)
+                while parent_node.get_edge_length() < args.cutoff:
+                    # Go up a level
+                    child_node = parent_node
+                    parent_node = child_node.get_parent()
+                    if parent_node.is_root():
+                        cut_clusters.add(child_node)
+                        break
+                    if (child_node.get_edge_length() < args.cutoff and \
+                        parent_node.get_edge_length() > args.cutoff):
+                        cut_clusters.add(child_node)
+                        break
 
     # In the case where a grand-parent node's average core distance is smaller
     # than child node's both great parent node and child node will be selected