Merge pull request #39 from andrewjpage/reroot_around_edge

Reroot around edge

run_gubbins.py

@@ -35,10 +35,35 @@ def reroot_tree_with_outgroup(tree_name, outgroup):
  tree.root_with_outgroup({'name': outgroup})
  Phylo.write(tree, tree_name, 'newick')
 
+def split_all_non_bi_nodes(node):
+ if node.is_leaf():
+ return None
+ elif len(node.child_nodes()) > 2:
+ split_child_nodes(node)
+
+ for child_node in node.child_nodes():
+ split_all_non_bi_nodes(child_node)
+
+ return None
+
+def split_child_nodes(node):
+ all_child_nodes = node.child_nodes()
+ #skip over the first node
+ first_child = all_child_nodes.pop()
+ # create a placeholder node to hang everything else off
+ new_child_node = node.new_child(edge_length=0)
+ # move the subtree into the placeholder
+ new_child_node.set_child_nodes(all_child_nodes)
+ # probably not really nessisary
+ node.set_child_nodes((first_child,new_child_node))
+
 def reroot_tree_at_midpoint(tree_name):
  tree = dendropy.Tree.get_from_path(tree_name, 'newick')
- tree.reroot_at_midpoint(update_splits=False, delete_outdegree_one=False)
+ split_all_non_bi_nodes(tree.seed_node)
+
+ tree.reroot_at_midpoint(update_splits=True, delete_outdegree_one=False)
  tree.deroot()
+ tree.update_splits()
  tree.write_to_path(
  tree_name, 
  'newick',