[Biopython] Phylo: rerooting a tree with a terminal node

[Robert Beiko]

Hi,

I have been experimenting with the excellent Phylo package in BioPython, 
and am having a bit of trouble with the 'root_with_outgroup' method.

Specifically, it seems to work fine when I apply it to internal nodes, 
but when I try to root on a terminal, I get an error:

---------------

Traceback (most recent call last):
   File "C:/Projects/10000/Phylogenomics/TestTrees/test.py", line 16, in 
<module>
     tree.root_with_outgroup(leaf)
   File "C:\Python26\lib\site-packages\Bio\Phylo\BaseTree.py", line 777, 
in root_with_outgroup
     parent.clades.pop(parent.clades.index(new_parent))
ValueError: list.index(x): x not in list

---------------

Here is an example script:

import io
import sys
from Bio import Phylo

infile = 'Example1.tre'
trees = Phylo.parse(infile,'newick')

for tree in trees:
     leafList = tree.get_terminals()
     for leaf in leafList:
         tree.root_with_outgroup(leaf)

---------------

And here is the file 'Example1.tre'

((AAA,BBB),(CCC,DDD));

[I have tried many permutations of the tree, and in no case have I been 
able to root using a terminal].

Line 777 in 'BaseTree.py' is:
parent.clades.pop(parent.clades.index(new_parent))

so it appears that new_parent is not in the list 'parent.clades'. My 
Python is rather rudimentary so I haven't been able to figure out why 
this might arise.

If I change 'get_terminals()' to 'get_nonterminals()' in the script 
above, everything works fine. I imagine I could get things to work by 
introducing a dummy sister node for each terminal I would like to root 
on, and then rooting on the LCA of the terminal and its dummy sister. 
But is there something I am doing wrong in the script above, that could 
easily be remedied without a hack?

Python version is 2.6, BioPython 1.56.

Best wishes and thanks,
Rob Beiko