[Biopython] Phylo: rerooting a tree with a terminal node
Robert Beiko
beiko at cs.dal.ca
Wed Jan 12 09:06:43 EST 2011
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
More information about the Biopython
mailing list