BioPython, PhyloXML and duplication nodes

Question

[abascalfederico]

Hi, I am parsing some trees from Ensembl's Compara that are in PhyloXML format. Internal nodes within these trees have several attributes, one of which indicates whether the node is a gene-duplication node or not.

I can't find the way to properly identify the duplication nodes using BioPython and the PhyloXML module (it seems much easier with my old BioPerl friend). I guess I have to do something with the class Events. Any help or clue?

Thanks!

Federico

Answer 1

[Eric T.]

Could you post an example snippet from one of these files? You can iterate over the nodes with the tree methods find_clades() or get_nonterminals(), or search for the Event tags themselves with find_elements(PhyloXML.Events) -- assuming the information you want is in the "events" tag. But check the XML file or the documentation to confirm that this is the tag you want, and try playing with it in a Python interpreter (e.g. IPython, ipython-notebook) to see how to get the exact information you want.

[abascalfederico]

Thank you! I didn't see your reply until now.