[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update 10: PhyloXML for Biopython

[Brad Chapman]

Hi Eric;
Thanks for taking on this reorganization into Tree/TreeIO. That is
turning out really nice and provides a great general framework for
plugging other phylogeny modules into.

>     - Bioperl's phyloXML driver was written for version 1.00 and might hurl
> if given a v1.10 file -- so that's a potential problem if Biopython
> defaults to writing v1.10 files. Should Writer take a option to specify the
> file format version number? Right now it only writes valid phyloXML v1.00.

I tend to agree with Mark and Hilmar's assessment; PhyloXML is in
development right now so we want to push towards the latest version.
Reading Christian's summary of changes:

http://phyloxml.blogspot.com/2009/06/proposed-changes-and-additions-for.html

it seems like much of this is fixes. It would be worth pinging
BioPerl to be sure someone will handle updates to the latest version
but otherwise I would go with what is easiest. You want to be
careful not to get trapped in version purgatory.

>     - Above, I've listed more enhancements than I'll probably be able to finish
>       this week. Which should have higher priority? I know merging Bio.Nexus
>       and Bio.Tree would be the most useful, but since (1) Biopython
>       development still happens on CVS, not Git, and (2) another Tree-based
>       GSoC project is expected to land around the same time as mine, I think
>       doing the integration right now would be kind of painful. So I can focus
>       either on laying the groundwork in Bio.Tree.BaseTree, copying rather than
>       moving the relevant Nexus code, or else work mainly on exporting to other
>       useful object representations like networkx graphs, or any Biopython
>       classes I've missed (e.g. alignments). Suggestions?

What are you most interested in? You've certainly earned the right
to work on what you think may be most useful to you in the future.
Any of the listed projects are a good step forward. If you really
really want my votes, they are for adding common tree manipulation
methods to the base Tree class and working towards PhyloDB storage
compatibility.

Brad