[Biopython-dev] [Wg-phyloinformatics] BioGeography update

Tue Jul 7 18:12:10 UTC 2009

Hi all,

I am just now back in town and would love to co-coordinate on this.  I 
agree having multiple newick parsers etc. is undesirable, I just found I 
was forced to that this spring when BioPython didn't have what I need 
even for pretty standard Newick files.  I have also made use of 
Mailund's newick parser in the past.

I am booked this afternoon but will go through the thread more this 
evening and comment further. Cheers!
Nick

Eric Talevich wrote:
> On Tue, Jul 7, 2009 at 9:02 AM, Brad Chapman <chapmanb at 50mail.com 
> <mailto:chapmanb at 50mail.com>> wrote:
> 
>     Hi Stephen;
> 
>     We can require lagrange to be installed and use imports to
>     grab the needed code. The other option is that y'all can explicitly
>     relicense a subset of the code under the Biopython license.
> 
> 
> Trivia: it looks like lagrange in turn depends on scipy, but quickly 
> glancing through the code, I only see numpy functions being used. Since 
> some other Biopython modules already depend on numpy, could the 
> installation of lagrange for Bio.Geography be made simpler by just 
> changing the import to numpy?
> 
>      > I can see however
>      > where the Bio.Nexus functionality might not be sufficient for tree
>      > manipulation. I am not a contributor to the BioPython dev group so I
>      > cannot speak to those specifics, but as a user I can see separating
>      > out the tree functions from the Nexus package (and tree I/O in
>      > general) as logically a phylogenetic tree structure has little to do
>      > with the nexus file format. It can be somewhat awkward to deal
>     with in
>      > the current form. A more general implementation might be a Bio.Tree
>      > package with I/O readers in Nexus and Newick and XML, etc.
> 
>     Definitely. Eric has been discussing this with regards to the
>     PhyloXML project and we had been looking at other Tree
>     representations: in PyCogent and Thomas Mailund's Newick module.
>     Considering the lagrange tree model makes a lot of sense as well.
>     What I'd like to see is a stab at a generalized Tree object that
>     supports the operations you need and that the Bio.Nexus parser can
>     produce, exactly as you describe. Eric and Nick, what do you think
>     about coordinating on this?
> 
> 
> Sounds great to me. My impression is that most tree representations are 
> based on a recursive Node element with a few associated attributes and a 
> number of useful methods; phyloXML has a Clade object roughly 
> corresponding to that, but also a bunch of other element types for 
> extensive annotation of the tree. So two options spring to mind:
> 
> 1. Let the Bio.PhyloXML.Tree objects be a superset of everything needed 
> by any phylogenetic tree representation, ever. (It's already pretty 
> close.) Refactor Nexus and Newick to use these objects; merge the 
> features of lagrange so the rest of the Biopython environment can 
> benefit. Only export to external object structures that are something 
> other than a straight phylogenetic tree -- e.g. networkx or graphviz for 
> plotting, numpy/scipy for crunching.
> 
> 2. Factor a simple tree structure out of lagrange and Bio.Nexus, and let 
> that be the Biopython default representation. Add a function in 
> Bio.PhyloXML to export its enhanced tree structure to this simpler 
> Bio.Tree representation.
> 
> I wrote Bio.PhyloXML.Tree to use the naming conventions of phyloXML, but 
> otherwise be independent of that specific file format. It doesn't depend 
> on any XML library directly, and both child nodes and XML node 
> attributes appear as plain ol' object attributes in the tree. But the 
> Nexus module looked like the parser was kind of tied to the tree 
> representation, so I haven't reused any of that code yet. So #1 is my 
> preference, but it put the burden of inter-module compatibility on 
> whoever is maintaining Bio.Nexus, whereas #2 leaves my code on a quiet 
> little island for the rest of the summer.
> 
> All the best,
> Eric

-- 
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

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