[Biopython-dev] GSoC final update: PhyloXML for Biopython
Eric Talevich
eric.talevich at gmail.com
Mon Aug 17 21:47:22 UTC 2009
Hi all,
Here's a final changelog for Aug. 10-14:
- Added a 'terminal' argument to the find() method on BaseTree.Tree, for
filtering internal/external nodes. This makes get_leaf_nodes() a trivial
function, and total_branch_length is pretty simple too.
- Updated the example phyloXML files to v1.10 schema-compliant copies from
phyloxml.org; couple bug fixes.
- Removed the project's README.rst file, so Bio/PhyloXML/ is no longer
controlled by Git. I'll merge any useful information from there into the
Biopython wiki documentation.
- Pulled the Biopython 1.51 release into my master branch, and merged that
into the phyloxml branch, so this branch (and the required GSoC patch
tarball) will apply cleanly to the publicly released Biopython 1.51 source
tree.
- Documented most of what's been done on the Biopython wiki:
http://www.biopython.org/wiki/PhyloXML
http://www.biopython.org/wiki/TreeIO
http://www.biopython.org/wiki/Tree
*Future plans*
There are a few tangential projects that deserve more attention over the
next few months, and I'm going to create separate Git branches for each of
them, to make it easier to share:
- Port the Newick tree parser and methods from Bio.Newick to Bio.Tree
and
TreeIO.
- Improve the graph drawing and networkx integration
- BioSQL adapter between Bio.Tree.BaseTree and PhyloDB tables
- Possibly, play with other tree representations -- nested-set, as
PhyloDB
does, and relationship matrix, which could bring NumPy into play (in a
separate Bio.Tree.Matrix module)
Finally, massive thanks to Brad and Christian for mentoring, Hilmar for
overseeing the whole project, Peter and the Biopython folks for their
guidance, and the various BioPerl monks and BioRubyists who shared their
wisdom.
All the best,
Eric
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Biopython_support_for_parsing_and_writing_phyloXML
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