[Biopython-dev] GSoC Weekly Update 12: PhyloXML for Biopython
Eric Talevich
eric.talevich at gmail.com
Mon Aug 10 13:44:31 EDT 2009
Hi folks,
Previously I (Aug. 3-7):
- Refactored the PhyloXML parser somewhat, to behave more like the other
Biopython parsers and also handle 'other' elements better
- Reorganized Bio.Tree a bit, generalizing the Tree base class and
improving BaseTree-PhyloXML interoperability
- Worked on networkx export and graphviz display
- Added some more tests (thanks, Diana!)
- Added TreeIO.convert(), to match the AlignIO and SeqIO modules
Next week (Aug. 10-14) I will:
- Update the wiki documentation
- Fix any surprises that come up during testing
Automated testing:
- Check unit tests for complete coverage
- Re-run performance benchmarks
- Run tests and benchmarks on alternate platforms
- Check epydoc's generated API documentation
Remarks:
- Performance of the I/O functions is close to what it was before, in
the
best of times; parsing Taxonomy nodes incrementally seems to have
helped.
- Drawing trees with Graphviz is still ugly. Hopefully I can fix it this
week, but if not, I'll probably do it after GSoC because I like pretty
things.
- Presumably, any discussion of merging with Biopython will have to wait
until after the biopython-1.51 release. I'll be around. For GSoC
requirements, I'm planning on just dumping the Bio.Tree and Bio.TreeIO
modules along with the unit test suite as standalone files, rather
than
as a patch set since the last upstream revision I pulled was just a
random untagged one around the time of the last beta release.
Cheers,
Eric
http://github.com/etal/biopython/tree/phyloxml/Bio/PhyloXML
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Biopython_support_for_parsing_and_writing_phyloXML
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