[Biopython-dev] [Bug 3044] PhyloXMLIO, assigning node_id causes failures on write after re-reading

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3044





------- Comment #1 from eric.talevich at gmail.com  2010-04-06 19:02 EST -------
Hi Joel,

Thanks for testing! It's great to get this stuff ironed out before the first
stable release.

(In reply to comment #0)
> I updated my biopython from git and archaeoptryx from cvs on Friday and now
> several things work differently, mostly for the better.

Heads up: I pushed another change to GitHub yesterday that *might* have broken
your code. Would you mind pulling another update and seeing if everything still
works? (The main effect is that "tree.get_path(code='OCTVU')" will work now.)


> I have problems with writing any phyloXML tree which was read with node_id's
> defined.  Writing the tree the first time doesn't fail, and the tree can be
> subsequently read, but a failure occurs on the second write.

OK, I'll check this out soon. This may be due to a shim I added to make
PhyloXML.Id object behave like a primitive type in some cases, for
compatibility with non-PhyloXML trees.

Best,
Eric


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