[Treebase-devel] NEXML bug?

[Roderic P. <r....@bi...>]

I'm parsing NEXML from TreeBASE as part of a project to build a TreeBASE browser. 

In some cases I'm getting files where the OTU labels (in the <otus> tags) don't match the trees. I'm using XML files a grabbed late last year so I'm not sure if the issue ahs been fixed, but I can't get a more recent verison from TreeBASE - http://treebase.org/treebase-web/search/downloadAStudy.html?id=2048&format=nexml keeps timing out (sigh).

The file for S2048 has three trees and three <otus> blocks. These don't seem to match. For example, tree #trees663275 claims it's OTUs are labelled by otus650205, but these otus only partially match the tree, leaving large gaps when I draw the tree.

Something has gone badly amiss. It's been a hassle to get to the bottom of this partly because of the verbosity of NEXML, and partly because the labels are separated from the tree, making it a hassle to extract the two sets of labels and discover that there's a problem.

Any thoughts on why the list of <otus> referred to by a tree would lack all the labels? I've attached the file that I'm working with.

Regards

Rod