Re: [Treebase-devel] NEXUS output problems

[William P. <wil...@ya...>]

On Apr 21, 2011, at 11:09 PM, Mark Holder wrote:

> Hi,
> 	I just downloaded S2012.nex (I can send it along if needed, but I won't clutter your inboxes unless it is needed. The urlishttp://purl.org/phylo/treebase/phylows/study/TB2:S2012 ).
> 
> 	My NEXUS parser is choking on a couple of things:
> 		1. The names of the CHARSET commands in the SETS block have spaces, but the names have not been "escaped" to convert them to single NEXUS tokens.  
> 
> 		2. There are multiple TAXA blocks but the TREES blocks do not use the LINK command to disambiguate.  Mesquite is smart enough to figure out which TAXA block is correct.  I suppose I could add taxa-block-detection code to NCL (the NEXUS parsing library that I use), but it would be much easier if TreeBase used LINK to clarify the connections.
> 
> all the best,
> Mark


We need to fix those things. Thanks for reporting. The LINK issue seems to work if analyses are downloaded individually, e.g.:

http://treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=4172&id=2012
http://treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=4173&id=2012

But indeed the CHARSETs are still not escaped properly. 

To be added to the bug list...

bp