Friday, June 8, 2007

PhyImport: Bio::TreeIO and Nexus problems

I was able to get nodes and edges loaded into the database for the example newick file using Bio::TreeIO. This is working for newick and New Hampshire extended files. However, I can't find a nexus file that Bio::TreeIO can seem to handle. :(. Perhaps this is due to the general chaos surrounding the NEXUS "standard", but I would like to get the import working for nearly all NEXUS files.

Maybe I should switch to the Bio::Phylo object, but I wanted to use the object model that was most tightly integrated with bioperl. I am trying to see if I can generate at least one "nexus" file that I can parse.

Since I can not even convert from a newick file to nexus, I seem to be having trouble with my installation of bioperl similar to a recent discussion: (http://portal.open-bio.org/pipermail/bioperl-l/2007-February/024829.html).

2 comments:

Hilmar said...

Have you tried and emailed that to the BioPerl list? Sendu Bala may be able to help (or know that that's an issue.

Sasilvia said...
This comment has been removed by a blog administrator.