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