Hi Mark, Brian and others,
Mark Holder wrote on 25/03/2011 23:12:
Hi all,
Adding a command skipping feature to ape, might make it a good bit
more robust to some of the weird files that are out there. I'm afraid
that I'm not familiar enough with the code to suggest where those
changes should go.
It's done. I've also fixed a bug in write.nexus() at the same occasion.
I've just submitted ape 2.7-1 to CRAN. For those who'd like to try it
right now, I've updated svn and uploaded the sources here:
http://ape.mpl.ird.fr/ape_2.7-1.tar.gz
Cheers,
Emmanuel
The NEXUS standard indicates that parsers should skip commands that
they don't understand. This can lead to problems (if there were multiple
taxa blocks in the same file and you ignore the LINK commands, for
instance). But in many cases, skipping these commands will work fine.
Skipping a command simply entails reading NEXUS tokens until the
token; is encountered. The tokenization rules are spec (
http://www.ncbi.nlm.nih.gov/pubmed/11975335 ).
Mesquite also occasionally uses a BLOCKID command (in pretty much any
block).
all the best,
Mark
On Mar 25, 2011, at 10:58 AM, Brian O'Meara wrote:
TITLE and LINK are used by Mesquite but not many other Nexus-reading
programs (TITLE appears as a future reserved command name in the Maddison et
al. (1997) nexus specification but I don't see LINK there).
Brian
_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
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On Fri, Mar 25, 2011 at 11:28 AM, Hilmar Lapp <hl...@nescent.org> wrote:
Thanks for tracking this down, Emmanuel. I'm forwarding this to the
TreeBASE developers list for consideration.
BTW the phylobase implementation uses NCL (NEXUS Class Library, in C++) for
parsing NEXUS. Given the difference, probably ape does not?
-hilmar
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