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.
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
On Mar 25, 2011, at 12:00
Hello,
I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files
downloaded from treebase with URLs parsed from xml files. I can't manually edit
each file as I want to read a lot of these files. Is there an easy fix? One of
the files is copied below.
Thanks!
Scott
Hi Scott,
Which version of phylobase are you using and which architecture? I can
read the file on my machine.
Cheers,
-- François
On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.comwrote:
Hello,
I can't get read.nexus (ape) or readNexus (phylobase) to read nexus
Scott,
readNexus (phylobase) can read your tree but not read.nexus (ape). The
problem is the two lines inserted within the TREES block:
BEGIN TREES;
TITLE Tb10793;
LINK TAXA = M4787;
TREE Fig._3c = [R]
If you delete them, it's OK. FigTree also cannot read this file.
Cheers,
