[Biopython-dev] Bio.Phylo tutorial

[Eric Talevich]

On Wed, Dec 3, 2014 at 9:05 AM, Tiago Antao <tra at popgen.net> wrote:

> Hi,
>
> I am back with trying to get the tutorial running with Python 3 (after
> the bugs were solved). I am hitting a problem (with both 2 and 3):
>
> Phylo.convert("data/tree1.dnd", "newick", "data/tree1.xml", "nexml")
>
> This fails, see:
>
>
> http://localhost:8888/notebooks/13%20-%20Phylogenetics%20with%20Bio.Phylo.ipynb
>
> It says that the file tree1.dnd does not exist.
>
> Question: Is there a file missing in the tutorial? Or it is just a case
> that simple.dnd or opuntia.dnd should be used instead (and the
> tutorial amended)?
>

The file was supposed to be created in the previous step, but unfortunately
the file names did not match: created as "tree1.nwk", used later as
"tree1.dnd". I just fixed it here:
https://github.com/biopython/biopython/commit/4b732e6fae40c1f0e26e770be2667bf1bf72cfe6

HTH,
Eric
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