<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Wed, Dec 3, 2014 at 9:05 AM, Tiago Antao <span dir="ltr"><<a href="mailto:tra@popgen.net" target="_blank">tra@popgen.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
I am back with trying to get the tutorial running with Python 3 (after<br>
the bugs were solved). I am hitting a problem (with both 2 and 3):<br>
<br>
Phylo.convert("data/tree1.dnd", "newick", "data/tree1.xml", "nexml")<br>
<br>
This fails, see:<br>
<br>
<a href="http://localhost:8888/notebooks/13%20-%20Phylogenetics%20with%20Bio.Phylo.ipynb" target="_blank">http://localhost:8888/notebooks/13%20-%20Phylogenetics%20with%20Bio.Phylo.ipynb</a><br>
<br>
It says that the file tree1.dnd does not exist.<br>
<br>
Question: Is there a file missing in the tutorial? Or it is just a case<br>
that simple.dnd or opuntia.dnd should be used instead (and the<br>
tutorial amended)?<br></blockquote><div><br></div><div>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:<br><a href="https://github.com/biopython/biopython/commit/4b732e6fae40c1f0e26e770be2667bf1bf72cfe6">https://github.com/biopython/biopython/commit/4b732e6fae40c1f0e26e770be2667bf1bf72cfe6</a><br></div></div><br></div><div class="gmail_extra">HTH,<br></div><div class="gmail_extra">Eric<br></div></div>