[Biopython-dev] Bio.Phylo, Python 3 and Notebooks

[Tiago Antao]

Hi,

Sorry for the convoluted email, but the 3 topics of Bio.Phylo, Python 3
and Notebooks are related.

So, Biopython currently does not support Python3 completely because of
Bio.Phylo dependency on networkx, which itself depends on either
pygraphviz or pydot. Neither of which supports Python3. The pygraphviz
version on github (not released) currently supports Python3 and it is
good enough to at least run the cookbook. I am going to contact the
pygraphviz developers with an encouragement to release whenever
possible. So, that problem is probably be solved soon.

I am trying to wrap up the notebook of Bio.Phylo (which is a copy of
the chapter cookbook with a few adaptations). I have stumbled on a few
problems. This will be used for reference:


http://nbviewer.ipython.org/github/tiagoantao/biopython-notebook/blob/master/notebooks/13%20-%20Phylogenetics%20with%20Bio.Phylo.ipynb

1. Input 13 on the notebook above: There seems to be a Python3 problem
(the typical str/bytes issue)? Potential P3 bug?

2. 14: Do you know where I can find the file other_trees.xml ? Could
not find it

3. 15: The same from tree1.dnd

4. 42: It seems that paml is not generating a 'lnL max' (just see the
full dictionary appended there)? Potential cookbook bug?

Tiago