[Biopython-dev] Fw: Bio.Phylo tutorial

Tiago Antao tra at popgen.net
Thu Dec 4 18:24:22 UTC 2014

Sorry, sent this to Eric and forgot to Cc the list...

Begin forwarded message:

Date: Thu, 4 Dec 2014 18:23:29 +0000
From: Tiago Antao <tra at popgen.net>
To: Eric Talevich <eric.talevich at gmail.com>
Subject: Re: [Biopython-dev] Bio.Phylo tutorial


There are 3 problems:

Problem 1:
On Python 2 this (from the Tutorial) is failing:

trees = Phylo.parse("data/phyloxml_examples.xml", "phyloxml")
trees = list(trees)
for tree in trees:


Bio/Phylo/BaseTree.pyc in print_tree(obj, indent)
    953             This closes over textlines and modifies it in-place.
    954             """
--> 955             textlines.append(TAB * indent + repr(obj))
    956             indent += 1
    957             for attr in obj.__dict__:

UnicodeEncodeError: 'ascii' codec can't encode character u'\xfc' in
position 24: ordinal not in range(128)

This works on Python 3! But see problem 3 below

Problem 2:

On Python 3 this dialect does not work

trees = list(Phylo.parse("../../Tests/PhyloXML/phyloxml_examples.xml",
"phyl oxml"))
>>> tree1 = trees[0]
>>> others = trees[1:]

(trees is a generator). There are different solutions here (like doing

Problem 3:

While the code of problem 1 works on Python 3, the bit after does not
(I do not know with Python 2):

Phylo.write(tree1, "data/tree1.xml", "phyloxml")


Bio/Phylo/PhyloXMLIO.py in write(self, file, encoding, indent)
    675         if indent:
    676             _indent(self._tree.getroot())
--> 677         self._tree.write(file, encoding)
    678         return len(self._tree.getroot())

TypeError: must be str, not bytes

Maybe putting all this on automated docstring test would be a good


More information about the Biopython-dev mailing list