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# Copyright (C) 2009 by Eric Talevich (
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for Bio.Phylo functions with external dependencies."""
# Check for any missing dependencies at the top level so we can skip
from Bio import MissingExternalDependencyError
import matplotlib
except ImportError:
raise MissingExternalDependencyError(
"Install matplotlib if you want to use Bio.Phylo._utils.")
# Don't use the Wx backend for matplotlib, use the simpler postscript
# backend -- we're not going to display or save the plot anyway, so it
# doesn't matter much, as long as it's not Wx. See:
from matplotlib import pyplot
import networkx
except ImportError:
raise MissingExternalDependencyError(
"Install NetworkX if you want to use Bio.Phylo._utils.")
import pygraphviz
except ImportError:
import pydot
except ImportError:
raise MissingExternalDependencyError(
"Install PyGraphviz or Pydot if you want to use "
# OK, we can go ahead
import unittest
from cStringIO import StringIO
from Bio import Phylo
# Example PhyloXML file
EX_DOLLO = 'PhyloXML/o_tol_332_d_dollo.xml'
EX_APAF = 'PhyloXML/apaf.xml'
class UtilTests(unittest.TestCase):
"""Tests for various utility functions."""
def test_draw(self):
"""Run the tree layout algorithm, but don't display it."""
pyplot.ioff() # Turn off interactive display
dollo =, 'phyloxml')
apaf =, 'phyloxml')
Phylo.draw(dollo, do_show=False)
Phylo.draw(apaf, do_show=False)
# Fancier options
Phylo.draw(apaf, do_show=False, branch_labels={apaf.root: 'Root'})
Phylo.draw(apaf, do_show=False, branch_labels=lambda c: c.branch_length)
def test_draw_ascii(self):
"""Tree to Graph conversion, if networkx is available."""
handle = StringIO()
tree =, 'phyloxml')
Phylo.draw_ascii(tree, file=handle)
Phylo.draw_ascii(tree, file=handle, column_width=120)
def test_to_networkx(self):
"""Tree to Graph conversion, if networkx is available."""
tree =, 'phyloxml')
G = Phylo.to_networkx(tree)
self.assertEqual(len(G.nodes()), 659)
# ---------------------------------------------------------
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
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