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# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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
try:
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:
# http://lists.open-bio.org/pipermail/biopython-dev/2012-April/009559.html
matplotlib.use('ps')
try:
from matplotlib import pyplot
except ImportError:
#Can fail here with font problems
raise MissingExternalDependencyError(
"Install matplotlib installation if you want to use Bio.Phylo._utils.")
try:
import networkx
except ImportError:
#We'll skip any tests requiring this below...
networkx = None
try:
import pygraphviz
except ImportError:
#We'll skip any tests requiring this below...
pygraphviz = None
# OK, we can go ahead
import unittest
from Bio._py3k 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 = Phylo.read(EX_DOLLO, 'phyloxml')
apaf = Phylo.read(EX_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."""
handle = StringIO()
tree = Phylo.read(EX_APAF, 'phyloxml')
Phylo.draw_ascii(tree, file=handle)
Phylo.draw_ascii(tree, file=handle, column_width=120)
handle.close()
if networkx:
def test_to_networkx(self):
"""Tree to Graph conversion, if networkx is available."""
tree = Phylo.read(EX_DOLLO, 'phyloxml')
G = Phylo.to_networkx(tree)
self.assertEqual(len(G.nodes()), 659)
# ---------------------------------------------------------
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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