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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."""
import unittest
from Bio._py3k import StringIO
from Bio import Phylo
# Check for any missing dependencies at the top level so we can skip
from Bio import MissingExternalDependencyError
try:
import networkx
except ImportError:
raise MissingExternalDependencyError(
"Install networkx if you wish to use it with Bio.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_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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