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test_Phylo_networkx.py
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test_Phylo_networkx.py
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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
# Check for any missing dependencies at the top level so we can skip
from Bio import MissingExternalDependencyError
from Bio import Phylo
try:
import networkx
except ImportError:
raise MissingExternalDependencyError(
"Install networkx if you wish to use it with Bio.Phylo"
) from None
# 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)