1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
# 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 networkx
except ImportError:
raise MissingExternalDependencyError(
"Install NetworkX if you want to use Bio.Phylo._utils.")
try:
import pygraphviz
except ImportError:
try:
import pydot
except ImportError:
raise MissingExternalDependencyError(
"Install PyGraphviz or Pydot if you want to use "
"Bio.Phylo._utils.")
# OK, we can go ahead
import unittest
from Bio import Phylo
# Example PhyloXML file
EX_DOLLO = 'PhyloXML/o_tol_332_d_dollo.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)
|
