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96 lines
3.4 KiB
Python
96 lines
3.4 KiB
Python
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Unit tests for Bio.Phylo functions with external dependencies."""
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import unittest
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from Bio._py3k import StringIO
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from Bio import Phylo
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# Check for any missing dependencies at the top level so we can skip
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from Bio import MissingExternalDependencyError
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try:
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import matplotlib
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except ImportError:
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raise MissingExternalDependencyError(
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"Install matplotlib if you want to use Bio.Phylo._utils.")
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# Don't use the Wx backend for matplotlib, use the simpler postscript
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# backend -- we're not going to display or save the plot anyway, so it
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# doesn't matter much, as long as it's not Wx. See:
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# http://lists.open-bio.org/pipermail/biopython-dev/2012-April/009559.html
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matplotlib.use('ps')
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try:
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from matplotlib import pyplot
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except ImportError:
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# Can fail here with font problems
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raise MissingExternalDependencyError(
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"Install matplotlib if you want to use Bio.Phylo._utils.")
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# Example PhyloXML file
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EX_DOLLO = 'PhyloXML/o_tol_332_d_dollo.xml'
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EX_APAF = 'PhyloXML/apaf.xml'
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class UtilTests(unittest.TestCase):
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"""Tests for various utility functions."""
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def test_draw(self):
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"""Run the tree layout algorithm, but don't display it."""
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pyplot.ioff() # Turn off interactive display
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dollo = Phylo.read(EX_DOLLO, 'phyloxml')
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apaf = Phylo.read(EX_APAF, 'phyloxml')
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Phylo.draw(dollo, do_show=False)
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Phylo.draw(apaf, do_show=False)
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# Fancier options
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Phylo.draw(apaf, do_show=False, branch_labels={apaf.root: 'Root'})
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Phylo.draw(apaf, do_show=False, branch_labels=lambda c: c.branch_length)
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def test_draw_with_label_colors_dict(self):
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"""Run the tree layout algorithm with a label_colors argument passed in
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as a dictionary. Don't display tree."""
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pyplot.ioff() # Turn off interactive display
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dollo = Phylo.read(EX_DOLLO, 'phyloxml')
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apaf = Phylo.read(EX_APAF, 'phyloxml')
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label_colors_dollo = {
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'f_50': 'red',
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'f_34': 'blue',
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}
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label_colors_apaf = {
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'22_MOUSE': 'red',
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'18_NEMVE': 'blue',
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}
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Phylo.draw(dollo, label_colors=label_colors_dollo, do_show=False)
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Phylo.draw(apaf, label_colors=label_colors_apaf, do_show=False)
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def test_draw_with_label_colors_callable(self):
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"""Run the tree layout algorithm with a label_colors argument passed in
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as a callable. Don't display tree."""
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pyplot.ioff() # Turn off interactive display
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dollo = Phylo.read(EX_DOLLO, 'phyloxml')
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apaf = Phylo.read(EX_APAF, 'phyloxml')
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label_colors_dollo = lambda label: 'r' if label == 'f_50' else 'k'
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label_colors_apaf = lambda label: 'r'
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Phylo.draw(dollo, label_colors=label_colors_dollo, do_show=False)
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Phylo.draw(apaf, label_colors=label_colors_apaf, do_show=False)
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def test_draw_ascii(self):
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"""Tree to Graph conversion."""
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handle = StringIO()
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tree = Phylo.read(EX_APAF, 'phyloxml')
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Phylo.draw_ascii(tree, file=handle)
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Phylo.draw_ascii(tree, file=handle, column_width=120)
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handle.close()
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if __name__ == '__main__':
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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