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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 the Bio.Phylo module."""
import sys
import unittest
from cStringIO import StringIO
from Bio import Phylo
from Bio.Phylo import PhyloXML, NewickIO
# Example Newick and Nexus files
EX_NEWICK = 'Nexus/int_node_labels.nwk'
EX_NEXUS = 'Nexus/test_Nexus_input.nex'
# Example PhyloXML files
EX_APAF = 'PhyloXML/apaf.xml'
EX_BCL2 = 'PhyloXML/bcl_2.xml'
EX_PHYLO = 'PhyloXML/phyloxml_examples.xml'
class IOTests(unittest.TestCase):
"""Tests for parsing and writing the supported formats."""
def test_newick_read_single(self):
"""Read a Newick file with one tree."""
tree = Phylo.read(EX_NEWICK, 'newick')
self.assertEqual(len(tree.get_terminals()), 28)
def test_newick_read_multiple(self):
"""Parse a Nexus file with multiple trees."""
trees = list(Phylo.parse(EX_NEXUS, 'nexus'))
self.assertEqual(len(trees), 3)
for tree in trees:
self.assertEqual(len(tree.get_terminals()), 9)
def test_newick_write(self):
"""Parse a Nexus file with multiple trees."""
# Tree with internal node labels
mem_file = StringIO()
tree = Phylo.read(StringIO('(A,B,(C,D)E)F;'), 'newick')
Phylo.write(tree, mem_file, 'newick')
mem_file.seek(0)
tree2 = Phylo.read(mem_file, 'newick')
# Sanity check
self.assertEqual(tree2.count_terminals(), 4)
# Check internal node labels were retained
internal_names = set(c.name
for c in tree2.get_nonterminals()
if c is not None)
self.assertEqual(internal_names, set(('E', 'F')))
def test_format_branch_length(self):
"""Custom format string for Newick branch length serialization."""
tree = Phylo.read(StringIO('A:0.1;'), 'newick')
mem_file = StringIO()
Phylo.write(tree, mem_file, 'newick', format_branch_length='%.0e')
# Py2.5 compat: Windows with Py2.5- represents this as 1e-001;
# on all other platforms it's 1e-01
self.assertTrue(mem_file.getvalue().strip()
in ['A:1e-01;', 'A:1e-001;'])
def test_convert(self):
"""Convert a tree between all supported formats."""
mem_file_1 = StringIO()
mem_file_3 = StringIO()
if sys.version_info[0] == 3:
from io import BytesIO
mem_file_2 = BytesIO()
else:
mem_file_2 = StringIO()
Phylo.convert(EX_NEWICK, 'newick', mem_file_1, 'nexus')
mem_file_1.seek(0)
Phylo.convert(mem_file_1, 'nexus', mem_file_2, 'phyloxml')
mem_file_2.seek(0)
Phylo.convert(mem_file_2, 'phyloxml', mem_file_3, 'newick')
mem_file_3.seek(0)
tree = Phylo.read(mem_file_3, 'newick')
self.assertEqual(len(tree.get_terminals()), 28)
class TreeTests(unittest.TestCase):
"""Tests for methods on BaseTree.Tree objects."""
def test_root_with_outgroup(self):
"""Tree.root_with_outgroup: reroot at a given clade."""
# On a large realistic tree, at a deep internal node
tree = Phylo.read(EX_APAF, 'phyloxml')
orig_num_tips = len(tree.get_terminals())
orig_tree_len = tree.total_branch_length()
tree.root_with_outgroup('19_NEMVE', '20_NEMVE')
self.assertEqual(orig_num_tips, len(tree.get_terminals()))
self.assertAlmostEqual(orig_tree_len, tree.total_branch_length())
# On small contrived trees, testing edge cases
for small_nwk in (
'(A,B,(C,D));',
'((E,F),((G,H)),(I,J));',
'((Q,R),(S,T),(U,V));',
'(X,Y);',
):
tree = Phylo.read(StringIO(small_nwk), 'newick')
orig_tree_len = tree.total_branch_length()
for node in list(tree.find_clades()):
tree.root_with_outgroup(node)
self.assertAlmostEqual(orig_tree_len,
tree.total_branch_length())
# Magic method
def test_str(self):
"""Tree.__str__: pretty-print to a string.
NB: The exact line counts are liable to change if the object
constructors change.
"""
for source, count in zip((EX_APAF, EX_BCL2), (386, 747)):
tree = Phylo.read(source, 'phyloxml')
output = str(tree)
self.assertEqual(len(output.splitlines()), count)
class MixinTests(unittest.TestCase):
"""Tests for TreeMixin methods."""
def setUp(self):
self.phylogenies = list(Phylo.parse(EX_PHYLO, 'phyloxml'))
# Traversal methods
def test_find_elements(self):
"""TreeMixin: find_elements() method."""
# From the docstring example
tree = self.phylogenies[5]
matches = list(tree.find_elements(PhyloXML.Taxonomy, code='OCTVU'))
self.assertEqual(len(matches), 1)
self.assertTrue(isinstance(matches[0], PhyloXML.Taxonomy))
self.assertEqual(matches[0].code, 'OCTVU')
self.assertEqual(matches[0].scientific_name, 'Octopus vulgaris')
# Iteration and regexps
tree = self.phylogenies[10]
for point, alt in zip(tree.find_elements(geodetic_datum=r'WGS\d{2}'),
(472, 10, 452)):
self.assertTrue(isinstance(point, PhyloXML.Point))
self.assertEqual(point.geodetic_datum, 'WGS84')
self.assertAlmostEqual(point.alt, alt)
# class filter
tree = self.phylogenies[4]
events = list(tree.find_elements(PhyloXML.Events))
self.assertEqual(len(events), 2)
self.assertEqual(events[0].speciations, 1)
self.assertEqual(events[1].duplications, 1)
# string filter & find_any
tree = self.phylogenies[3]
taxonomy = tree.find_any("B. subtilis")
self.assertEqual(taxonomy.scientific_name, "B. subtilis")
# integer filter
tree = Phylo.read(EX_APAF, 'phyloxml')
domains = list(tree.find_elements(start=5))
self.assertEqual(len(domains), 8)
for dom in domains:
self.assertEqual(dom.start, 5)
self.assertEqual(dom.value, 'CARD')
def test_find_clades(self):
"""TreeMixin: find_clades() method."""
# boolean filter
for clade, name in zip(self.phylogenies[10].find_clades(name=True),
list('ABCD')):
self.assertTrue(isinstance(clade, PhyloXML.Clade))
self.assertEqual(clade.name, name)
# finding deeper attributes
octo = list(self.phylogenies[5].find_clades(code='OCTVU'))
self.assertEqual(len(octo), 1)
self.assertTrue(isinstance(octo[0], PhyloXML.Clade))
self.assertEqual(octo[0].taxonomies[0].code, 'OCTVU')
# string filter
dee = self.phylogenies[10].find_clades('D').next()
self.assertEqual(dee.name, 'D')
def test_find_terminal(self):
"""TreeMixin: find_elements() with terminal argument."""
for tree, total, extern, intern in zip(
self.phylogenies,
(6, 6, 7, 18, 21, 27, 7, 9, 9, 19, 15, 9, 6),
(3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3),
(3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3),
):
self.assertEqual(len(list(tree.find_elements())), total)
self.assertEqual(len(list(tree.find_elements(terminal=True))),
extern)
self.assertEqual(len(list(tree.find_elements(terminal=False))),
intern)
def test_get_path(self):
"""TreeMixin: get_path() method."""
path = self.phylogenies[1].get_path('B')
self.assertEqual(len(path), 2)
self.assertAlmostEqual(path[0].branch_length, 0.06)
self.assertAlmostEqual(path[1].branch_length, 0.23)
self.assertEqual(path[1].name, 'B')
def test_trace(self):
"""TreeMixin: trace() method."""
tree = self.phylogenies[1]
path = tree.trace('A', 'C')
self.assertEqual(len(path), 3)
self.assertAlmostEqual(path[0].branch_length, 0.06)
self.assertAlmostEqual(path[2].branch_length, 0.4)
self.assertEqual(path[2].name, 'C')
# Information methods
def test_common_ancestor(self):
"""TreeMixin: common_ancestor() method."""
tree = self.phylogenies[1]
lca = tree.common_ancestor('A', 'B')
self.assertEqual(lca, tree.clade[0])
lca = tree.common_ancestor('A', 'C')
self.assertEqual(lca, tree.clade)
tree = self.phylogenies[10]
lca = tree.common_ancestor('A', 'B', 'C')
self.assertEqual(lca, tree.clade[0])
def test_depths(self):
"""TreeMixin: depths() method."""
tree = self.phylogenies[1]
depths = tree.depths()
self.assertEqual(len(depths), 5)
for found, expect in zip(sorted(depths.values()),
[0, 0.060, 0.162, 0.290, 0.400]):
self.assertAlmostEqual(found, expect)
def test_distance(self):
"""TreeMixin: distance() method."""
t = self.phylogenies[1]
self.assertAlmostEqual(t.distance('A'), 0.162)
self.assertAlmostEqual(t.distance('B'), 0.29)
self.assertAlmostEqual(t.distance('C'), 0.4)
self.assertAlmostEqual(t.distance('A', 'B'), 0.332)
self.assertAlmostEqual(t.distance('A', 'C'), 0.562)
self.assertAlmostEqual(t.distance('B', 'C'), 0.69)
def test_is_bifurcating(self):
"""TreeMixin: is_bifurcating() method."""
for tree, is_b in zip(self.phylogenies,
(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1)):
self.assertEqual(tree.is_bifurcating(), is_b)
def test_is_monophyletic(self):
"""TreeMixin: is_monophyletic() method."""
tree = self.phylogenies[10]
abcd = tree.get_terminals()
abc = tree.clade[0].get_terminals()
ab = abc[:2]
d = tree.clade[1].get_terminals()
self.assertEqual(tree.is_monophyletic(abcd), tree.root)
self.assertEqual(tree.is_monophyletic(abc), tree.clade[0])
self.assertEqual(tree.is_monophyletic(ab), False)
self.assertEqual(tree.is_monophyletic(d), tree.clade[1])
# Alternate argument form
self.assertEqual(tree.is_monophyletic(*abcd), tree.root)
def test_total_branch_length(self):
"""TreeMixin: total_branch_length() method."""
tree = self.phylogenies[1]
self.assertAlmostEqual(tree.total_branch_length(), 0.792)
self.assertAlmostEqual(tree.clade[0].total_branch_length(), 0.392)
# Tree manipulation methods
def test_collapse(self):
"""TreeMixin: collapse() method."""
tree = self.phylogenies[1]
parent = tree.collapse(tree.clade[0])
self.assertEqual(len(parent), 3)
for clade, name, blength in zip(parent,
('C', 'A', 'B'),
(0.4, 0.162, 0.29)):
self.assertEqual(clade.name, name)
self.assertAlmostEqual(clade.branch_length, blength)
def test_collapse_all(self):
"""TreeMixin: collapse_all() method."""
tree = Phylo.read(EX_APAF, 'phyloxml')
d1 = tree.depths()
tree.collapse_all()
d2 = tree.depths()
# Total branch lengths should not change
for clade in d2:
self.assertAlmostEqual(d1[clade], d2[clade])
# No internal nodes should remain except the root
self.assertEqual(len(tree.get_terminals()), len(tree.clade))
self.assertEqual(len(list(tree.find_clades(terminal=False))), 1)
# Again, with a target specification
tree = Phylo.read(EX_APAF, 'phyloxml')
d1 = tree.depths()
internal_node_ct = len(tree.get_nonterminals())
tree.collapse_all(lambda c: c.branch_length < 0.1)
d2 = tree.depths()
# Should have collapsed 7 internal nodes
self.assertEqual(len(tree.get_nonterminals()), internal_node_ct - 7)
for clade in d2:
self.assertAlmostEqual(d1[clade], d2[clade])
def test_ladderize(self):
"""TreeMixin: ladderize() method."""
def ordered_names(tree):
return [n.name for n in tree.get_terminals()]
tree = self.phylogenies[10]
self.assertEqual(ordered_names(tree), list('ABCD'))
tree.ladderize()
self.assertEqual(ordered_names(tree), list('DABC'))
tree.ladderize(reverse=True)
self.assertEqual(ordered_names(tree), list('ABCD'))
def test_prune(self):
"""TreeMixin: prune() method."""
tree = self.phylogenies[10]
# Taxon in a trifurcation -- no collapse afterward
parent = tree.prune(name='B')
self.assertEqual(len(parent.clades), 2)
self.assertEqual(parent.clades[0].name, 'A')
self.assertEqual(parent.clades[1].name, 'C')
self.assertEqual(len(tree.get_terminals()), 3)
self.assertEqual(len(tree.get_nonterminals()), 2)
# Taxon in a bifurcation -- collapse
tree = self.phylogenies[0]
parent = tree.prune(name='A')
self.assertEqual(len(parent.clades), 2)
for clade, name, blen in zip(parent, 'BC', (.29, .4)):
self.assertTrue(clade.is_terminal())
self.assertEqual(clade.name, name)
self.assertAlmostEqual(clade.branch_length, blen)
self.assertEqual(len(tree.get_terminals()), 2)
self.assertEqual(len(tree.get_nonterminals()), 1)
# Taxon just below the root -- don't screw up
tree = self.phylogenies[1]
parent = tree.prune(name='C')
self.assertEqual(parent, tree.root)
self.assertEqual(len(parent.clades), 2)
for clade, name, blen in zip(parent, 'AB', (.102, .23)):
self.assertTrue(clade.is_terminal())
self.assertEqual(clade.name, name)
self.assertAlmostEqual(clade.branch_length, blen)
self.assertEqual(len(tree.get_terminals()), 2)
self.assertEqual(len(tree.get_nonterminals()), 1)
def test_split(self):
"""TreeMixin: split() method."""
tree = self.phylogenies[0]
C = tree.clade[1]
C.split()
self.assertEqual(len(C), 2)
self.assertEqual(len(tree.get_terminals()), 4)
self.assertEqual(len(tree.get_nonterminals()), 3)
C[0].split(3, .5)
self.assertEqual(len(tree.get_terminals()), 6)
self.assertEqual(len(tree.get_nonterminals()), 4)
for clade, name, blen in zip(C[0],
('C00', 'C01', 'C02'),
(0.5, 0.5, 0.5)):
self.assertTrue(clade.is_terminal())
self.assertEqual(clade.name, name)
self.assertEqual(clade.branch_length, blen)
# ---------------------------------------------------------
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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