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test_Phylo.py

# 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

#TODO - Remove this hack
#This will raise MissingPythonDependencyError if we don't have ElementTree
#and thus skip the all these tests. A couple of them could be run without
#ElementTree, but we're about drop Python 2.4 support so I don't mind.
from Bio.Phylo import PhyloXMLIO as PXIO
del PXIO

# 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'


00032 class IOTests(unittest.TestCase):
    """Tests for parsing and writing the supported formats."""

00035     def test_newick(self):
        """Read a Newick file with one tree."""
        tree = Phylo.read(EX_NEWICK, 'newick')
        self.assertEqual(len(tree.get_terminals()), 28)

00040     def test_newick(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)

00047     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)


00066 class TreeTests(unittest.TestCase):
    """Tests for methods on BaseTree.Tree objects."""
00068     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
00092     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)


00104 class MixinTests(unittest.TestCase):
    """Tests for TreeMixin methods."""
    def setUp(self):
        self.phylogenies = list(Phylo.parse(EX_PHYLO, 'phyloxml'))

    # Traversal methods

00111     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')

00145     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')


00162     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)

00176     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')

00184     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

00195     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])

00206     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)

00215     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)

00225     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)

00231     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)

00245     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

00253     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)

00264     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])

00287     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'))

00298     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)

00330     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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