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test_tree_compare.py
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test_tree_compare.py
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#!/usr/bin/env python
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.3.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
"""tests the tree_compare.py module."""
from cogent.util.unit_test import TestCase, main
from qiime.parse import parse_newick
import qiime.tree_compare as tc
class TreeCompareTests(TestCase):
""" tests only top level functions
"""
def test_bootstrap_support(self):
""" bootstrap_support should have correct bootstrap for a tree with
unlabeled internal nodes
"""
master_tree = parse_newick('((a:2,b:3):2,(c:1,d:2):7);')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2):2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33):2,d:7);') # abc are siblings
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2])
self.assertFloatEqual(sorted(bootstraps.values()),sorted([1.0, .5, .5]))
def test_bootstrap_support_labeled(self):
""" bootstrap_support should have correct bootstrap on a tree
with labeled internal nodes
"""
master_tree = parse_newick('((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2)hi:2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33)ho:2,d:7);') # abc are siblings
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2])
expected = dict([('ab', .5),('cd',.5),('rt',1.0)])
self.assertFloatEqual(bootstraps, expected)
def test_bootstrap_support_subset(self):
""" bootstrap_support should have correct bootstrap on a tree
when one support tree is missing a tip
"""
master_tree = parse_newick('((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2)hi:2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33)ho:2,d:7);') # abc are siblings
t3 = parse_newick('((a:6)hi:2,(c:1,d:2):7);') # b missing
t4 = parse_newick('(a:8,(c:1,d:2):7);') # b missing, and pruned
new_master, bootstraps = tc.bootstrap_support(master_tree,
[t1, t2,t3,t4])
expected = dict([('cd',.75),('rt',1.0)])
self.assertFloatEqual(bootstraps, expected)
def test_tree_support(self):
""" tree_support should correctly modify node.bootstrap_support
"""
master_tree = parse_newick('((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t2 = parse_newick('((a:2,b:3,c:33)ho:2,d:7);') # abc are siblings
tc.tree_support(master_tree, t2)
self.assertFloatEqual(\
master_tree.getNodeMatchingName('rt').bootstrap_support,1.0)
def test_setup_master_tree_alltips(self):
"""tests setup_master_tree"""
master_tree = parse_newick('((a:2,b:3):2,(c:1,d:2)foo:7);')
t1 = parse_newick('((a:6,b:8.2):2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33):2,d:7);') # abc are siblings
support_tree_tipnames = ['a','b','c','d']
exp = "((a:2.0,b:3.0)node1:2.0,(c:1.0,d:2.0)foo:7.0)node0;"
new_master = tc.setup_master_tree(master_tree, [t1,t2])
self.assertEqual(new_master.getNewick(with_distances=True),exp)
desc_tips_root = frozenset(['a','b','c','d'])
desc_tips_c0 = frozenset(['a','b'])
desc_tips_c1 = frozenset(['c','d'])
desc_tips_c0c0 = frozenset(['a'])
desc_tips_c0c1 = frozenset(['b'])
desc_tips_c1c0 = frozenset(['c'])
desc_tips_c1c1 = frozenset(['d'])
self.assertEqual(frozenset(new_master.getTipNames()), desc_tips_root)
self.assertEqual(frozenset(new_master.Children[0].getTipNames()), desc_tips_c0)
self.assertEqual(frozenset(new_master.Children[1].getTipNames()), desc_tips_c1)
c0 = master_tree.Children[0]
c1 = master_tree.Children[1]
self.assertEqual(frozenset(c0.Children[0].getTipNames()), desc_tips_c0c0)
self.assertEqual(frozenset(c0.Children[1].getTipNames()), desc_tips_c0c1)
self.assertEqual(frozenset(c1.Children[0].getTipNames()), desc_tips_c1c0)
self.assertEqual(frozenset(c1.Children[1].getTipNames()), desc_tips_c1c1)
def test_setup_master_tree_missingtips(self):
"""tests setup_master_tree"""
master_tree = parse_newick('((a:2,b:3):2,(c:1,d:2)foo:7);')
t1 = parse_newick('((a:6,b:8.2):2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,c:33):2,d:7);') # where's b?
support_tree_tipnames = ['a','c','d']
exp = "((c:1.0,d:2.0)foo:7.0,a:4.0)node0;"
new_master = tc.setup_master_tree(master_tree, [t1,t2])
self.assertEqual(new_master.getNewick(with_distances=True),exp)
desc_tips_root = frozenset(['a','c','d'])
desc_tips_c1 = frozenset(['a'])
desc_tips_c0 = frozenset(['c','d'])
desc_tips_c0c0 = frozenset(['c'])
desc_tips_c0c1 = frozenset(['d'])
self.assertEqual(frozenset(new_master.getTipNames()), desc_tips_root)
self.assertEqual(frozenset(new_master.Children[0].getTipNames()), desc_tips_c0)
self.assertEqual(frozenset(new_master.Children[1].getTipNames()), desc_tips_c1)
c0 = new_master.Children[0]
self.assertEqual(frozenset(c0.Children[0].getTipNames()), desc_tips_c0c0)
self.assertEqual(frozenset(c0.Children[1].getTipNames()), desc_tips_c0c1)
if __name__ =='__main__':
main()