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#!/usr/bin/env python
import unittest
import os
from cogent import LoadTree
from cogent.parse.tree import DndParser
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Andrew Butterfield",
"Matthew Wakefield", "Daniel McDonald", "Justin Kuczynski"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
base_path = os.getcwd()
data_path = os.path.join(base_path, 'data')
# Missing tests: edge attributes (Name, Length, Children) only get tested
# in passing by some of these tests. See also xxx's
class TreeInterfaceForLikelihoodFunction(unittest.TestCase):
default_newick = "((A:1,B:2)ab:3,((C:4,D:5)cd,E:6)cde:7)"
def _maketree(self, treestring=None):
if treestring is None:
treestring = self.default_newick
return LoadTree(treestring=treestring, underscore_unmunge=True)
def setUp(self):
self.default_tree = self._maketree()
def test_getEdgeNames(self):
tree = self._maketree()
for (a, b, outgroup, result) in [
('A', 'B', None, ['A', 'B']),
('E', 'C', None, ['C', 'D', 'cd', 'E']),
('C', 'D', 'E', ['C', 'D'])]:
self.assertEqual(tree.getEdgeNames(
a, b, True, False, outgroup), result)
def test_parser(self):
"""nasty newick"""
nasty = "( (A :1.0,'B (b)': 2) [com\nment]pair:3,'longer name''s':4)dash_ed;"
nice = "((A:1.0,'B (b)':2.0)pair:3.0,'longer name''s':4.0)dash_ed;"
tree = self._maketree(nasty)
tidied = tree.getNewick(with_distances=1)
self.assertEqual(tidied, nice)
# Likelihood Function Interface
def test_getEdgeNames(self):
tree = self.default_tree
clade = tree.getEdgeNames('C', 'E', getstem=0, getclade=1)
clade.sort()
self.assertEqual(clade, ['C', 'D', 'E', 'cd'])
all = tree.getEdgeNames('C', 'E', getstem=1, getclade=1)
all.sort()
self.assertEqual(all, ['C', 'D', 'E', 'cd', 'cde'])
stem = tree.getEdgeNames('C', 'E', getstem=1, getclade=0)
self.assertEqual(stem, ['cde'])
def test_getEdgeNamesUseOutgroup(self):
t1 = LoadTree(treestring="((A,B)ab,(F,(C,D)cd)cdf,E)root;")
# a, e, ogroup f
t2 = LoadTree(treestring="((E,(A,B)ab)abe,F,(C,D)cd)root;")
expected = ['A', 'B', 'E', 'ab']
for t in [t1, t2]:
edges = t.getEdgeNames('A', 'E', getstem = False, getclade = True,
outgroup_name = "F")
edges.sort()
self.assertEqual(expected, edges)
def test_getConnectingNode(self):
tree = self.default_tree
self.assertEqual(tree.getConnectingNode('A', 'B').Name, 'ab')
self.assertEqual(tree.getConnectingNode('A', 'C').Name, 'root')
def test_getNodeMatchingName(self):
tree = self.default_tree
for (name, expect_tip) in [('A', True), ('ab', False)]:
edge = tree.getNodeMatchingName(name)
self.assertEqual(edge.Name, name)
self.assertEqual(edge.istip(), expect_tip)
def test_getEdgeVector(self):
tree = self.default_tree
names = [e.Name for e in tree.getEdgeVector()]
self.assertEqual(names,
['A', 'B', 'ab', 'C', 'D', 'cd', 'E', 'cde', 'root'])
def test_getNewickRecursive(self):
orig = "((A:1.0,B:2.0)ab:3.0,((C:4.0,D:5.0)cd:6.0,E:7.0)cde:8.0)all;"
unlen = "((A,B)ab,((C,D)cd,E)cde)all;"
tree = self._maketree(orig)
self.assertEqual(tree.getNewickRecursive(with_distances=1), orig)
self.assertEqual(tree.getNewickRecursive(), unlen)
tree.Name = "a'l"
ugly_name = "((A,B)ab,((C,D)cd,E)cde)a'l;"
ugly_name_esc = "((A,B)ab,((C,D)cd,E)cde)'a''l';"
self.assertEqual(tree.getNewickRecursive(escape_name=True), \
ugly_name_esc)
self.assertEqual(tree.getNewickRecursive(escape_name=False), ugly_name)
tree.Name = "a_l"
ugly_name = "((A,B)ab,((C,D)cd,E)cde)a_l;"
ugly_name_esc = "((A,B)ab,((C,D)cd,E)cde)'a_l';"
self.assertEqual(tree.getNewickRecursive(escape_name=True), \
ugly_name_esc)
self.assertEqual(tree.getNewickRecursive(escape_name=False), ugly_name)
tree.Name = "a l"
ugly_name = "((A,B)ab,((C,D)cd,E)cde)a l;"
ugly_name_esc = "((A,B)ab,((C,D)cd,E)cde)a_l;"
self.assertEqual(tree.getNewickRecursive(escape_name=True), \
ugly_name_esc)
self.assertEqual(tree.getNewickRecursive(escape_name=False), ugly_name)
tree.Name = "'a l'"
quoted_name = "((A,B)ab,((C,D)cd,E)cde)'a l';"
quoted_name_esc = "((A,B)ab,((C,D)cd,E)cde)'a l';"
self.assertEqual(tree.getNewickRecursive(escape_name=True), \
quoted_name_esc)
self.assertEqual(tree.getNewickRecursive(escape_name=False),quoted_name)
def test_getNewick(self):
orig = "((A:1.0,B:2.0)ab:3.0,((C:4.0,D:5.0)cd:6.0,E:7.0)cde:8.0)all;"
unlen = "((A,B)ab,((C,D)cd,E)cde)all;"
tree = self._maketree(orig)
self.assertEqual(tree.getNewick(with_distances=1), orig)
self.assertEqual(tree.getNewick(), unlen)
tree.Name = "a'l"
ugly_name = "((A,B)ab,((C,D)cd,E)cde)a'l;"
ugly_name_esc = "((A,B)ab,((C,D)cd,E)cde)'a''l';"
self.assertEqual(tree.getNewick(escape_name=True), ugly_name_esc)
self.assertEqual(tree.getNewick(escape_name=False), ugly_name)
tree.Name = "a_l"
ugly_name = "((A,B)ab,((C,D)cd,E)cde)a_l;"
ugly_name_esc = "((A,B)ab,((C,D)cd,E)cde)'a_l';"
self.assertEqual(tree.getNewickRecursive(escape_name=True), \
ugly_name_esc)
self.assertEqual(tree.getNewickRecursive(escape_name=False), ugly_name)
tree.Name = "a l"
ugly_name = "((A,B)ab,((C,D)cd,E)cde)a l;"
ugly_name_esc = "((A,B)ab,((C,D)cd,E)cde)a_l;"
self.assertEqual(tree.getNewickRecursive(escape_name=True), \
ugly_name_esc)
self.assertEqual(tree.getNewickRecursive(escape_name=False), ugly_name)
tree.Name = "'a l'"
quoted_name = "((A,B)ab,((C,D)cd,E)cde)'a l';"
quoted_name_esc = "((A,B)ab,((C,D)cd,E)cde)'a l';"
self.assertEqual(tree.getNewick(escape_name=True), \
quoted_name_esc)
self.assertEqual(tree.getNewick(escape_name=False),quoted_name)
def test_XML(self):
# should add some non-length parameters
orig = self.default_tree
xml = orig.getXML()
parsed = LoadTree(treestring=xml)
self.assertEqual(str(orig), str(parsed))
# Magic methods
def test_str(self):
"""testing (well, exercising at least), __str__"""
str(self.default_tree)
def test_repr(self):
"""testing (well, exercising at least), __repr__"""
repr(self.default_tree)
def test_eq(self):
"""testing (well, exercising at least), __eq__"""
# xxx not good enough!
t1 = self._maketree()
t2 = self._maketree()
self.assertTrue(t1 == t1)
self.assertFalse(t1 == t2)
def test_balanced(self):
"""balancing an unrooted tree"""
t = LoadTree(treestring='((a,b),((c1,(c2,(c3,(c4,(c5,(c6,c7)))))),(d,e)),f)')
b = LoadTree(treestring='(c1,(c2,(c3,(c4,(c5,(c6,c7))))),((d,e),((a,b),f)))')
self.assertEqual(str(t.balanced()), str(b))
def test_params_merge(self):
t = LoadTree(treestring='((((a,b)ab,c)abc),d)')
for (label, length, beta) in [('a',1, 20),('b',3,2.0),('ab',4,5.0),]:
t.getNodeMatchingName(label).params = {'length':length, 'beta':beta}
t = t.getSubTree(['b', 'c', 'd'])
self.assertEqual(t.getNodeMatchingName('b').params,
{'length':7, 'beta':float(2*3+4*5)/(3+4)})
self.assertRaises(ValueError, t.getSubTree, ['b','c','xxx'])
self.assertEqual(str(t.getSubTree(['b','c','xxx'],ignore_missing=True)),
'(b:7,c)root;')
def test_making_from_list(self):
tipnames_with_spaces = ['a_b','a b',"T'lk"]
tipnames_with_spaces.sort()
t = LoadTree(tip_names=tipnames_with_spaces)
result = t.getTipNames()
result.sort()
assert result == tipnames_with_spaces
def test_getsetParamValue(self):
"""test getting, setting of param values"""
t = LoadTree(treestring='((((a:.2,b:.3)ab:.1,c:.3)abc:.4),d:.6)')
self.assertEqual(t.getParamValue('length', 'ab'), 0.1, 2)
t.setParamValue('zz', 'ab', 4.321)
node = t.getNodeMatchingName('ab')
self.assertEqual(4.321, node.params['zz'], 4)
class SmallTreeReshapeTestClass(unittest.TestCase):
def test_rootswaps(self):
"""testing (well, exercising at least), unrooted"""
new_tree = LoadTree(treestring="((a,b),(c,d))")
new_tree = new_tree.unrooted()
self.assert_(len(new_tree.Children) > 2, 'not unrooted right')
def test_reroot(self):
tree = LoadTree(treestring="((a,b),(c,d),e)")
tree2 = tree.rootedWithTip('b')
self.assertEqual(tree2.getNewick(), "(a,b,((c,d),e));")
def test_sameShape(self):
"""test topology assessment"""
t1 = LoadTree(treestring="(((s1,s5),s3),s2,s4);")
t2 = LoadTree(treestring="((s1,s5),(s2,s4),s3);")
t3 = LoadTree(treestring="((s1,s4),(s2,s5),s3);")
assert t1.sameTopology(t2), (t1, t2)
assert not t1.sameTopology(t3), (t1, t3)
assert not t2.sameTopology(t3), (t2, t3)
#=============================================================================
# these are tests involving tree manipulation methods
# hence, testing them for small and big trees
# the tests are written once for the small tree, the big tree
# tests are performed by inheriting from this class, but over-riding
# the setUp.
class TestTree(unittest.TestCase):
"""tests for a single tree-type"""
def setUp(self):
self.name = 'small tree - '
self.otu_names = ['NineBande', 'Mouse', 'HowlerMon', 'DogFaced']
self.otu_names.sort()
self.newick = '(((Human,HowlerMon),Mouse),NineBande,DogFaced);'
self.newick_sorted = '(DogFaced,((HowlerMon,Human),Mouse),NineBande);'
self.newick_reduced = '((HowlerMon,Mouse),NineBande,DogFaced);'
self.tree = LoadTree(treestring = self.newick)
def test_sorttree(self):
"""testing (well, exercising at least) treesort"""
new_tree = self.tree.sorted()
if hasattr(self, 'newick_sorted'):
self.assertEqual(
self.newick_sorted,
new_tree.getNewick(with_distances=0))
def test_getsubtree(self):
"""testing getting a subtree"""
subtree = self.tree.unrooted().getSubTree(self.otu_names)
new_tree = LoadTree(treestring = self.newick_reduced).unrooted()
# check we get the same names
self.assertEqual(*[len(t.Children) for t in (subtree,new_tree)])
self.assertEqual(str(subtree), str(new_tree))
def test_ascii(self):
self.tree.asciiArt()
# unlabeled internal node
tr = DndParser("(B:0.2,(C:0.3,D:0.4):0.6)F;")
tr.asciiArt(show_internal=True, compact=False)
tr.asciiArt(show_internal=True, compact=True)
tr.asciiArt(show_internal=False, compact=False)
# the following class repeats the above tests but using a big tree and big data-set
class BigTreeSingleTests(TestTree):
"""using the big-tree for single-tree tests"""
def setUp(self):
self.name = 'big tree - '
self.otu_names = ['Horse', 'TombBat', 'Rhino', 'Pig', 'AsianElep',
'SpermWhal', 'Cat', 'Gorilla', 'Orangutan',
'bandicoot', 'Hedgehog', 'Sloth', 'HairyArma',
'Manatee', 'GoldenMol', 'Pangolin']
self.otu_names.sort()
self.newick = '((((((((FlyingFox,DogFaced),((FreeTaile,LittleBro),(TombBat,RoundEare))),(FalseVamp,LeafNose)),(((Horse,Rhino),(Pangolin,(Cat,Dog))),(Llama,(Pig,(Cow,(Hippo,(SpermWhal,HumpbackW))))))),(Mole,Hedgehog)),(TreeShrew,(FlyingLem,((Jackrabbit,(FlyingSqu,(OldWorld,(Mouse,Rat)))),(Galago,(HowlerMon,(Rhesus,(Orangutan,(Gorilla,(Human,Chimpanzee)))))))))),(((NineBande,HairyArma),(Anteater,Sloth)),(((Dugong,Manatee),((AfricanEl,AsianElep),(RockHyrax,TreeHyrax))),(Aardvark,((GoldenMol,(Madagascar,Tenrec)),(LesserEle,GiantElep)))))),(caenolest,(phascogale,(wombat,bandicoot))));'
self.newick_reduced = '(((((TombBat,(((Horse,Rhino),(Pangolin,Cat)),(Pig,SpermWhal))),Hedgehog),(Orangutan,Gorilla)),((HairyArma,Sloth),((Manatee,AsianElep),GoldenMol))),bandicoot);'
self.tree = LoadTree(treestring = self.newick)
def test_getEdgeNames(self):
"""testing (well, exercising at least), getedgenames"""
# Fell over on small tree because "stem descended from root
# joiner was a tip"
a,b = self.otu_names[:2]
clade = self.tree.getEdgeNames(a, b, True, False)
def test_getTipNames(self):
"""testing (well, exercising at least), getTipNames"""
a,b = self.otu_names[:2]
tips = self.tree.getTipNames()
self.assertEqual(len(tips), 55)
if __name__ == '__main__':
unittest.main()
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