class TestTree(TestCase):
def setUp(self):
self.tree = Tree('((a,b),(c,d),e)')
assert sorted(self.tree.taxa) == list('abcde')
def test_getDistanceToRoot(self):
assert self.tree.getDistanceToRoot('a') == 2
def test_get_LCA(self):
assert str(self.tree.get_LCA('a', 'b')) == '(a,b);'
def test_get_distance(self):
tree_a = Tree('((a:1,b:1):1,(c:1,d:1):1)')
tree_b = Tree('((a:1,c:1):1,(b:1,d:1):1)')
assert tree_a.get_distance(tree_b, 'grf') == 1.0
assert tree_a.get_distance(tree_b, 'rf') == 1.0
assert tree_a.get_distance(tree_b, 'symmetric') == 2
assert tree_a.get_distance(tree_b, 'grf') == 1.0
def test_get_distance_unknown(self):
"""test failure with unknown distance"""
with self.assertRaises(ValueError):
Tree('(a,b)').get_distance(Tree('(a,b)'), 'xxx')
def test_init_from_file(self):
tree = Tree(test_data('phybo.tre'))
assert len(tree.taxa) == 40, "should have a taxa attribute and 40 tips"
def test_init_from_list(self):
tree = Tree(['Simon', 'Mattis', 'Robert'])
assert len(tree.taxa) == 3, "should have a taxa attribute and 3 tips"
class TestTree(object):
def setup(self):
self.tree = Tree('((a,b),(c,d),e)')
assert sorted(self.tree.taxa) == list('abcde')
def test_getDistanceToRoot(self):
assert self.tree.getDistanceToRoot('a') == 2
def test_get_LCA(self):
assert str(self.tree.get_LCA('a','b')) == '(a,b);'
def test_get_distance(self):
treeA = Tree('((a:1,b:1):1,(c:1,d:1):1)')
treeB = Tree('((a:1,c:1):1,(b:1,d:1):1)')
assert treeA.get_distance(treeB,'grf') == 1.0
assert treeA.get_distance(treeB,'rf') == 1.0
assert treeA.get_distance(treeB,'symmetric') == 2
assert treeA.get_distance(treeB,'grf') == 1.0
def test_random_tree():
taxa = list('abcdefg')
t1 = Tree(random_tree(taxa, branch_lengths=False))
t2 = Tree(random_tree(taxa, branch_lengths=True))
assert sorted(t1.taxa) == sorted(t2.taxa)
assert str(t1) != str(t2)
assert ':' in str(t2) and ':' not in str(t1)
def test_get_distance(self):
tree_a = Tree('((a:1,b:1):1,(c:1,d:1):1)')
tree_b = Tree('((a:1,c:1):1,(b:1,d:1):1)')
assert tree_a.get_distance(tree_b, 'grf') == 1.0
assert tree_a.get_distance(tree_b, 'rf') == 1.0
assert tree_a.get_distance(tree_b, 'symmetric') == 2
assert tree_a.get_distance(tree_b, 'grf') == 1.0
class TestTree(TestCase):
def setUp(self):
self.tree = Tree('((a,b),(c,d),e)')
assert sorted(self.tree.taxa) == list('abcde')
def test_getDistanceToRoot(self):
assert self.tree.getDistanceToRoot('a') == 2
def test_get_LCA(self):
assert str(self.tree.get_LCA('a', 'b')) == '(a,b);'
def test_get_distance(self):
treeA = Tree('((a:1,b:1):1,(c:1,d:1):1)')
treeB = Tree('((a:1,c:1):1,(b:1,d:1):1)')
assert treeA.get_distance(treeB, 'grf') == 1.0
assert treeA.get_distance(treeB, 'rf') == 1.0
assert treeA.get_distance(treeB, 'symmetric') == 2
assert treeA.get_distance(treeB, 'grf') == 1.0
def test_init_from_list(self):
tree = Tree(['Simon', 'Mattis', 'Robert'])
assert len(tree.taxa) == 3, "should have a taxa attribute and 3 tips"
def test_init_from_file(self):
tree = Tree(test_data('phybo.tre'))
assert len(tree.taxa) == 40, "should have a taxa attribute and 40 tips"
def test_get_distance_unknown(self):
"""test failure with unknown distance"""
with self.assertRaises(ValueError):
Tree('(a,b)').get_distance(Tree('(a,b)'), 'xxx')
def setUp(self):
self.tree = Tree('((a,b),(c,d),e)')
assert sorted(self.tree.taxa) == list('abcde')
def test_nwk2tree_matrix():
newick = '(((a,b),(c,d)),e);'
matrix, taxa = tree.nwk2tree_matrix(newick)
assert taxa == Tree(newick).taxa
def test_get_distance_unknown():
"""test failure with unknown distance"""
with pytest.raises(ValueError):
Tree('(a,b)').get_distance(Tree('(a,b)'), 'xxx')
def tree():
return Tree('((a,b),(c,d),e)')
def setUp(self):
WithTempDir.setUp(self)
self.newick = '(((a,b),(c,d)),e);'
self.tree = Tree(self.newick)