def test_get_or_create(self):
t = Tree('root', ['A', 'B'])
c = t.get_or_create("C")
c.get_or_create("c1")
c.get_or_create("c2")
t.get("B").add('b1')
assert str(t) == "(A,b1,(c1,c2))"
def test_is_tip(self):
t = Tree('root', ['A', 'B'])
t.get("B").add("sub", ["b1", "b2"])
assert t.get("A").is_tip
assert t.get("B").is_tip is False
assert t.get("b1").is_tip
assert t.get("b2").is_tip
def test_get_or_create(self):
t = Tree('root', ['A', 'B'])
c = t.get_or_create("C")
c.get_or_create("c1")
c.get_or_create("c2")
t.get("B").add('b1')
assert str(t) == "(A,b1,(c1,c2))"
def test_sanitise(self):
with self.assertRaises(ValueError):
Tree('a;', ['A', 'B'])
with self.assertRaises(ValueError):
Tree('a', ['A(', 'B'])
with self.assertRaises(ValueError):
Tree('a;', ['A', 'B)'])
def test_get(self):
t = Tree('root', ['A', 'B', 'C'])
c = t.get("C")
c.add("c1")
c.add("c2")
t.get("B").add('b1')
assert str(t) == "(A,b1,(c1,c2))"
# try from different depths
assert t.get('c1').node == 'c1'
assert c.get('c1').node == 'c1'
def test_example(self):
t = Tree('root')
a = t.add("family a")
a1 = a.add("subgroup 1")
a1.add("A1")
a2 = a.add("subgroup 2")
a2.add("A2")
b = t.add("family b")
b1 = b.add("subgroup 1")
b1.add("B1a")
b1.add("B1b")
b2 = b.add("subgroup 2")
b2.add("B2")
assert str(t) == '((A1,A2),((B1a,B1b),B2))'
def test_example(self):
t = Tree('root')
a = t.add("family a")
a1 = a.add("subgroup 1")
a1.add("A1")
a2 = a.add("subgroup 2")
a2.add("A2")
b = t.add("family b")
b1 = b.add("subgroup 1")
b1.add("B1a")
b1.add("B1b")
b2 = b.add("subgroup 2")
b2.add("B2")
assert str(t) == '((A1,A2),((B1a,B1b),B2))'
def test_example(self):
t = Tree('root', show_nodelabels=True)
a = t.add("family a")
a1 = a.add("subgroup 1")
a1.add("A1")
a2 = a.add("subgroup 2")
a2.add("A2")
b = t.add("family b")
b1 = b.add("subgroup 1")
b1.add("B1a")
b1.add("B1b")
b2 = b.add("subgroup 2")
b2.add("B2")
assert str(
t) == '((A1,A2)family a,((B1a,B1b)subgroup 1,B2)family b)root'
def test_real(self):
# yon Trans-New Guinea, Ok-Awyu, Ok, Lowland
# bhl Trans-New Guinea, Ok-Awyu, Ok, Mountain
# fai Trans-New Guinea, Ok-Awyu, Ok, Mountain
# yir Trans-New Guinea, Ok-Awyu, Awyu-Dumut, Awyu
# aax Trans-New Guinea, Ok-Awyu, Awyu-Dumut, Dumut
# bwp Trans-New Guinea, Ok-Awyu, Awyu-Dumut, Dumut
t = Tree("Ok-Awyu")
Ok = t.add('Ok', ['Mountain', 'Lowland'])
Ok.get('Lowland').add('yon')
Ok.get('Mountain').add('bhl')
Ok.get('Mountain').add('fai')
AD = t.add('Awyu-Dumut', ['Awyu', 'Dumut'])
AD.get('Awyu').add('yir')
AD.get('Dumut').add('aax')
AD.get('Dumut').add('bwp')
assert str(t) == "((yir,(aax,bwp)),(yon,(bhl,fai)))"
def test_real(self):
# yon Trans-New Guinea, Ok-Awyu, Ok, Lowland
# bhl Trans-New Guinea, Ok-Awyu, Ok, Mountain
# fai Trans-New Guinea, Ok-Awyu, Ok, Mountain
# yir Trans-New Guinea, Ok-Awyu, Awyu-Dumut, Awyu
# aax Trans-New Guinea, Ok-Awyu, Awyu-Dumut, Dumut
# bwp Trans-New Guinea, Ok-Awyu, Awyu-Dumut, Dumut
t = Tree("Ok-Awyu")
Ok = t.add('Ok', ['Mountain', 'Lowland'])
Ok.get('Lowland').add('yon')
Ok.get('Mountain').add('bhl')
Ok.get('Mountain').add('fai')
AD = t.add('Awyu-Dumut', ['Awyu', 'Dumut'])
AD.get('Awyu').add('yir')
AD.get('Dumut').add('aax')
AD.get('Dumut').add('bwp')
assert str(t) == "((yir,(aax,bwp)),(yon,(bhl,fai)))"
def test_is_tip(self):
t = Tree('root', ['A', 'B'])
t.get("B").add("sub", ["b1", "b2"])
assert t.get("A").is_tip
assert t.get("B").is_tip is False
assert t.get("b1").is_tip
assert t.get("b2").is_tip
def test_get(self):
t = Tree('root', ['A', 'B', 'C'])
c = t.get("C")
c.add("c1")
c.add("c2")
t.get("B").add('b1')
assert str(t) == "(A,b1,(c1,c2))"
# try from different depths
assert t.get('c1').node == 'c1'
assert c.get('c1').node == 'c1'
def test_tips(self):
t = Tree('root', ['A', 'B'])
t.get("B").add("sub", ["b1", "b2"])
assert list([t.node for t in t.tips()]) == ['A', 'b1', 'b2']
def test_recursive_add(self):
t = Tree('root', ['A', 'B'])
t.get("B").add("sub", ["b1", "b2"])
assert str(t) == "(A,(b1,b2))"
def test_simple(self):
t = Tree('root', ['A', 'B', 'C'])
assert str(t) == "(A,B,C)"
def test_add(self):
t = Tree('root', ['A', 'B'])
t.add("C")
assert str(t) == "(A,B,C)"
def test_conflicts(self):
t = Tree('root', ['A', 'B'])
t.get("A").add("sub", ["b1", "b2"])
t.get("B").add("sub", ["b1", "b2"])
assert str(t) == '((b1,b2),(b1,b2))'
def test_singleton_tree(self):
assert str(Tree("root")) == "root"
def test_repr(self):
assert repr(Tree('a')) == "<Tree: a>"
def test_deep_tree(self):
t = Tree('root', show_nodelabels=True)
taxon = t
for i in range(0, 10):
taxon = taxon.add(i, [i])
assert str(t) == "(0,(1,(2,(3,(4,(5,(6,(7,(8,9)8)7)6)5)4)3)2)1)0"
def test_eq(self):
assert Tree("a") == Tree("a")
def test_conflicts(self):
t = Tree('root', ['A', 'B'])
t.get("A").add("sub", ["b1", "b2"])
t.get("B").add("sub", ["b1", "b2"])
assert str(t) == '((b1,b2),(b1,b2))'
def test_add(self):
t = Tree('root', ['A', 'B'])
t.add("C")
assert str(t) == "(A,B,C)"
def test_gt(self):
assert Tree("a") < Tree("b")
def test_deep_tree(self):
t = Tree('root')
taxon = t
for i in range(0, 10):
taxon = taxon.add(i, [i])
assert str(t) == "(0,(1,(2,(3,(4,(5,(6,(7,(8,9)))))))))"
def test_recursive_add(self):
t = Tree('root', ['A', 'B'])
t.get("B").add("sub", ["b1", "b2"])
assert str(t) == "(A,(b1,b2))"
def test_empty_tree(self):
assert str(Tree()) == ""
def test_simple(self):
t = Tree('root', ['A', 'B', 'C'], show_nodelabels=True)
assert str(t) == "(A,B,C)root"
def test_lt(self):
assert Tree("b") > Tree("a")
def test_tips(self):
t = Tree('root', ['A', 'B'])
t.get("B").add("sub", ["b1", "b2"])
assert list([t.node for t in t.tips()]) == ['A', 'b1', 'b2']
def test_recursive_add(self):
t = Tree('root', ['A', 'B'], show_nodelabels=True)
t.get("B").add("sub", ["b1", "b2"])
assert str(t) == "(A,(b1,b2)sub)root"
