def test_same_topology(self):
p = skbio.TreeNode.read(['((a,b),c);'])
s = skbio.TreeNode.read(['((a,b),c);'])
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s)
for n in internal:
self.assertEqual(n.support_count, 1)
def test_same_topology(self):
p = skbio.TreeNode.read(['((a,b),c);'])
s = skbio.TreeNode.read(['((a,b),c);'])
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s)
for n in internal:
self.assertEqual(n.support_count, 1)
def test_differing_topology(self):
p = skbio.TreeNode.read(['(((a,b),c),d);'])
s = skbio.TreeNode.read(['(((a,c),b),d);'])
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s)
a_b = p.find('a').parent
a_b_c = a_b.parent
self.assertEqual(a_b.support_count, 0)
self.assertEqual(a_b_c.support_count, 1)
def test_differing_topology(self):
p = skbio.TreeNode.read(['(((a,b),c),d);'])
s = skbio.TreeNode.read(['(((a,c),b),d);'])
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s)
a_b = p.find('a').parent
a_b_c = a_b.parent
self.assertEqual(a_b.support_count, 0)
self.assertEqual(a_b_c.support_count, 1)
def test_extra_node(self):
p = skbio.TreeNode.read(['(((a,b),c),d);'])
s = skbio.TreeNode.read(['((a,b),(c,d));'])
# The first node that has a, b, and c, also has d as a descendant
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s)
a_b = p.find('a').parent
a_b_c = a_b.parent
self.assertEqual(a_b.support_count, 1)
self.assertEqual(a_b_c.support_count, 0)
def test_extra_node(self):
p = skbio.TreeNode.read(['(((a,b),c),d);'])
s = skbio.TreeNode.read(['((a,b),(c,d));'])
# The first node that has a, b, and c, also has d as a descendant
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s)
a_b = p.find('a').parent
a_b_c = a_b.parent
self.assertEqual(a_b.support_count, 1)
self.assertEqual(a_b_c.support_count, 0)
def test_multiple_calls_with_outgroup(self):
p = skbio.TreeNode.read(['((((a,b),c),d),e);'])
s1 = skbio.TreeNode.read(['(((c,b),(a,d)),e);'])
s2 = skbio.TreeNode.read(['((((a,c),b),d),e);'])
# e is the outgroup here
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s1)
_add_support_count(internal, s2)
a_b = p.find('a').parent
a_b_c = a_b.parent
a_b_c_d = a_b_c.parent
self.assertEqual(a_b.support_count, 0)
self.assertEqual(a_b_c.support_count, 1)
self.assertEqual(a_b_c_d.support_count, 2)
def test_multiple_calls_with_outgroup(self):
p = skbio.TreeNode.read(['((((a,b),c),d),e);'])
s1 = skbio.TreeNode.read(['(((c,b),(a,d)),e);'])
s2 = skbio.TreeNode.read(['((((a,c),b),d),e);'])
# e is the outgroup here
internal = list(p.non_tips())
for n in internal:
n.support_count = 0
_add_support_count(internal, s1)
_add_support_count(internal, s2)
a_b = p.find('a').parent
a_b_c = a_b.parent
a_b_c_d = a_b_c.parent
self.assertEqual(a_b.support_count, 0)
self.assertEqual(a_b_c.support_count, 1)
self.assertEqual(a_b_c_d.support_count, 2)
