def test_fitch_descendants_missing_data(self):
"""fitch_descendants should work with missing data"""
#tree and envs for testing missing values
t_str = '(((a:1,b:2):4,(c:3,d:1):2):1,(e:2,f:1):3);'
env_str = """a A
b B
c D
d C
e C
f D"""
t = DndParser(t_str, UniFracTreeNode)
node_index, nodes = index_tree(t)
env_counts = count_envs(env_str.split('\n'))
count_array, unique_envs, env_to_index, node_to_index = \
index_envs(env_counts, node_index)
branch_lengths = get_branch_lengths(node_index)
#test just the AB pair
ab_counts = count_array[:, 0:2]
bindings = bind_to_array(nodes, ab_counts)
changes = fitch_descendants(bindings, counter=FitchCounter)
self.assertEqual(changes, 1)
orig_result = ab_counts.copy()
#check that the original Fitch counter gives the expected
#incorrect parsimony result
changes = fitch_descendants(bindings, counter=FitchCounterDense)
self.assertEqual(changes, 5)
new_result = ab_counts.copy()
#check that the two versions fill the array with the same values
self.assertEqual(orig_result, new_result)
def test_fitch_descendants_missing_data(self):
"""fitch_descendants should work with missing data"""
#tree and envs for testing missing values
t_str = '(((a:1,b:2):4,(c:3,d:1):2):1,(e:2,f:1):3);'
env_str = """a A
b B
c D
d C
e C
f D"""
t = DndParser(t_str, UniFracTreeNode)
node_index, nodes = index_tree(t)
env_counts = count_envs(env_str.split('\n'))
count_array, unique_envs, env_to_index, node_to_index = \
index_envs(env_counts, node_index)
branch_lengths = get_branch_lengths(node_index)
#test just the AB pair
ab_counts = count_array[:, 0:2]
bindings = bind_to_array(nodes, ab_counts)
changes = fitch_descendants(bindings, counter=FitchCounter)
self.assertEqual(changes, 1)
orig_result = ab_counts.copy()
#check that the original Fitch counter gives the expected
#incorrect parsimony result
changes = fitch_descendants(bindings, counter=FitchCounterDense)
self.assertEqual(changes, 5)
new_result = ab_counts.copy()
#check that the two versions fill the array with the same values
self.assertEqual(orig_result, new_result)
def test_fitch_descendants(self):
"""fitch_descendants should assign states by fitch parsimony, ret. #"""
id_, child = index_tree(self.t3)
a = zeros((11, 3)) + 99 # fill with junk
bindings = bind_to_array(child, a)
# load in leaf envs
a[0] = a[1] = a[2] = a[7] = [0, 1, 0]
a[3] = [1, 0, 0]
a[6] = [0, 0, 1]
changes = fitch_descendants(bindings)
self.assertEqual(changes, 2)
self.assertEqual(
a,
array(
[
[0, 1, 0],
[0, 1, 0],
[0, 1, 0],
[1, 0, 0],
[0, 1, 0],
[1, 0, 0],
[0, 0, 1],
[0, 1, 0],
[1, 1, 0],
[0, 1, 1],
[0, 1, 0],
]
),
)
def test_fitch_descendants(self):
"""fitch_descendants should assign states by fitch parsimony, ret. #"""
id_, child = index_tree(self.t3)
a = zeros((11, 3)) + 99 #fill with junk
bindings = bind_to_array(child, a)
#load in leaf envs
a[0] = a[1] = a[2] = a[7] = [0, 1, 0]
a[3] = [1, 0, 0]
a[6] = [0, 0, 1]
changes = fitch_descendants(bindings)
self.assertEqual(changes, 2)
self.assertEqual(a, \
array([[0,1,0],[0,1,0],[0,1,0],[1,0,0],[0,1,0],[1,0,0],\
[0,0,1],[0,1,0],[1,1,0],[0,1,1],[0,1,0]])
)
