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 setUp(self):
"""Define a couple of standard trees"""
self.t1 = DndParser("(((a,b),c),(d,e))", UniFracTreeNode)
self.t2 = DndParser("(((a,b),(c,d)),(e,f))", UniFracTreeNode)
self.t3 = DndParser("(((a,b,c),(d)),(e,f))", UniFracTreeNode)
self.t4 = DndParser("((c)b,((f,g,h)e,i)d)", UniFracTreeNode)
self.t4.Name = "a"
self.t_str = "((a:1,b:2):4,(c:3,(d:1,e:1):2):3)"
self.t = DndParser(self.t_str, UniFracTreeNode)
self.env_str = """
a A 1
a C 2
b A 1
b B 1
c B 1
d B 3
e C 1"""
self.env_counts = count_envs(self.env_str.splitlines())
self.node_index, self.nodes = index_tree(self.t)
self.count_array, self.unique_envs, self.env_to_index, self.node_to_index = index_envs(
self.env_counts, self.node_index
)
self.branch_lengths = get_branch_lengths(self.node_index)
self.old_t_str = "((org1:0.11,org2:0.22,(org3:0.12,org4:0.23)g:0.33)b:0.2,(org5:0.44,org6:0.55)c:0.3,org7:0.4)"
self.old_t = DndParser(self.old_t_str, UniFracTreeNode)
self.old_env_str = """
org1 env1 1
org1 env2 1
org2 env2 1
org3 env2 1
org4 env3 1
org5 env1 1
org6 env1 1
org7 env3 1
"""
self.old_env_counts = count_envs(self.old_env_str.splitlines())
self.old_node_index, self.old_nodes = index_tree(self.old_t)
self.old_count_array, self.old_unique_envs, self.old_env_to_index, self.old_node_to_index = index_envs(
self.old_env_counts, self.old_node_index
)
self.old_branch_lengths = get_branch_lengths(self.old_node_index)
def setUp(self):
"""Define a couple of standard trees"""
self.t1 = DndParser('(((a,b),c),(d,e))', UniFracTreeNode)
self.t2 = DndParser('(((a,b),(c,d)),(e,f))', UniFracTreeNode)
self.t3 = DndParser('(((a,b,c),(d)),(e,f))', UniFracTreeNode)
self.t4 = DndParser('((c)b,((f,g,h)e,i)d)', UniFracTreeNode)
self.t4.Name = 'a'
self.t_str = '((a:1,b:2):4,(c:3,(d:1,e:1):2):3)'
self.t = DndParser(self.t_str, UniFracTreeNode)
self.env_str = """
a A 1
a C 2
b A 1
b B 1
c B 1
d B 3
e C 1"""
self.env_counts = count_envs(self.env_str.splitlines())
self.node_index, self.nodes = index_tree(self.t)
self.count_array, self.unique_envs, self.env_to_index, \
self.node_to_index = index_envs(self.env_counts, self.node_index)
self.branch_lengths = get_branch_lengths(self.node_index)
self.old_t_str = '((org1:0.11,org2:0.22,(org3:0.12,org4:0.23)g:0.33)b:0.2,(org5:0.44,org6:0.55)c:0.3,org7:0.4)'
self.old_t = DndParser(self.old_t_str, UniFracTreeNode)
self.old_env_str = """
org1 env1 1
org1 env2 1
org2 env2 1
org3 env2 1
org4 env3 1
org5 env1 1
org6 env1 1
org7 env3 1
"""
self.old_env_counts = count_envs(self.old_env_str.splitlines())
self.old_node_index, self.old_nodes = index_tree(self.old_t)
self.old_count_array, self.old_unique_envs, self.old_env_to_index, \
self.old_node_to_index = index_envs(self.old_env_counts, self.old_node_index)
self.old_branch_lengths = get_branch_lengths(self.old_node_index)
def setUp(self):
"""Define some standard trees."""
self.t_str = '((a:1,b:2):4,(c:3,(d:1,e:1):2):3)'
self.t = DndParser(self.t_str, UniFracTreeNode)
self.env_str = """
a A 1
a C 2
b A 1
b B 1
c B 1
d B 3
e C 1"""
self.env_counts = count_envs(self.env_str.splitlines())
self.missing_env_str = """
a A 1
a C 2
e C 1"""
self.missing_env_counts = count_envs(self.missing_env_str.splitlines())
self.extra_tip_str = """
q A 1
w C 2
e A 1
r B 1
t B 1
y B 3
u C 1"""
self.extra_tip_counts = count_envs(self.extra_tip_str.splitlines())
self.wrong_tip_str = """
q A 1
w C 2
r B 1
t B 1
y B 3
u C 1"""
self.wrong_tip_counts = count_envs(self.wrong_tip_str.splitlines())
self.t2_str = '(((a:1,b:1):1,c:5):2,d:4)'
self.t2 = DndParser(self.t2_str, UniFracTreeNode)
self.env2_str = """
a B 1
b A 1
c A 2
c C 2
d B 1
d C 1"""
self.env2_counts = count_envs(self.env2_str.splitlines())
self.trees = [self.t, self.t2]
self.envs = [self.env_counts, self.env2_counts]
self.mc_1 = array([.5, .4, .3, .2, .1, .6, .7, .8, .9, 1.0])
# from old EnvsNode tests
self.old_t_str = '((org1:0.11,org2:0.22,(org3:0.12,org4:0.23)g:0.33)b:0.2,(org5:0.44,org6:0.55)c:0.3,org7:0.4)'
self.old_t = DndParser(self.old_t_str, UniFracTreeNode)
self.old_env_str = """
org1 env1 1
org1 env2 1
org2 env2 1
org3 env2 1
org4 env3 1
org5 env1 1
org6 env1 1
org7 env3 1
"""
self.old_env_counts = count_envs(self.old_env_str.splitlines())
self.old_node_index, self.old_nodes = index_tree(self.old_t)
self.old_count_array, self.old_unique_envs, self.old_env_to_index, \
self.old_node_to_index = index_envs(self.old_env_counts, self.old_node_index)
self.old_branch_lengths = get_branch_lengths(self.old_node_index)
def setUp(self):
"""Define some standard trees."""
self.t_str = '((a:1,b:2):4,(c:3,(d:1,e:1):2):3)'
self.t = DndParser(self.t_str, UniFracTreeNode)
self.env_str = """
a A 1
a C 2
b A 1
b B 1
c B 1
d B 3
e C 1"""
self.env_counts = count_envs(self.env_str.splitlines())
self.missing_env_str = """
a A 1
a C 2
e C 1"""
self.missing_env_counts = count_envs(self.missing_env_str.splitlines())
self.extra_tip_str = """
q A 1
w C 2
e A 1
r B 1
t B 1
y B 3
u C 1"""
self.extra_tip_counts = count_envs(self.extra_tip_str.splitlines())
self.wrong_tip_str = """
q A 1
w C 2
r B 1
t B 1
y B 3
u C 1"""
self.wrong_tip_counts = count_envs(self.wrong_tip_str.splitlines())
self.t2_str = '(((a:1,b:1):1,c:5):2,d:4)'
self.t2 = DndParser(self.t2_str, UniFracTreeNode)
self.env2_str = """
a B 1
b A 1
c A 2
c C 2
d B 1
d C 1"""
self.env2_counts = count_envs(self.env2_str.splitlines())
self.trees = [self.t, self.t2]
self.envs = [self.env_counts, self.env2_counts]
self.mc_1 = array([.5, .4, .3, .2, .1, .6, .7, .8, .9, 1.0])
# from old EnvsNode tests
self.old_t_str = '((org1:0.11,org2:0.22,(org3:0.12,org4:0.23)g:0.33)b:0.2,(org5:0.44,org6:0.55)c:0.3,org7:0.4)'
self.old_t = DndParser(self.old_t_str, UniFracTreeNode)
self.old_env_str = """
org1 env1 1
org1 env2 1
org2 env2 1
org3 env2 1
org4 env3 1
org5 env1 1
org6 env1 1
org7 env3 1
"""
self.old_env_counts = count_envs(self.old_env_str.splitlines())
self.old_node_index, self.old_nodes = index_tree(self.old_t)
self.old_count_array, self.old_unique_envs, self.old_env_to_index, \
self.old_node_to_index = index_envs(self.old_env_counts, self.old_node_index)
self.old_branch_lengths = get_branch_lengths(self.old_node_index)
def test_get_branch_lengths(self):
"""get_branch_lengths should make array of branch lengths from index"""
result = get_branch_lengths(self.node_index)
self.assertEqual(result, array([1,2,1,1,3,2,4,3,0]))
def test_get_branch_lengths(self):
"""get_branch_lengths should make array of branch lengths from index"""
result = get_branch_lengths(self.node_index)
self.assertEqual(result, array([1, 2, 1, 1, 3, 2, 4, 3, 0]))