def test_bind_to_parent_array(self):
"""bind_to_parent_array should bind tree to array correctly"""
a = reshape(arange(33), (11, 3))
index_tree(self.t3)
bindings = bind_to_parent_array(self.t3, a)
self.assertEqual(len(bindings), 10)
self.assertEqual(bindings[0][0], a[8])
self.assertEqual(bindings[0][1], a[10])
self.assertEqual(bindings[1][0], a[4])
self.assertEqual(bindings[1][1], a[8])
self.assertEqual(bindings[2][0], a[0])
self.assertEqual(bindings[2][1], a[4])
self.assertEqual(bindings[3][0], a[1])
self.assertEqual(bindings[3][1], a[4])
self.assertEqual(bindings[4][0], a[2])
self.assertEqual(bindings[4][1], a[4])
self.assertEqual(bindings[5][0], a[5])
self.assertEqual(bindings[5][1], a[8])
self.assertEqual(bindings[6][0], a[3])
self.assertEqual(bindings[6][1], a[5])
self.assertEqual(bindings[7][0], a[9])
self.assertEqual(bindings[7][1], a[10])
self.assertEqual(bindings[8][0], a[6])
self.assertEqual(bindings[8][1], a[9])
self.assertEqual(bindings[9][0], a[7])
self.assertEqual(bindings[9][1], a[9])
def test_bind_to_parent_array(self):
"""bind_to_parent_array should bind tree to array correctly"""
a = reshape(arange(33), (11,3))
index_tree(self.t3)
bindings = bind_to_parent_array(self.t3, a)
self.assertEqual(len(bindings), 10)
self.assertEqual(bindings[0][0], a[8])
self.assertEqual(bindings[0][1], a[10])
self.assertEqual(bindings[1][0], a[4])
self.assertEqual(bindings[1][1], a[8])
self.assertEqual(bindings[2][0], a[0])
self.assertEqual(bindings[2][1], a[4])
self.assertEqual(bindings[3][0], a[1])
self.assertEqual(bindings[3][1], a[4])
self.assertEqual(bindings[4][0], a[2])
self.assertEqual(bindings[4][1], a[4])
self.assertEqual(bindings[5][0], a[5])
self.assertEqual(bindings[5][1], a[8])
self.assertEqual(bindings[6][0], a[3])
self.assertEqual(bindings[6][1], a[5])
self.assertEqual(bindings[7][0], a[9])
self.assertEqual(bindings[7][1], a[10])
self.assertEqual(bindings[8][0], a[6])
self.assertEqual(bindings[8][1], a[9])
self.assertEqual(bindings[9][0], a[7])
self.assertEqual(bindings[9][1], a[9])
def test_index_tree(self):
"""index_tree should produce correct index and node map"""
#test for first tree: contains singleton outgroup
t1 = self.t1
id_1, child_1 = index_tree(t1)
nodes_1 = [n._leaf_index for n in t1.traverse(self_before=False, \
self_after=True)]
self.assertEqual(nodes_1, [0, 1, 2, 3, 6, 4, 5, 7, 8])
self.assertEqual(child_1, [(2, 0, 1), (6, 2, 3), (7, 4, 5), (8, 6, 7)])
#test for second tree: strictly bifurcating
t2 = self.t2
id_2, child_2 = index_tree(t2)
nodes_2 = [n._leaf_index for n in t2.traverse(self_before=False, \
self_after=True)]
self.assertEqual(nodes_2, [0, 1, 4, 2, 3, 5, 8, 6, 7, 9, 10])
self.assertEqual(child_2, [(4, 0, 1), (5, 2, 3), (8, 4, 5), (9, 6, 7),
(10, 8, 9)])
#test for third tree: contains trifurcation and single-child parent
t3 = self.t3
id_3, child_3 = index_tree(t3)
nodes_3 = [n._leaf_index for n in t3.traverse(self_before=False, \
self_after=True)]
self.assertEqual(nodes_3, [0, 1, 2, 4, 3, 5, 8, 6, 7, 9, 10])
self.assertEqual(child_3, [(4, 0, 2), (5, 3, 3), (8, 4, 5), (9, 6, 7),
(10, 8, 9)])
def test_sum_descendants(self):
"""sum_descendants should sum total descendants w/ each state"""
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]
sum_descendants(bindings)
self.assertEqual(
a,
array(
[
[0, 1, 0],
[0, 1, 0],
[0, 1, 0],
[1, 0, 0],
[0, 3, 0],
[1, 0, 0],
[0, 0, 1],
[0, 1, 0],
[1, 3, 0],
[0, 1, 1],
[1, 4, 1],
]
),
)
def test_bool_descendants(self):
"""bool_descendants should be true if any descendant true"""
# self.t3 = DndParser('(((a,b,c),(d)),(e,f))', UniFracTreeNode)
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]
bool_descendants(bindings)
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],
[1, 1, 1],
]
),
)
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 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 test_delete_empty_parents(self):
"""delete_empty_parents should remove empty parents from bound indices"""
id_to_node, node_first_last = index_tree(self.t)
bound_indices = bind_to_array(node_first_last, self.count_array[:,0:1])
bool_descendants(bound_indices)
self.assertEqual(len(bound_indices), 4)
deleted = delete_empty_parents(bound_indices)
self.assertEqual(len(deleted), 2)
for d in deleted:
self.assertEqual(d[0][0], 1)
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 test_index_tree(self):
"""index_tree should produce correct index and node map"""
# test for first tree: contains singleton outgroup
t1 = self.t1
id_1, child_1 = index_tree(t1)
nodes_1 = [n._leaf_index for n in t1.traverse(self_before=False, self_after=True)]
self.assertEqual(nodes_1, [0, 1, 2, 3, 6, 4, 5, 7, 8])
self.assertEqual(child_1, [(2, 0, 1), (6, 2, 3), (7, 4, 5), (8, 6, 7)])
# test for second tree: strictly bifurcating
t2 = self.t2
id_2, child_2 = index_tree(t2)
nodes_2 = [n._leaf_index for n in t2.traverse(self_before=False, self_after=True)]
self.assertEqual(nodes_2, [0, 1, 4, 2, 3, 5, 8, 6, 7, 9, 10])
self.assertEqual(child_2, [(4, 0, 1), (5, 2, 3), (8, 4, 5), (9, 6, 7), (10, 8, 9)])
# test for third tree: contains trifurcation and single-child parent
t3 = self.t3
id_3, child_3 = index_tree(t3)
nodes_3 = [n._leaf_index for n in t3.traverse(self_before=False, self_after=True)]
self.assertEqual(nodes_3, [0, 1, 2, 4, 3, 5, 8, 6, 7, 9, 10])
self.assertEqual(child_3, [(4, 0, 2), (5, 3, 3), (8, 4, 5), (9, 6, 7), (10, 8, 9)])
def test_delete_empty_parents(self):
"""delete_empty_parents should remove empty parents from bound indices"""
id_to_node, node_first_last = index_tree(self.t)
bound_indices = bind_to_array(node_first_last, self.count_array[:,
0:1])
bool_descendants(bound_indices)
self.assertEqual(len(bound_indices), 4)
deleted = delete_empty_parents(bound_indices)
self.assertEqual(len(deleted), 2)
for d in deleted:
self.assertEqual(d[0][0], 1)
def test_sum_descendants(self):
"""sum_descendants should sum total descendants w/ each state"""
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]
sum_descendants(bindings)
self.assertEqual(a, \
array([[0,1,0],[0,1,0],[0,1,0],[1,0,0],[0,3,0],[1,0,0],\
[0,0,1],[0,1,0],[1,3,0],[0,1,1],[1,4,1]])
)
def test_traverse_reduce(self):
"""traverse_reduce should reduce array in traversal order."""
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]
f = logical_or.reduce
traverse_reduce(bindings, f)
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],
[1, 1, 1],
]
),
)
f = sum
traverse_reduce(bindings, f)
self.assertEqual(
a,
array(
[
[0, 1, 0],
[0, 1, 0],
[0, 1, 0],
[1, 0, 0],
[0, 3, 0],
[1, 0, 0],
[0, 0, 1],
[0, 1, 0],
[1, 3, 0],
[0, 1, 1],
[1, 4, 1],
]
),
)
def test_bool_descendants(self):
"""bool_descendants should be true if any descendant true"""
#self.t3 = DndParser('(((a,b,c),(d)),(e,f))', UniFracTreeNode)
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]
bool_descendants(bindings)
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],[1,1,1]])
)
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_traverse_reduce(self):
"""traverse_reduce should reduce array in traversal order."""
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]
f = logical_or.reduce
traverse_reduce(bindings, f)
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],[1,1,1]])
)
f = sum
traverse_reduce(bindings, f)
self.assertEqual( a, \
array([[0,1,0],[0,1,0],[0,1,0],[1,0,0],[0,3,0],[1,0,0],\
[0,0,1],[0,1,0],[1,3,0],[0,1,1],[1,4,1]])
)
def test_bind_to_array(self):
"""bind_to_array should return correct array ranges"""
a = reshape(arange(33), (11,3))
id_, child = index_tree(self.t3)
bindings = bind_to_array(child, a)
self.assertEqual(len(bindings), 5)
self.assertEqual(bindings[0][0], a[4])
self.assertEqual(bindings[0][1], a[0:3])
self.assertEqual(bindings[0][1].shape, (3,3))
self.assertEqual(bindings[1][0], a[5])
self.assertEqual(bindings[1][1], a[3:4])
self.assertEqual(bindings[1][1].shape, (1,3))
self.assertEqual(bindings[2][0], a[8])
self.assertEqual(bindings[2][1], a[4:6])
self.assertEqual(bindings[2][1].shape, (2,3))
self.assertEqual(bindings[3][0], a[9])
self.assertEqual(bindings[3][1], a[6:8])
self.assertEqual(bindings[3][1].shape, (2,3))
self.assertEqual(bindings[4][0], a[10])
self.assertEqual(bindings[4][1], a[8:10])
self.assertEqual(bindings[4][1].shape, (2,3))
def test_bind_to_array(self):
"""bind_to_array should return correct array ranges"""
a = reshape(arange(33), (11, 3))
id_, child = index_tree(self.t3)
bindings = bind_to_array(child, a)
self.assertEqual(len(bindings), 5)
self.assertEqual(bindings[0][0], a[4])
self.assertEqual(bindings[0][1], a[0:3])
self.assertEqual(bindings[0][1].shape, (3, 3))
self.assertEqual(bindings[1][0], a[5])
self.assertEqual(bindings[1][1], a[3:4])
self.assertEqual(bindings[1][1].shape, (1, 3))
self.assertEqual(bindings[2][0], a[8])
self.assertEqual(bindings[2][1], a[4:6])
self.assertEqual(bindings[2][1].shape, (2, 3))
self.assertEqual(bindings[3][0], a[9])
self.assertEqual(bindings[3][1], a[6:8])
self.assertEqual(bindings[3][1].shape, (2, 3))
self.assertEqual(bindings[4][0], a[10])
self.assertEqual(bindings[4][1], a[8:10])
self.assertEqual(bindings[4][1].shape, (2, 3))
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)
