Пример #1
0
    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)
Пример #2
0
    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)
Пример #3
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)
Пример #4
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)
Пример #5
0
    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)
Пример #6
0
    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)