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]]) )