def generate_factor(treeFile, columnFile, prior, cpd, domain):
# Build the binary tree and find the interior nodes
tree = BinaryTree()
tree.parse_from_string(read_nh_file_into_single_line(treeFile))
interior_nodes = []
tree.assign_idx(interior_nodes, [0])
animal_to_idx={}
idx_to_animal={}
factors=[]
def build_prior_factor(idx):
factor=Factor()
factor.scope = [idx]
factor.card = [len(domain)]
factor.val = prior
return factor
def build_evolution_factor(i2,i1):
factor=Factor()
factor.scope = [i2,i1]
factor.card = [len(domain),len(domain)]
factor.val = cpd
return factor
def assign_index(TreeNode):
animal_to_idx[TreeNode.data]=TreeNode.idx+1
idx_to_animal[TreeNode.idx+1]=TreeNode.data
if TreeNode.left!=None:
f_e=build_evolution_factor(TreeNode.left.idx+1,TreeNode.idx+1)
f_e.name = TreeNode.left.data+'<--'+TreeNode.data
factors.append(f_e)
assign_index(TreeNode.left)
if TreeNode.right!=None:
f_e=build_evolution_factor(TreeNode.right.idx+1,TreeNode.idx+1)
f_e.name = TreeNode.right.data+'<--'+TreeNode.data
factors.append(f_e)
assign_index(TreeNode.right)
f_p=build_prior_factor(tree.idx+1)
f_p.name=tree.data
factors.append(f_p)
assign_index(tree)
sequences = read_sequences(columnFile,animal_to_idx)
domain_to_idx = {domain[i]: i for i in xrange(len(domain))}
return sequences,tree,factors
def generate_factor(treeFile, columnFile, prior, cpd, domain):
# Build the binary tree and find the interior nodes
tree = BinaryTree()
tree.parse_from_string(read_nh_file_into_single_line(treeFile))
interior_nodes = []
tree.assign_idx(interior_nodes, [0])
animal_to_idx = {}
idx_to_animal = {}
factors = []
def build_prior_factor(idx):
factor = Factor()
factor.scope = [idx]
factor.card = [len(domain)]
factor.val = prior
return factor
def build_evolution_factor(i2, i1):
factor = Factor()
factor.scope = [i2, i1]
factor.card = [len(domain), len(domain)]
factor.val = cpd
return factor
def assign_index(TreeNode):
animal_to_idx[TreeNode.data] = TreeNode.idx + 1
idx_to_animal[TreeNode.idx + 1] = TreeNode.data
if TreeNode.left != None:
f_e = build_evolution_factor(TreeNode.left.idx + 1,
TreeNode.idx + 1)
f_e.name = TreeNode.left.data + '<--' + TreeNode.data
factors.append(f_e)
assign_index(TreeNode.left)
if TreeNode.right != None:
f_e = build_evolution_factor(TreeNode.right.idx + 1,
TreeNode.idx + 1)
f_e.name = TreeNode.right.data + '<--' + TreeNode.data
factors.append(f_e)
assign_index(TreeNode.right)
f_p = build_prior_factor(tree.idx + 1)
f_p.name = tree.data
factors.append(f_p)
assign_index(tree)
sequences = read_sequences(columnFile, animal_to_idx)
domain_to_idx = {domain[i]: i for i in xrange(len(domain))}
return sequences, tree, factors
