def extract_tree_with_taxa(tree, taxa, suppress_unifurcations=True):
taxon_to_leaf = {}
for n in tree.preorder_node_iter():
n.keep = False
if n.is_leaf():
taxon_to_leaf[n.taxon] = n
for t in taxa:
for n in taxon_to_leaf[t].ancestor_iter(inclusive=True):
n.keep = True
out = Tree()
q_old = Queue()
q_old.put(tree.seed_node)
q_new = Queue()
q_new.put(out.seed_node)
while not q_old.empty():
n_old = q_old.get()
n_new = q_new.get()
for c_old in n_old.child_node_iter():
if c_old.keep:
c_new = Node(taxon=c_old.taxon,
label=c_old.label,
edge_length=c_old.edge_length)
n_new.add_child(c_new)
q_old.put(c_old)
q_new.put(c_new)
if suppress_unifurcations:
out.suppress_unifurcations()
return out
results = line.strip().split(',')
tree = Tree()
root = Node()
root.__dict__['label'] = results[0].replace("\"", "")
nodes_dict[results[0].replace("\"", "")] = root
prune = ['1']
#Add root node to tree
tree.__dict__['_seed_node'].add_child(root)
for line in lines:
results = line.strip().split(',')
node = Node()
node.__dict__['label'] = results[0].replace("\"", "")
node.taxon = Taxon(results[0].replace("\"", ""))
nodes_dict[results[0].replace("\"", "")] = node
nodes_dict[results[1].replace("\"", "")].add_child(node)
if results[0].replace("\"", "") not in species:
prune.append(results[0].replace("\"", ""))
for taxa in prune:
nodes_dict[taxa].label = ''
# tree.delete_outdegree_one_nodes()
tree.suppress_unifurcations()
output = open(taxonomyTree, 'w')
output.write(str(tree) + ";")
output.close()
lines.close()
