def simplify_tree(self, tree):
root_label = self._simplify_tree(tree)
if tree.label in ['Arg1', 'Arg2', 'Conn', 'none']:
tree.children = self.get_leave_node(tree)
return
for i, c in enumerate(tree.children):
if self.deeperthan1(c):
self.simplify_tree(c)
else:
n = TreeNode()
n.children = [c]
n.label = c.label
tree.children[i] = n
def coalesce_paths(self, child_paths, t0):
"""
Create a new TreeNode and assign a given list of child nodes and its host node.
:param child_paths: A list of TreeNodes in the pathogen tree.
:param t0: Time of pathogen coalescence as height
:return: A tuple containing:
1. TreeNode object for the new pathogen lineage.
2. updated extant list
"""
assert len(child_paths
) == 2, 'Can only coalesce 2 pathogen lineages at a time'
p1, p2 = child_paths
assert p1 in self.extant_p and p2 in self.extant_p, 'Both pathogen lineages must be extant'
assert p1.host == p2.host, 'Can only coalesce pathogen lineages in the same host'
host = p1.host
assert p1.height < t0 and p2.height < t0, \
'Pathogen lineage heights %f %f cannot exceed coalescent event %f' % (p1.height, p2.height, t0)
# create new pathogen lineage
new_path = TreeNode(name='_'.join([x.name for x in child_paths]),
dist=0)
new_path.add_features(host=host, height=t0)
# cast child_paths as a List because ete3.Tree.children requires it
new_path.children = list(child_paths)
self.extant_p.append(new_path)
# coalesced pathogen lineages are no longer extant
for node in child_paths:
node.up = new_path
node.dist = t0 - node.height # when node was created, we stored the height
self.extant_p.remove(node)
self.not_extant_p.append(node)
return new_path
