def calc_nonepitope_star_distance(tree, attr="ne_star", seasons=[]):
"""
calculates the distance at nonepitope sites of any tree node to ref
tree -- dendropy tree
attr -- the attribute name used to save the result
"""
if not hasattr(tree, "nonepitope_star_distance_assigned") or tree.nonepitope_star_distance_assigned == False:
for node in tree.postorder_node_iter():
if len(node.tips) and node != tree.seed_node:
if not hasattr(node, "aa"):
node.aa = translate(node.seq)
tmp_node = node.parent_node
cur_season = min(node.tips.keys())
prev_season = seasons[max(0, seasons.index(cur_season) - 1)]
while True:
if tmp_node != tree.seed_node:
if prev_season in tmp_node.tips and len(tmp_node.tips[prev_season]) > 0:
break
else:
tmp_node = tmp_node.parent_node
else:
break
if not hasattr(tmp_node, "aa"):
tmp_node.aa = translate(tmp_node.seq)
node.__setattr__(attr, nonepitope_distance(node.aa, tmp_node.aa))
else:
node.__setattr__(attr, np.nan)
tree.nonepitope_star_distance_assigned = True
def calc_nonepitope_distance(tree, attr="ne", ref=None):
"""
calculates the distance at nonepitope sites of any tree node to ref
tree -- dendropy tree
attr -- the attribute name used to save the result
"""
if not hasattr(tree, "nonepitope_distance_assigned") or tree.nonepitope_distance_assigned == False:
if ref == None:
ref = translate(tree.seed_node.seq)
for node in tree.postorder_node_iter():
if not hasattr(node, "aa"):
node.aa = translate(node.seq)
node.__setattr__(attr, nonepitope_distance(node.aa, ref))
tree.nonepitope_distance_assigned = True
