How to collapse leaves with the same name in ETE3 tree?
I'm trying to collapse leaves that have the same name in ETE3's tree. I think I almost got it. Two leaves in my example (
A. thaliana) have been combined into a single leaf, but not named. I would like it to have the same name as its components.
from ete3 import Tree def collapsed_leaf(node): if len(node2labels[node]) == 1: return True else: return False t1 = Tree('(("A. thaliana":0.723274,"A. thaliana":0.567784):0.067192,("B":0.279326,"H":0.756049):0.807788);', quoted_node_names=True) node2labels = t1.get_cached_content(store_attr="name") print(t1) # /-A. thaliana # /-| # | -A. thaliana # --| # | /-B # -| # -H t2 = Tree(t1.write(is_leaf_fn=collapsed_leaf, quoted_node_names=True), quoted_node_names=True) print(t2) # /- # --| # | /-B # -| # -H
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