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
•
written
by
Andrzej Zielezinski
Hi Andrzej,
I was looking for something similar and ended up developing the following code.
def name_internal_nodes(T):
for node in T.traverse():
if node.is_leaf()==False:
# list names of leaves
leaf_names=[leaf.name for leaf in node.iter_leaves()]
names_unique = list(set(leaf_names))
# if all leaves have the same name, give that name to the node
if (len(names_unique)==1):
node.name = names_unique[0]
Basically, this function adds a name to an internal node if all children leaves of that node have the same name. Then, collapsed_leaf will keep the internal name with its support value.
On your example, it gives the following:
t1 = Tree('(("A. thaliana":0.723274,"A. thaliana":0.567784):0.067192,("B":0.279326,"H":0.756049):0.807788);', quoted_node_names=True)
print(t1.get_ascii(show_internal=True))
# /-A. thaliana
# /-|
# | \-A. thaliana
#--|
# | /-B
# \-|
# \-H
name_internal_nodes(t1)
print(t1.get_ascii(show_internal=True))
# /-A. thaliana
# /A. thaliana
# | \-A. thaliana
#--|
# | /-B
# \-|
# \-H
# Cache node content
node2labels = t1.get_cached_content(store_attr="name")
# Collapse tree
t2 = Tree( t1.write(is_leaf_fn=collapsed_leaf, quoted_node_names=True), quoted_node_names=True)
print(t2.get_ascii(show_internal=True))
# /-A. thaliana
#--|
# | /-B
# \-|
# \-H
print (t2.write())
#(A. thaliana:0.067192,(B:0.279326,H:0.756049)1:0.807788);
Thank you, Kevin. This is exactly what I was looking for. You saved my life :)
Hi, I have tried to adapt this to collapse a tree based on the first string in leaf labels (being a genus name), but it is not being collapsed or renamed. Can you suggest what the problem might be?
Thanks for any help.
test.tree = (("Arabidopsis_thaliana1":0.723274,"Arabidopsis_thaliana2":0.567784):0.067192,("B":0.279326,"H":0.756049):0.807788);
import ete3
import sys
def name_internal_nodes(T):
for node in T.traverse():
if node.is_leaf()==False:
# list names of leaves
leaf_names=[leaf.name.split("_")[0] for leaf in node.iter_leaves()]
names_unique = list(set(leaf_names))
print(names_unique)
# if all leaves have the same name, give that name to the node
if (len(names_unique)==1):
node.name = names_unique[0]
return T
def collapsed_leaf(node):
if len(node2labels[node]) == 1:
return True
else:
return False
#global
t1 = ete3.Tree(sys.argv[1], quoted_node_names=True)
node2labels = t1.get_cached_content(store_attr="name")
g=open(sys.argv[2],'w')
print(t1.get_ascii(show_internal=True))
t2=name_internal_nodes(t1)
print(t2.get_ascii(show_internal=True))
node2labels = t2.get_cached_content(store_attr="name")
t3 = ete3.Tree( t2.write(is_leaf_fn=collapsed_leaf, quoted_node_names=True), quoted_node_names=True)
print(t3.get_ascii(show_internal=True))
g.write(str(t3.write()))
•
written
by
susan.klein •
Ok, think I solved it - had to also rename the leaves:
#!/usr/bin/env python3
import ete3
import sys
def name_internal_nodes(T):
for node in T.traverse():
if node.is_leaf()==False:
# list names of leaves
leaf_names=[leaf.name.split("_")[0] for leaf in node.iter_leaves()]
c=-1
for leaf in node.iter_leaves():
c=c+1
leaf.name=leaf_names[c]
names_unique = list(set(leaf_names))
print(names_unique)
# if all leaves have the same name, give that name to the node
if (len(names_unique)==1):
node.name = names_unique[0]
return T
def collapsed_leaf(node):
if len(node2labels[node]) == 1:
return True
else:
return False
#global
t1 = ete3.Tree(sys.argv[1], quoted_node_names=True)
node2labels = t1.get_cached_content(store_attr="name")
g=open(sys.argv[2],'w')
print(t1.get_ascii(show_internal=True))
t2=name_internal_nodes(t1)
print(t2.get_ascii(show_internal=True))
node2labels = t2.get_cached_content(store_attr="name")
t3 = ete3.Tree(t2.write(is_leaf_fn=collapsed_leaf, quoted_node_names=True), quoted_node_names=True)
print(t3.get_ascii(show_internal=True))
g.write(str(t3.write()))
Log in to answer this question.
