File: getting_leaves.py

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python-ete3 3.1.2%2Bdfsg-3
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from ete3 import Tree
# Loads a basic tree
t = Tree( '(A:0.2,(B:0.4,(C:1.1,D:0.45):0.5):0.1);' )
print(t)
#          /-A
#---------|
#         |          /-B
#          \--------|
#                   |          /-C
#                    \--------|
#                              \-D
# Counts leaves within the tree
nleaves = 0
for leaf in t.get_leaves():
    nleaves += 1
print("This tree has", nleaves, "terminal nodes")
# But, like this is much simpler :)
nleaves = len(t)
print("This tree has", nleaves, "terminal nodes [proper way: len(tree) ]")
# Counts leaves within the tree
ninternal = 0
for node in t.get_descendants():
    if not node.is_leaf():
        ninternal +=1
print("This tree has", ninternal,  "internal nodes")
# Counts nodes with whose distance is higher than 0.3
nnodes = 0
for node in t.get_descendants():
    if node.dist >  0.3:
        nnodes +=1
# or, translated into a better pythonic
nnodes = len([n for n in t.get_descendants() if n.dist>0.3])
print("This tree has", nnodes,  "nodes with a branch length > 0.3")