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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"
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