Python Tree.get_leavesの例

コード例 #1

ファイル: getting_leaves.py プロジェクト: MikeTrizna/ete

from ete_dev 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

コード例 #2

import time
from ete_dev import Tree
# Creates a random tree with 10,000 leaf nodes
tree = Tree()
tree.populate(10000)
# This code should be faster
t1 = time.time()
for leaf in tree.iter_leaves():
    if "aw" in leaf.name:
        print "found a match:", leaf.name,
        break
print "Iterating: ellapsed time:", time.time() - t1
# This slower
t1 = time.time()
for leaf in tree.get_leaves():
    if "aw" in leaf.name:
        print "found a match:", leaf.name,
        break
print "Getting: ellapsed time:", time.time() - t1
# Results in something like:
# found a match: guoaw Iterating: ellapsed time: 0.00436091423035 secs
# found a match: guoaw Getting: ellapsed time: 0.124316930771 secs

コード例 #3

ファイル: iterators.py プロジェクト: MikeTrizna/ete

import time
from ete_dev import Tree
# Creates a random tree with 10,000 leaf nodes
tree = Tree()
tree.populate(10000)
# This code should be faster
t1 = time.time()
for leaf in tree.iter_leaves():
    if "aw" in leaf.name:
        print "found a match:", leaf.name,
        break
print "Iterating: ellapsed time:", time.time()-t1
# This slower
t1 = time.time()
for leaf in tree.get_leaves():
    if "aw" in leaf.name:
        print "found a match:", leaf.name,
        break
print "Getting: ellapsed time:", time.time()-t1
# Results in something like:
# found a match: guoaw Iterating: ellapsed time: 0.00436091423035 secs
# found a match: guoaw Getting: ellapsed time: 0.124316930771 secs

コード例 #4

ファイル: getting_leaves.py プロジェクト: tarah28/ete

from ete_dev 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