本文整理汇总了Python中cogent.LoadTree.getTipNames方法的典型用法代码示例。如果您正苦于以下问题：Python LoadTree.getTipNames方法的具体用法？Python LoadTree.getTipNames怎么用？Python LoadTree.getTipNames使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类cogent.LoadTree的用法示例。
在下文中一共展示了LoadTree.getTipNames方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: BigTreeSingleTests
# 需要导入模块: from cogent import LoadTree [as 别名]
# 或者: from cogent.LoadTree import getTipNames [as 别名]
class BigTreeSingleTests(TestTree):
"""using the big-tree for single-tree tests"""
def setUp(self):
self.name = 'big tree - '
self.otu_names = ['Horse', 'TombBat', 'Rhino', 'Pig', 'AsianElep',
'SpermWhal', 'Cat', 'Gorilla', 'Orangutan',
'bandicoot', 'Hedgehog', 'Sloth', 'HairyArma',
'Manatee', 'GoldenMol', 'Pangolin']
self.otu_names.sort()
self.newick = '((((((((FlyingFox,DogFaced),((FreeTaile,LittleBro),(TombBat,RoundEare))),(FalseVamp,LeafNose)),(((Horse,Rhino),(Pangolin,(Cat,Dog))),(Llama,(Pig,(Cow,(Hippo,(SpermWhal,HumpbackW))))))),(Mole,Hedgehog)),(TreeShrew,(FlyingLem,((Jackrabbit,(FlyingSqu,(OldWorld,(Mouse,Rat)))),(Galago,(HowlerMon,(Rhesus,(Orangutan,(Gorilla,(Human,Chimpanzee)))))))))),(((NineBande,HairyArma),(Anteater,Sloth)),(((Dugong,Manatee),((AfricanEl,AsianElep),(RockHyrax,TreeHyrax))),(Aardvark,((GoldenMol,(Madagascar,Tenrec)),(LesserEle,GiantElep)))))),(caenolest,(phascogale,(wombat,bandicoot))));'
self.newick_reduced = '(((((TombBat,(((Horse,Rhino),(Pangolin,Cat)),(Pig,SpermWhal))),Hedgehog),(Orangutan,Gorilla)),((HairyArma,Sloth),((Manatee,AsianElep),GoldenMol))),bandicoot);'
self.tree = LoadTree(treestring = self.newick)
def test_getEdgeNames(self):
"""testing (well, exercising at least), getedgenames"""
# Fell over on small tree because "stem descended from root
# joiner was a tip"
a,b = self.otu_names[:2]
clade = self.tree.getEdgeNames(a, b, True, False)
def test_getTipNames(self):
"""testing (well, exercising at least), getTipNames"""
a,b = self.otu_names[:2]
tips = self.tree.getTipNames()
self.assertEqual(len(tips), 55)示例2: test_making_from_list
# 需要导入模块: from cogent import LoadTree [as 别名]
# 或者: from cogent.LoadTree import getTipNames [as 别名]
def test_making_from_list(self):
tipnames_with_spaces = ['a_b','a b',"T'lk"]
tipnames_with_spaces.sort()
t = LoadTree(tip_names=tipnames_with_spaces)
result = t.getTipNames()
result.sort()
assert result == tipnames_with_spaces示例3: load_de_numericized_newick_tree
# 需要导入模块: from cogent import LoadTree [as 别名]
# 或者: from cogent.LoadTree import getTipNames [as 别名]
def load_de_numericized_newick_tree(tree_in,before="'",after="'",root=False):
from cogent.core.tree import PhyloNode
from cogent import LoadTree
import os.path
if os.path.isfile(tree_in):
tree = LoadTree(tree_in)
else:
tree = LoadTree(treestring=tree_in)
terminals = tree.getTipNames()
rename_dict = {}
for tip in terminals:
rename_dict[tip] = before + str(tip) + after
tree.reassignNames(rename_dict)
if root:
tree = tree.rootAtMidpoint()
treestring = tree.getNewick(with_distances=True)
return treestring