本文整理汇总了Python中ete3.Tree.get_monophyletic方法的典型用法代码示例。如果您正苦于以下问题：Python Tree.get_monophyletic方法的具体用法？Python Tree.get_monophyletic怎么用？Python Tree.get_monophyletic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ete3.Tree的用法示例。
在下文中一共展示了Tree.get_monophyletic方法的1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: len
# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_monophyletic [as 别名]
#euk sequence is a singleton nested within a clade of bacteria, and there is only one eukaryote sequence in the tree
if len(eukaryote_seqs) == 1: #this is, I guess, an LGT candidate
print sys.argv[1] + "\tSingleton"
#euk sequence is a singleton nested within a clade of bacteria, and the eukaryotes are not monophyletic in the tree
#print len(eukaryote_seqs)
else:
try:
answer = tree.check_monophyly(values=eukaryote_seqs, target_attr="name")
if answer[0] == True:
ca = tree.get_common_ancestor(eukaryote_seqs)
print sys.argv[1] + "\tEuks monophyletic\t" + str(len(eukaryote_seqs)) + "\t" + str(ca.support)
elif answer[0] == False:
mono_groups = []
target_group = ''
for node in tree.get_monophyletic(values=['Eukaryote'], target_attr="domain"):
if target_leaf in node:
target_group = node
else:
mono_groups.append(node)
size_target_group = len(target_group)
#get distance
shortest_distance = 999999999999999.0
closest_other_group = ''
for subtree in mono_groups:
curr_distance = tree.get_distance(target_group, subtree, topology_only=True)
if curr_distance < shortest_distance:
shortest_distance = curr_distance
closest_other_group = subtree
#attempt to calculate distance on a version of the tree in which branches below some support threshold have been deleted
# closest_leaves = []