本文整理汇总了Python中dendropy.Tree.find_node_with_label方法的典型用法代码示例。如果您正苦于以下问题：Python Tree.find_node_with_label方法的具体用法？Python Tree.find_node_with_label怎么用？Python Tree.find_node_with_label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dendropy.Tree的用法示例。
在下文中一共展示了Tree.find_node_with_label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: createTreeFile
# 需要导入模块: from dendropy import Tree [as 别名]
# 或者: from dendropy.Tree import find_node_with_label [as 别名]
def createTreeFile(logFilname,quick,nRobots,gTime,cutDeadLeaf):
print "############################"
print "## Parsing of the logFile ##"
fileContentArray = open(options.logFile,'r').readlines()
currentTimeStamp = -1 # Detection of changement in the timestamps
precTimeStamp = -1 # Detection of changement in the timestamps
removeDone = False
beg= int(options.begin)
nGen = int(options.end)
step = int(options.step)
if(quick):table=[[-1 for i in range(nRobots)] for i in range(nGen + 1)]
allPhy = []
newAllPhy=allPhy
print "G",
for line in fileContentArray:
# A line is valid only if it starts by an interation number
#timeStampDescription = 'Info\(([0-9]+)\) : robot nb.([0-9]+) take the genome from the robot nb.([0-9]+)'
timeStampDescription = '([0-9]+) : ([0-9]+) take ([0-9]+)'
timeStampEvaluation = re.compile(timeStampDescription)
match = timeStampEvaluation.search(line)
if ( match ):
#Mechanism to detect a changement in the timestamps ( There might be many lines with the same timeStamp)
timeStamp = (int(match.group(1))+1)#/gTime
if (timeStamp > int(options.end)):
break
if ( currentTimeStamp == -1):
precTimeStamp = timeStamp
else:
precTimeStamp = currentTimeStamp
currentTimeStamp = timeStamp
newGeneration = not (precTimeStamp == currentTimeStamp)
#We continue to parse the file while we have not reached the first generation wanted
if (timeStamp >= beg) :
if(timeStamp == beg and allPhy == []) : allPhy = initAllPhy(beg-1,nRobots)
if ( newGeneration ):
print "-"+str(timeStamp),
stdout.flush()
allRoot=[]
allPhy=newAllPhy
newAllPhy = []
father = int(match.group(3))
son = int(match.group(2))
################## tree dendropy creation
sonId = str(timeStamp) + ' ' + str(son)
fatherId = str(timeStamp - 1) + ' ' + str(father)
for tree in allPhy :
if(cutDeadLeaf):
if(newGeneration):
leaves= tree.leaf_nodes()
for l in leaves:
if ( (l.level() < (timeStamp-1)) and (l.level() > 1)):
p= l.parent_node
p.remove_child(l)
while(p.is_leaf() and p.level() > 1) :
f= p.parent_node
f.remove_child(p)
p=f
n = None
ancestor = None #ancestor at the level N-S
allNodes = tree.nodes()
#Why look all node and not leaves only? Not sure but the dendropy function which gives us all leaves is faster than looking for leaves manually. And if you choose to look leaves only, be sure to no forget that they change during a generation.
for node in allNodes :
if(node.label == fatherId) :
n=node
if(n is not None):
son=n.new_child(label=sonId)
son.edge_length = 1
sonI= son.label.split(' ')[1]
gene = son.label.split(' ')[0]
if((int(timeStamp) > beg + int(step) -1) and quick ):#used to cut everythng no more useful
ancestor=son.parent_node
while( (int(getGen(son))-int(getGen(ancestor))) != int(step ) ):
ancestor = ancestor.parent_node
ancestorId = ancestor.label.split(' ')[1]
#Create a new tree using the ancestor as root
new_tree = Tree(tree)
mrca_node = new_tree.find_node_with_label(ancestor.label)
new_tree.seed_node=mrca_node
new_tree.seed_node.parent_node = None
addTree(new_tree,newAllPhy)
table[int(timeStamp)][int(sonI)]=ancestorId
else :
newAllPhy = allPhy
print "# Parsing done. #"
print "############################"
if(quick):
s=""
allFather=0
for i in table:
for j in i :
s+= str(j)+","
#.........这里部分代码省略.........