本文整理汇总了Python中tree.Node.isleaf方法的典型用法代码示例。如果您正苦于以下问题：Python Node.isleaf方法的具体用法？Python Node.isleaf怎么用？Python Node.isleaf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tree.Node的用法示例。
在下文中一共展示了Node.isleaf方法的2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: parse_trees
# 需要导入模块: from tree import Node [as 别名]
# 或者: from tree.Node import isleaf [as 别名]
def parse_trees(e, otus):
"""
Get trees from an etree object
Args:
e: A nexml document parsed by etree
otus: OTUs returned by parse_otus
Returns:
list: A list of ivy Storage objects each
containing every node of a tree.
"""
from tree import Node
v = []
for tb in e.findall(NEXML+"trees"):
for te in tb.findall(NEXML+"tree"):
t = storage.Storage()
t.attrib = storage.Storage(te.attrib)
t.nodes = {}
for n in te.findall(NEXML+"node"):
node = Node()
if n.attrib.get("otu"):
node.isleaf = True
node.otu = otus[n.attrib["otu"]]
node.label = node.otu.label
t.nodes[n.attrib["id"]] = node
for edge in te.findall(NEXML+"edge"):
d = edge.attrib
n = t.nodes[d["target"]]
p = t.nodes[d["source"]]
length = d.get("length")
if length:
n.length = float(length)
p.add_child(n)
r = [ n for n in t.nodes.values() if not n.parent ]
assert len(r)==1
r = r[0]
r.isroot = True
for i, n in enumerate(r): n.id = i+1
t.root = r
v.append(t)
return v示例2: parse
# 需要导入模块: from tree import Node [as 别名]
# 或者: from tree.Node import isleaf [as 别名]
def parse(data, ttable=None, treename=None):
"""
Parse a newick string.
Args:
data: Any file-like object that can be coerced into shlex, or
a string (converted to StringIO)
ttable (dict): Mapping of node labels in the newick string
to other values.
Returns:
Node: The root node.
"""
from tree import Node
if type(data) in types.StringTypes:
data = StringIO(data)
start_pos = data.tell()
tokens = Tokenizer(data)
node = None; root = None
lp=0; rp=0; rooted=1
previous = None
ni = 0 # node id counter (preorder) - zero-based indexing
li = 0 # leaf index counter
ii = 0 # internal node index counter
pi = 0 # postorder sequence
while 1:
token = tokens.get_token()
#print token,
if token == ';' or token == tokens.eof:
assert lp == rp, \
"unbalanced parentheses in tree description: (%s, %s)" \
% (lp, rp)
break
# internal node
elif token == '(':
lp = lp+1
newnode = Node()
newnode.ni = ni; ni += 1
newnode.isleaf = False
newnode.ii = ii; ii += 1
newnode.treename = treename
if node:
if node.children: newnode.left = node.children[-1].right+1
else: newnode.left = node.left+1
node.add_child(newnode)
else:
newnode.left = 1; newnode.right = 2
newnode.right = newnode.left+1
node = newnode
elif token == ')':
rp = rp+1
node = node.parent
node.pi = pi; pi += 1
if node.children:
node.right = node.children[-1].right + 1
elif token == ',':
node = node.parent
if node.children:
node.right = node.children[-1].right + 1
# branch length
elif token == ':':
token = tokens.get_token()
if token == '[':
node.length_comment = tokens.parse_embedded_comment()
token = tokens.get_token()
if not (token == ''):
try: brlen = float(token)
except ValueError:
raise ValueError, ("invalid literal for branch length, "
"'%s'" % token)
else:
raise 'NewickError', \
'unexpected end-of-file (expecting branch length)'
node.length = brlen
# comment
elif token == '[':
node.comment = tokens.parse_embedded_comment()
if node.comment[0] == '&':
# metadata
meta = META.findall(node.comment[1:])
if meta:
node.meta = {}
for k, v in meta:
v = eval(v.replace('{','(').replace('}',')'))
node.meta[k] = v
# leaf node or internal node label
else:
if previous != ')': # leaf node
#.........这里部分代码省略.........