def parse(data, ttable=None, treename=None):
"""
Parse a newick string.
*data* is any file-like object that can be coerced into shlex, or
a string (converted to StringIO)
*ttable* is a dictionary mapping node labels in the newick string
to other values.
Returns: the root node.
"""
from ivy.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
if ttable:
try:
ttoken = (ttable.get(int(token)) or ttable.get(token))
except ValueError:
ttoken = ttable.get(token)
if ttoken:
token = ttoken
newnode = Node()
newnode.ni = ni
ni += 1
newnode.pi = pi
pi += 1
newnode.label = "_".join(token.split()).replace("'", "")
newnode.isleaf = True
newnode.li = li
li += 1
if node.children: newnode.left = node.children[-1].right + 1
else: newnode.left = node.left + 1
newnode.right = newnode.left + 1
newnode.treename = treename
node.add_child(newnode)
node = newnode
else: # label
if ttable:
node.label = ttable.get(token, token)
else:
node.label = token
previous = token
node.isroot = True
return node
def parse(data, ttable=None, treename=None):
"""
Parse a newick string.
*data* is any file-like object that can be coerced into shlex, or
a string (converted to StringIO)
*ttable* is a dictionary mapping node labels in the newick string
to other values.
Returns: the root node.
"""
from ivy.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
if ttable:
try:
ttoken = (ttable.get(int(token)) or
ttable.get(token))
except ValueError:
ttoken = ttable.get(token)
if ttoken:
token = ttoken
newnode = Node()
newnode.ni = ni; ni += 1
newnode.pi = pi; pi += 1
newnode.label = "_".join(token.split()).replace("'", "")
newnode.isleaf = True
newnode.li = li; li += 1
if node.children: newnode.left = node.children[-1].right+1
else: newnode.left = node.left+1
newnode.right = newnode.left+1
newnode.treename = treename
node.add_child(newnode)
node = newnode
else: # label
if ttable:
node.label = ttable.get(token, token)
else:
node.label = token
previous = token
node.isroot = True
return node
