class NXNewick(object):
def __init__(self, nxTree=None):
self.nxTree = None
self.bracketMatch = None
self.inString = None
self.nextId = 0
self.outString = None
def parseFile(self, path):
inFile = open(path)
self.parseString(inFile.read())
inFile.close()
return self.nxTree
def parseString(self, newickString, addImpliedRoots=True):
self.nxTree = NXTree()
self.inString = self.__filterWhitespace(newickString)
self.__createBracketTable()
self.nextId = 0
assert self.inString[-1] == ';'
self.__addNode(0, len(self.inString) - 1, None, addImpliedRoots)
self.nxTree.isTree()
return self.nxTree
def writeString(self, nxTree=None):
if nxTree:
self.nxTree = nxTree
self.outString = ""
self.__writeNode(self.nxTree.getRootId(), None)
self.outString += ";"
return self.outString
def writeFile(self, path, nxTree=None):
outFile = open(path, "w")
outFile.write(self.writeString(nxTree))
outFile.write("\n")
outFile.close()
return None
#### PRIVATE WRITING FUNCTIONS ####
def __writeNode(self, node, parent=None):
children = self.nxTree.getChildren(node)
if len(children) > 0:
self.outString += "("
for child in children:
self.__writeNode(child, node)
if child != children[-1]:
self.outString += ","
if len(children) > 0:
self.outString += ")"
name = self.nxTree.getName(node)
if len(name) > 0:
containsSpace = True in [c1 in name for c1 in ws]
if containsSpace:
self.outString += "\""
self.outString += name
if containsSpace:
self.outString += "\""
if parent is not None:
weight = self.nxTree.getWeight(parent, node, defaultValue=None)
if weight is not None:
self.outString += ":%s" % str(weight)
#### PRIVATE READING FUNCTIONS ####
def __filterWhitespace(self, newickString):
filteredString = ""
inQuote = False
for c in newickString:
if c == "\'" or c == "\"":
inQuote = not inQuote
elif inQuote or c not in ws:
filteredString += c
return filteredString
def __createBracketTable(self):
bracketStack = []
self.bracketMatch = dict()
index = 0
for c in self.inString:
if c == '(':
bracketStack.append(index)
elif c == ')':
leftIndex = bracketStack.pop()
self.bracketMatch[leftIndex] = index
index += 1
assert len(bracketStack) == 0
def __childRanges(self, start, length):
ranges = []
currentStart = start
i = currentStart
while i < start + length + 1:
if self.inString[i] == ',' or i == start + length:
ranges.append((currentStart, i - currentStart))
currentStart = i + 1
if i in self.bracketMatch:
i = self.bracketMatch[i]
i += 1
return ranges
def __parseName(self, nameString):
if nameString == ';':
return ('', '')
tokens = nameString.split(':')
assert len(tokens) == 1 or len(tokens) == 2
name = tokens[0]
weight = ''
if len(tokens) == 2:
weight = tokens[1]
return (name, weight)
def __addNode(self, start, length, parent=None, addImpliedRoots=True):
# parse the children (..,...,..)
children = []
if self.inString[start] == '(':
assert start in self.bracketMatch
chLength = self.bracketMatch[start] - start - 1
children = self.__childRanges(start + 1, chLength)
start = self.bracketMatch[start] + 1
length -= (chLength + 2)
# prase the name abc:123
name, weight = self.__parseName(self.inString[start:start + length])
id = self.nextId
self.nextId += 1
self.nxTree.nxDg.add_node(id)
if len(name) > 0:
self.nxTree.nxDg.node[id]['name'] = name
#update the graph
if parent is not None:
self.nxTree.nxDg.add_edge(parent, id)
if len(weight) > 0:
self.nxTree.nxDg[parent][id]['weight'] = float(weight)
#update the root (implied roots are added as a new node)
if self.nxTree.getRootId() is None:
assert parent is None
root = id
if len(weight) > 0:
if addImpliedRoots:
root = self.nextId
self.nextId += 1
self.nxTree.nxDg.add_edge(root, id)
self.nxTree.setWeight(root, id, weight)
self.nxTree.rootId = root
# recurse on children
for child in children:
self.__addNode(child[0], child[1], id)
def testRoot(self):
for tree in self.trees:
nxTree = NXTree(tree)
rootId = nxTree.getRootId()
assert rootId is not None
assert nxTree.getParent(rootId) is None
class NXNewick(object):
def __init__(self, nxTree = None):
self.nxTree = None
self.bracketMatch = None
self.inString = None
self.nextId = 0
self.outString = None
def parseFile(self, path):
inFile = open(path)
self.parseString(inFile.read())
inFile.close()
return self.nxTree
def parseString(self, newickString, addImpliedRoots = True):
self.nxTree = NXTree()
self.inString = self.__filterWhitespace(newickString)
self.__createBracketTable()
self.nextId = 0
assert self.inString[-1] == ';'
self.__addNode(0, len(self.inString)-1, None, addImpliedRoots)
self.nxTree.isTree()
return self.nxTree
def writeString(self, nxTree = None):
if nxTree:
self.nxTree = nxTree
self.outString = ""
self.__writeNode(self.nxTree.getRootId(), None)
self.outString += ";"
return self.outString
def writeFile(self, path, nxTree = None):
outFile = open(path, "w")
outFile.write(self.writeString(nxTree))
outFile.write("\n")
outFile.close()
return None
#### PRIVATE WRITING FUNCTIONS ####
def __writeNode(self, node, parent = None):
children = self.nxTree.getChildren(node)
if len(children) > 0:
self.outString += "("
for child in children:
self.__writeNode(child, node)
if child != children[-1]:
self.outString += ","
if len(children) > 0:
self.outString += ")"
name = self.nxTree.getName(node)
if len(name) > 0:
containsSpace = True in [c1 in name for c1 in ws]
if containsSpace:
self.outString += "\""
self.outString += name
if containsSpace:
self.outString += "\""
if parent is not None:
weight = self.nxTree.getWeight(parent, node, defaultValue=None)
if weight is not None:
self.outString += ":%s" % str(weight)
#### PRIVATE READING FUNCTIONS ####
def __filterWhitespace(self, newickString):
filteredString = ""
inQuote = False
for c in newickString:
if c == "\'" or c == "\"":
inQuote = not inQuote
elif inQuote or c not in ws:
filteredString += c
return filteredString
def __createBracketTable(self):
bracketStack = []
self.bracketMatch = dict()
index = 0
for c in self.inString:
if c == '(':
bracketStack.append(index)
elif c == ')':
leftIndex = bracketStack.pop()
self.bracketMatch[leftIndex] = index
index += 1
assert len(bracketStack) == 0
def __childRanges(self, start, length):
ranges = []
currentStart = start
i = currentStart
while i < start + length + 1:
if self.inString[i] == ',' or i == start + length:
ranges.append((currentStart, i - currentStart))
currentStart = i + 1
if i in self.bracketMatch:
i = self.bracketMatch[i]
i += 1
return ranges
def __parseName(self, nameString):
if nameString == ';':
return ('','')
tokens = nameString.split(':')
assert len(tokens) == 1 or len(tokens) == 2
name = tokens[0]
weight = ''
if len(tokens) == 2:
weight = tokens[1]
return (name, weight)
def __addNode(self, start, length, parent = None, addImpliedRoots = True):
# parse the children (..,...,..)
children = []
if self.inString[start] == '(':
assert start in self.bracketMatch
chLength = self.bracketMatch[start] - start - 1
children = self.__childRanges(start+1, chLength)
start = self.bracketMatch[start] + 1
length -= (chLength + 2)
# prase the name abc:123
name, weight = self.__parseName(self.inString[start:start+length])
id = self.nextId
self.nextId += 1
self.nxTree.nxDg.add_node(id)
if len(name) > 0:
self.nxTree.nxDg.node[id]['name'] = name
#update the graph
if parent is not None:
self.nxTree.nxDg.add_edge(parent, id)
if len(weight) > 0:
self.nxTree.nxDg[parent][id]['weight'] = float(weight)
#update the root (implied roots are added as a new node)
if self.nxTree.getRootId() is None:
assert parent is None
root = id
if len(weight) > 0:
if addImpliedRoots:
root = self.nextId
self.nextId += 1
self.nxTree.nxDg.add_edge(root, id)
self.nxTree.setWeight(root,id, weight)
self.nxTree.rootId = root
# recurse on children
for child in children:
self.__addNode(child[0], child[1], id)
def testRoot(self):
for tree in self.trees:
nxTree = NXTree(tree)
rootId = nxTree.getRootId()
assert rootId is not None
assert nxTree.getParent(rootId) is None