def __init__(self):
super(Phyloxml_Parser, self).__init__()
self.phyloTree = PhyloTree()
self.tagsOfInterest = {
"clade": "",
"name": "name",
"branch_length": "length",
"confidence": "bootstrap",
"events": "events"
}
def _parseNewickToJson(self, newickString, treeName=None, nameMap=None):
"""parses a newick representation of a tree into a PhyloTree data structure,
which can be easily converted to json"""
self.phyloTree = PhyloTree()
newickString = self.cleanNewickString(newickString)
if nameMap:
newickString = self._mapName(newickString, nameMap)
self.phyloTree.root = self.parseNode(newickString, 0)
if nameMap:
self.phyloTree.addAttributesToRoot({"treeName": treeName})
return self.phyloTree.generateJsonableDict()
def __init__(self):
super(Phyloxml_Parser, self).__init__()
self.phyloTree = PhyloTree()
self.tagsOfInterest = {
"clade": "",
"name" : "name",
"branch_length" : "length",
"confidence" : "bootstrap",
"events" : "events"
}
def _parseNewickToJson(self, newickString, treeName=None, nameMap=None):
"""parses a newick representation of a tree into a PhyloTree data structure,
which can be easily converted to json"""
self.phyloTree = PhyloTree()
newickString = self.cleanNewickString(newickString)
if nameMap:
newickString = self._mapName(newickString, nameMap)
self.phyloTree.root = self.parseNode(newickString, 0)
if nameMap:
self.phyloTree.addAttributesToRoot({"treeName": treeName})
return self.phyloTree.generateJsonableDict()
class Newick_Parser(Base_Parser):
"""For parsing trees stored in the newick format (.nhx)
It is necessarily more complex because this parser is later extended by Nexus for parsing newick as well.."""
def __init__(self):
super(Newick_Parser, self).__init__()
def parseFile(self, filePath):
"""Parses a newick file to obtain the string inside. Returns: jsonableDict"""
with open(filePath, "r") as newickFile:
newickString = newickFile.read()
newickString = newickString.replace("\n", "").replace("\r", "")
return [self.parseData(newickString)], "Success"
def parseData(self, newickString):
"""To be called on a newickString directly to parse it. Returns: jsonableDict"""
return self._parseNewickToJson(newickString)
def _parseNewickToJson(self, newickString, treeName=None, nameMap=None):
"""parses a newick representation of a tree into a PhyloTree data structure,
which can be easily converted to json"""
self.phyloTree = PhyloTree()
newickString = self.cleanNewickString(newickString)
if nameMap:
newickString = self._mapName(newickString, nameMap)
self.phyloTree.root = self.parseNode(newickString, 0)
if nameMap:
self.phyloTree.addAttributesToRoot({"treeName": treeName})
return self.phyloTree.generateJsonableDict()
def cleanNewickString(self, rawNewick):
"""removing semi colon, and illegal json characters (\,',") and white spaces"""
return re.sub(r'\s|;|\"|\'|\\', '', rawNewick)
def _makeNodesFromString(self, string, depth):
"""elements separated by comma could be empty"""
if string.find("(") != -1:
raise Exception("Tree is not well form, location: " + string)
childrenString = string.split(",")
childrenNodes = []
for childString in childrenString:
if len(childString) == 0:
continue
nodeInfo = childString.split(":")
name, length, bootstrap = "", None, -1
if len(nodeInfo) == 2: # has length info
length = nodeInfo[1]
# checking for bootstap values
name = nodeInfo[0]
try: # Nexus may bootstrap in names position
name = float(name)
if 0 <= name <= 1:
bootstrap = name
elif 1 <= name <= 100:
bootstrap = name / 100
name = ""
except ValueError:
name = nodeInfo[0]
else:
name = nodeInfo[0] # string only contains name
node = self.phyloTree.makeNode(name,
length=length,
depth=depth,
bootstrap=bootstrap)
childrenNodes += [node]
return childrenNodes
def _mapName(self, newickString, nameMap):
"""
Necessary to replace names of terms inside nexus representation
Also, its here because Mailaud's doesnt deal with id_strings outside of quotes(" ")
"""
newString = ""
start = 0
end = 0
for i in xrange(len(newickString)):
if newickString[i] == "(" or newickString[i] == ",":
if re.match(r"[,(]", newickString[i + 1:]):
continue
else:
end = i + 1
# i now refers to the starting position of the term to be replaced,
# we will next find j which is the ending pos of the term
for j in xrange(i + 1, len(newickString)):
enclosingSymbol = newickString[
j] # the immediate symbol after a common or left bracket which denotes the end of a term
if enclosingSymbol == ")" or enclosingSymbol == ":" or enclosingSymbol == ",":
termToReplace = newickString[end:j]
newString += newickString[start:end] + nameMap[
termToReplace] #+ "'" "'" +
start = j
break
newString += newickString[start:]
return newString
def parseNode(self, string, depth):
"""
Recursive method for parsing newick string, works by stripping down the string into substring
of newick contained with brackers, which is used to call itself.
Eg ... ( A, B, (D, E)C, F, G ) ...
We will make the preceeding nodes first A, B, then the internal node C, its children D, E,
and finally the succeeding nodes F, G
"""
# Base case where there is only an empty string
if string == "":
return
# Base case there its only an internal claude
if string.find("(") == -1:
return self._makeNodesFromString(string, depth)
nodes, children = [], [
] # nodes refer to the nodes on this level, children refers to the child of the
start = 0
lenOfPreceedingInternalNodeString = 0
bracketStack = []
for j in xrange(len(string)):
if string[
j] == "(": #finding the positions of all the open brackets
bracketStack.append(j)
continue
if string[
j] == ")": #finding the positions of all the closed brackets to extract claude
i = bracketStack.pop()
if len(bracketStack) == 0: # is child of current node
InternalNode = None
#First flat call to make nodes of the same depth but from the preceeding string.
startSubstring = string[
start + lenOfPreceedingInternalNodeString:i]
preceedingNodes = self._makeNodesFromString(
startSubstring, depth)
nodes += preceedingNodes
# Then We will try to see if the substring has any internal nodes first, make it then make nodes preceeding it and succeeding it.
if j + 1 < len(string):
stringRightOfBracket = string[
j +
1:] # Eg. '(b:0.4,a:0.3)c:0.3, stringRightOfBracket = c:0.3
match = re.search(r"[\)\,\(]", stringRightOfBracket)
if match:
indexOfNextSymbol = match.start()
stringRepOfInternalNode = stringRightOfBracket[:
indexOfNextSymbol]
internalNodes = self._makeNodesFromString(
stringRepOfInternalNode, depth)
if len(internalNodes) > 0:
InternalNode = internalNodes[0]
lenOfPreceedingInternalNodeString = len(
stringRepOfInternalNode)
else: # sometimes the node can be the last element of a string
InternalNode = self._makeNodesFromString(
string[j + 1:], depth)[0]
lenOfPreceedingInternalNodeString = len(string) - j
if InternalNode == None: #creating a generic node if it is unnamed
InternalNode = self.phyloTree.makeNode(
"", depth=depth,
isInternal=True) #"internal-" + str(depth)
lenOfPreceedingInternalNodeString = 0
# recussive call to make the internal claude
childSubString = string[i + 1:j]
InternalNode.addChildNode(
self.parseNode(childSubString, depth + 1))
nodes.append(
InternalNode
) # we append the internal node later to preserve order
start = j + 1
continue
if depth == 0: # if its the root node, we do nothing about it and return
return nodes[0]
# Adding last most set of children
endString = string[start:]
if string[
start -
1] == ")": # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse
match = re.search(r"[\)\,\(]", endString)
if match:
endOfNodeName = start + match.start() + 1
endString = string[endOfNodeName:]
nodes += self._makeNodesFromString(endString, depth)
return nodes
class Phyloxml_Parser(Base_Parser):
"""Parses a phyloxml file into a json file that will be passed to PhyloViz for display"""
def __init__(self):
super(Phyloxml_Parser, self).__init__()
self.phyloTree = PhyloTree()
self.tagsOfInterest = {
"clade": "",
"name" : "name",
"branch_length" : "length",
"confidence" : "bootstrap",
"events" : "events"
}
def parseFile(self, filePath):
"""passes a file and extracts its Phylogeny Tree content."""
phyloXmlFile = open(filePath, "r")
xmlTree = ElementTree.parse(phyloXmlFile)
xmlRoot = xmlTree.getroot()[0]
self.nameSpaceIndex = xmlRoot.tag.rfind("}") + 1 # used later by the clean tag method to remove the name space in every element.tag
phyloRoot = None
for child in xmlRoot:
childTag = self.cleanTag(child.tag)
if childTag == "clade":
phyloRoot = child
elif childTag == "name":
self.phyloTree.title = child.text
self.phyloTree.root = self.parseNode(phyloRoot, 0)
jsonDict = self.phyloTree.generateJsonableDict()
return [jsonDict], "Success"
def parseNode(self, node, depth):
"""Parses any node within a phyloxml tree and looks out for claude, which signals the creation of
nodes - internal OR leaf"""
tag = self.cleanTag(node.tag)
if not tag == "clade":
return None
hasInnerClade = False
# peeking once for parent and once for child to check if the node is internal
for child in node:
childTag = self.cleanTag(child.tag)
if childTag == "clade":
hasInnerClade = True
break
if hasInnerClade: # this node is an internal node
currentNode = self._makeInternalNode(node, depth=depth)
for child in node:
child = self.parseNode(child, depth + 1)
if isinstance(child, Node):
currentNode.addChildNode(child)
else: # this node is a leaf node
currentNode = self._makeLeafNode(node, depth=depth + 1)
return currentNode
def _makeLeafNode(self, leafNode, depth=0 ):
"""Makes leaf nodes by calling Phylotree methods"""
node = {}
for child in leafNode:
childTag = self.cleanTag(child.tag)
if childTag in self.tagsOfInterest:
key = self.tagsOfInterest[childTag] # need to map phyloxml terms to ours
node[key] = child.text
node["depth"] = depth
return self.phyloTree.makeNode(self._getNodeName(leafNode), **node)
def _getNodeName(self, node, depth=-1):
"""Gets the name of a claude. It handles the case where a taxonomy node is involved"""
def getTagFromTaxonomyNode(node):
"""Returns the name of a taxonomy node. A taxonomy node have to be treated differently as the name
is embedded one level deeper"""
phyloxmlTaxoNames = {
"common_name" : "",
"scientific_name" : "",
"code" : ""
}
for child in node:
childTag = self.cleanTag(child.tag)
if childTag in phyloxmlTaxoNames:
return child.text
return ""
nodeName = ""
for child in node:
childTag = self.cleanTag(child.tag)
if childTag == "name" :
nodeName = child.text
break
elif childTag == "taxonomy":
nodeName = getTagFromTaxonomyNode(child)
break
return nodeName
def _makeInternalNode(self, internalNode, depth=0):
""" Makes an internal node from an element object that is guranteed to be a parent node.
Gets the value of interests like events and appends it to a custom node object that will be passed to PhyloTree to make nodes
"""
node = {}
for child in internalNode:
childTag = self.cleanTag(child.tag)
if childTag == "clade":
continue
elif childTag in self.tagsOfInterest:
if childTag == "events": # events is nested 1 more level deeper than others
key, text = "events", self.cleanTag(child[0].tag)
else:
key = self.tagsOfInterest[childTag]
text = child.text
node[key] = text
return self.phyloTree.makeNode(self._getNodeName(internalNode, depth), **node)
def cleanTag(self, tagString):
return tagString[self.nameSpaceIndex:]
class Newick_Parser(Base_Parser):
"""For parsing trees stored in the newick format (.nhx)
It is necessarily more complex because this parser is later extended by Nexus for parsing newick as well.."""
def __init__(self):
super(Newick_Parser, self).__init__()
def parseFile(self, filePath):
"""Parses a newick file to obtain the string inside. Returns: jsonableDict"""
with open(filePath, "r") as newickFile:
newickString = newickFile.read()
newickString = newickString.replace("\n", "").replace("\r", "")
return [self.parseData(newickString)], "Success"
def parseData(self, newickString):
"""To be called on a newickString directly to parse it. Returns: jsonableDict"""
return self._parseNewickToJson(newickString)
def _parseNewickToJson(self, newickString, treeName=None, nameMap=None):
"""parses a newick representation of a tree into a PhyloTree data structure,
which can be easily converted to json"""
self.phyloTree = PhyloTree()
newickString = self.cleanNewickString(newickString)
if nameMap:
newickString = self._mapName(newickString, nameMap)
self.phyloTree.root = self.parseNode(newickString, 0)
if nameMap:
self.phyloTree.addAttributesToRoot({"treeName": treeName})
return self.phyloTree.generateJsonableDict()
def cleanNewickString(self, rawNewick):
"""removing semi colon, and illegal json characters (\,',") and white spaces"""
return re.sub(r'\s|;|\"|\'|\\', '', rawNewick)
def _makeNodesFromString(self, string, depth):
"""elements separated by comma could be empty"""
if string.find("(") != -1:
raise Exception("Tree is not well form, location: " + string)
childrenString = string.split(",")
childrenNodes = []
for childString in childrenString:
if len(childString) == 0:
continue
nodeInfo = childString.split(":")
name, length, bootstrap = "", None, -1
if len(nodeInfo) == 2: # has length info
length = nodeInfo[1]
# checking for bootstap values
name = nodeInfo[0]
try: # Nexus may bootstrap in names position
name = float(name)
if 0<= name <= 1:
bootstrap = name
elif 1 <= name <= 100:
bootstrap = name / 100
name = ""
except ValueError:
name = nodeInfo[0]
else:
name = nodeInfo[0] # string only contains name
node = self.phyloTree.makeNode(name, length=length, depth=depth, bootstrap= bootstrap)
childrenNodes += [node]
return childrenNodes
def _mapName(self, newickString, nameMap):
"""
Necessary to replace names of terms inside nexus representation
Also, it's here because Mailaud's doesnt deal with id_strings outside of quotes(" ")
"""
newString = ""
start = 0
end = 0
for i in xrange(len(newickString)):
if newickString[i] == "(" or newickString[i] == ",":
if re.match(r"[,(]", newickString[i+1:]):
continue
else:
end = i + 1
# i now refers to the starting position of the term to be replaced,
# we will next find j which is the ending pos of the term
for j in xrange(i+1, len(newickString)):
enclosingSymbol = newickString[j] # the immediate symbol after a common or left bracket which denotes the end of a term
if enclosingSymbol == ")" or enclosingSymbol == ":" or enclosingSymbol == ",":
termToReplace = newickString[end:j]
newString += newickString[start : end] + nameMap[termToReplace] #+ "'" "'" +
start = j
break
newString += newickString[start:]
return newString
def parseNode(self, string, depth):
"""
Recursive method for parsing newick string, works by stripping down the string into substring
of newick contained with brackers, which is used to call itself.
Eg ... ( A, B, (D, E)C, F, G ) ...
We will make the preceeding nodes first A, B, then the internal node C, its children D, E,
and finally the succeeding nodes F, G
"""
# Base case where there is only an empty string
if string == "":
return
# Base case there it's only an internal claude
if string.find("(") == -1:
return self._makeNodesFromString(string, depth)
nodes, children = [], [] # nodes refer to the nodes on this level, children refers to the child of the
start = 0
lenOfPreceedingInternalNodeString = 0
bracketStack = []
for j in xrange(len(string)):
if string[j] == "(": #finding the positions of all the open brackets
bracketStack.append(j)
continue
if string[j] == ")": #finding the positions of all the closed brackets to extract claude
i = bracketStack.pop()
if len(bracketStack) == 0: # is child of current node
InternalNode = None
#First flat call to make nodes of the same depth but from the preceeding string.
startSubstring = string[start + lenOfPreceedingInternalNodeString: i]
preceedingNodes = self._makeNodesFromString(startSubstring, depth)
nodes += preceedingNodes
# Then We will try to see if the substring has any internal nodes first, make it then make nodes preceeding it and succeeding it.
if j + 1 < len(string):
stringRightOfBracket = string[j+1:] # Eg. '(b:0.4,a:0.3)c:0.3, stringRightOfBracket = c:0.3
match = re.search(r"[\)\,\(]", stringRightOfBracket)
if match:
indexOfNextSymbol = match.start()
stringRepOfInternalNode = stringRightOfBracket[:indexOfNextSymbol]
internalNodes = self._makeNodesFromString( stringRepOfInternalNode, depth)
if len(internalNodes) > 0:
InternalNode = internalNodes[0]
lenOfPreceedingInternalNodeString = len(stringRepOfInternalNode)
else: # sometimes the node can be the last element of a string
InternalNode = self._makeNodesFromString(string[j+1:], depth)[0]
lenOfPreceedingInternalNodeString = len(string) - j
if InternalNode == None: #creating a generic node if it is unnamed
InternalNode = self.phyloTree.makeNode( "", depth=depth, isInternal=True ) #"internal-" + str(depth)
lenOfPreceedingInternalNodeString = 0
# recussive call to make the internal claude
childSubString = string[ i + 1 : j ]
InternalNode.addChildNode(self.parseNode(childSubString, depth + 1))
nodes.append(InternalNode) # we append the internal node later to preserve order
start = j + 1
continue
if depth == 0: # if it's the root node, we do nothing about it and return
return nodes[0]
# Adding last most set of children
endString = string[start:]
if string[start-1] == ")": # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse
match = re.search(r"[\)\,\(]", endString)
if match:
endOfNodeName = start + match.start() + 1
endString = string[endOfNodeName:]
nodes += self._makeNodesFromString(endString, depth)
return nodes
class Phyloxml_Parser(Base_Parser):
"""Parses a phyloxml file into a json file that will be passed to PhyloViz for display"""
def __init__(self):
super(Phyloxml_Parser, self).__init__()
self.phyloTree = PhyloTree()
self.tagsOfInterest = {
"clade": "",
"name": "name",
"branch_length": "length",
"confidence": "bootstrap",
"events": "events"
}
def parseFile(self, filePath):
"""passes a file and extracts its Phylogeny Tree content."""
phyloXmlFile = open(filePath, "r")
xmlTree = ElementTree.parse(phyloXmlFile)
xmlRoot = xmlTree.getroot()[0]
self.nameSpaceIndex = xmlRoot.tag.rfind(
"}"
) + 1 # used later by the clean tag method to remove the name space in every element.tag
phyloRoot = None
for child in xmlRoot:
childTag = self.cleanTag(child.tag)
if childTag == "clade":
phyloRoot = child
elif childTag == "name":
self.phyloTree.title = child.text
self.phyloTree.root = self.parseNode(phyloRoot, 0)
jsonDict = self.phyloTree.generateJsonableDict()
return [jsonDict], "Success"
def parseNode(self, node, depth):
"""Parses any node within a phyloxml tree and looks out for claude, which signals the creation of
nodes - internal OR leaf"""
tag = self.cleanTag(node.tag)
if not tag == "clade":
return None
hasInnerClade = False
# peeking once for parent and once for child to check if the node is internal
for child in node:
childTag = self.cleanTag(child.tag)
if childTag == "clade":
hasInnerClade = True
break
if hasInnerClade: # this node is an internal node
currentNode = self._makeInternalNode(node, depth=depth)
for child in node:
child = self.parseNode(child, depth + 1)
if isinstance(child, Node):
currentNode.addChildNode(child)
else: # this node is a leaf node
currentNode = self._makeLeafNode(node, depth=depth + 1)
return currentNode
def _makeLeafNode(self, leafNode, depth=0):
"""Makes leaf nodes by calling Phylotree methods"""
node = {}
for child in leafNode:
childTag = self.cleanTag(child.tag)
if childTag in self.tagsOfInterest:
key = self.tagsOfInterest[
childTag] # need to map phyloxml terms to ours
node[key] = child.text
node["depth"] = depth
return self.phyloTree.makeNode(self._getNodeName(leafNode), **node)
def _getNodeName(self, node, depth=-1):
"""Gets the name of a claude. It handles the case where a taxonomy node is involved"""
def getTagFromTaxonomyNode(node):
"""Returns the name of a taxonomy node. A taxonomy node have to be treated differently as the name
is embedded one level deeper"""
phyloxmlTaxoNames = {
"common_name": "",
"scientific_name": "",
"code": ""
}
for child in node:
childTag = self.cleanTag(child.tag)
if childTag in phyloxmlTaxoNames:
return child.text
return ""
nodeName = ""
for child in node:
childTag = self.cleanTag(child.tag)
if childTag == "name":
nodeName = child.text
break
elif childTag == "taxonomy":
nodeName = getTagFromTaxonomyNode(child)
break
return nodeName
def _makeInternalNode(self, internalNode, depth=0):
""" Makes an internal node from an element object that is guranteed to be a parent node.
Gets the value of interests like events and appends it to a custom node object that will be passed to PhyloTree to make nodes
"""
node = {}
for child in internalNode:
childTag = self.cleanTag(child.tag)
if childTag == "clade":
continue
elif childTag in self.tagsOfInterest:
if childTag == "events": # events is nested 1 more level deeper than others
key, text = "events", self.cleanTag(child[0].tag)
else:
key = self.tagsOfInterest[childTag]
text = child.text
node[key] = text
return self.phyloTree.makeNode(self._getNodeName(internalNode, depth),
**node)
def cleanTag(self, tagString):
return tagString[self.nameSpaceIndex:]