Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.visualization.data_providers.phyloviz.newickparser
import re
from .baseparser import (
Base_Parser,
PhyloTree,
)
[docs]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.."""
[docs] def parseFile(self, filePath):
"""Parses a newick file to obtain the string inside. Returns: jsonableDict"""
with open(filePath) as newickFile:
newickString = newickFile.read()
newickString = newickString.replace("\n", "").replace("\r", "")
return [self.parseData(newickString)], "Success"
[docs] 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()
[docs] def cleanNewickString(self, rawNewick):
r"""removing semi colon, and illegal json characters (\,',") and white spaces"""
return re.sub(r"\s|;|\"|\'|\\", r"", rawNewick)
def _makeNodesFromString(self, string, depth):
"""elements separated by comma could be empty"""
if string.find("(") != -1:
raise Exception(f"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, -1.0
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_as_float = float(name)
if 0 <= name_as_float <= 1:
bootstrap = name_as_float
elif 1 <= name_as_float <= 100:
bootstrap = name_as_float / 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 range(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 range(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
[docs] 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 = [] # nodes refer to the nodes on this level
start = 0
lenOfPreceedingInternalNodeString = 0
bracketStack = []
for j in range(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"[\)\,\(]", stringRightOfBracket)
if match:
indexOfNextSymbol = match.start()
stringRepOfInternalNode = stringRightOfBracket[:indexOfNextSymbol]
internalNodes = self._makeNodesFromString(stringRepOfInternalNode, depth)
if len(internalNodes) > 0:
InternalNode = internalNodes[0]
lenOfPreceedingInternalNodeString = len(stringRepOfInternalNode)
else: # sometimes the node can be the last element of a string
InternalNode = self._makeNodesFromString(string[j + 1 :], depth)[0]
lenOfPreceedingInternalNodeString = len(string) - j
if InternalNode is None: # creating a generic node if it is unnamed
InternalNode = self.phyloTree.makeNode(
"", depth=depth, isInternal=True
) # "internal-" + str(depth)
lenOfPreceedingInternalNodeString = 0
# recussive call to make the internal claude
childSubString = string[i + 1 : j]
InternalNode.addChildNode(self.parseNode(childSubString, depth + 1))
nodes.append(InternalNode) # we append the internal node later to preserve order
start = j + 1
continue
if depth == 0: # if it's the root node, we do nothing about it and return
return nodes[0]
# Adding last most set of children
endString = string[start:]
if (
string[start - 1] == ")"
): # if the symbol belongs to an internal node which is created previously, then we remove it from the string left to parse
match = re.search(r"[\)\,\(]", endString)
if match:
endOfNodeName = start + match.start() + 1
endString = string[endOfNodeName:]
nodes += self._makeNodesFromString(endString, depth)
return nodes