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Source code for galaxy.visualization.data_providers.phyloviz.nexusparser

from __future__ import with_statement
from newickparser import Newick_Parser
import re

MAX_READLINES = 200000


[docs]class Nexus_Parser(Newick_Parser):
[docs] def __init__(self): super(Nexus_Parser, self).__init__()
[docs] def parseFile(self, filePath): """passes a file and extracts its Nexus content.""" return self.parseNexus(filePath)
[docs] def parseNexus(self, filename): """ Nexus data is stored in blocks between a line starting with begin and another line starting with end; Commends inside square brackets are to be ignored, For more information: http://wiki.christophchamp.com/index.php/NEXUS_file_format Nexus can store multiple trees """ with open(filename, "rt") as nex_file: nexlines = nex_file.readlines() rowCount = 0 inTreeBlock = False # sentinel to check if we are in a tree block intranslateBlock = False # sentinel to check if we are in the translate region of the tree. Stores synonyms of the labellings self.inCommentBlock = False self.nameMapping = None # stores mapping representation used in nexus format treeNames = [] for line in nexlines: line = line.replace(";\n", "") lline = line.lower() if rowCount > MAX_READLINES or (not nex_file) : break rowCount += 1 # We are only interested in the tree block. if "begin" in lline and "tree" in lline and not inTreeBlock: inTreeBlock = True continue if inTreeBlock and "end" in lline[:3]: inTreeBlock, currPhyloTree = False, None continue if inTreeBlock: if "title" in lline: # Adding title to the tree continue if "translate" in lline: intranslateBlock = True self.nameMapping = {} continue if intranslateBlock: mappingLine = self.splitLinebyWhitespaces(line) key, value = mappingLine[1], mappingLine[2].replace(",", "").replace("'", "") # replacing illegal json characters self.nameMapping[key] = value # Extracting newick Trees if "tree" in lline: intranslateBlock = False treeLineCols = self.splitLinebyWhitespaces(line) treeName, newick = treeLineCols[2], treeLineCols[-1] if newick == "": # Empty lines can be found in tree blocks continue currPhyloTree = self._parseNewickToJson(newick, treeName, nameMap=self.nameMapping) self.phyloTrees.append(currPhyloTree) treeIndex = len(self.phyloTrees) - 1 treeNames.append((treeName, treeIndex)) # appending name of tree, and its index continue return self.phyloTrees, treeNames
[docs] def splitLinebyWhitespaces(self, line): """replace tabs and write spaces to a single write space, so we can properly split it.""" return re.split(r"\s+", line)
[docs] def checkComments(self, line): """Check to see if the line/lines is a comment.""" if not self.inCommentBlock: if "[" in line: if "]" not in line: self.inCommentBlock = True else: return "Nextline" # need to move on to the nextline after getting out of comment else : if "]" in line: if line.rfind("[") > line.rfind("]"): pass # a comment block is closed but another is open. else: self.inCommentBlock = False return "Nextline" # need to move on to the nextline after getting out of comment return ""