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

from galaxy.util import parse_xml
from .baseparser import (

[docs]class Phyloxml_Parser(Base_Parser): """Parses a phyloxml file into a json file that will be passed to PhyloViz for display"""
[docs] def __init__(self): super().__init__() self.phyloTree = PhyloTree() self.tagsOfInterest = { "clade": "", "name": "name", "branch_length": "length", "confidence": "bootstrap", "events": "events", }
[docs] def parseFile(self, filePath): """passes a file and extracts its Phylogeny Tree content.""" xmlTree = parse_xml(filePath) 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"
[docs] 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)
[docs] def cleanTag(self, tagString): return tagString[self.nameSpaceIndex :]