def startElement(self, name, attrs):
if self.current_XMLNode is None:
self.current_XMLNode = XMLNode(name=name, attrs=attrs)
else:
t = XMLNode(name=name, attrs=attrs)
self.current_XMLNode.addChild(t)
self.xmlnode_hierarchylist.append(self.current_XMLNode)
self.current_XMLNode = t
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NEXT-STEP": # NOT USED FOR THE MOMENT...
self.next_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STEP-INTERACTIONS":
self.step_interactions_xref.append(current_child.attrs["rdf:resource"])
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:PATHWAY-COMPONENTS":
#print "Adding component ",current_child.attrs["rdf:resource"]
self.pathway_components.append(
current_child.attrs["rdf:resource"])
BiopaxEntity.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CONTROLLER":
self.controller_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROLLED":
self.controlled_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROL-TYPE":
control_type = current_child.getValue()
if control_type == "ACTIVATION":
self.control_type = "activates"
elif control_type == "INHIBITION":
self.control_type = "inhibits"
elif control_type == "INHIBITION-ALLOSTERIC":
self.control_type = "allosteric_inhibition"
elif control_type == "INHIBITION-COMPETITIVE":
self.control_type = "competitive_inhibition"
elif control_type == "INHIBITION-IRREVERSIBLE":
self.control_type = "irreversible_inhibition"
elif control_type == "INHIBITION-NONCOMPETITIVE":
self.control_type = "non_competitive_inhibition"
elif control_type == "INHIBITION-OTHER":
self.control_type = "inhibits"
elif control_type == "INHIBITION-UNCOMPETITIVE":
self.control_type = "uncompetitive_inhibition"
elif control_type == "ACTIVATION-NONALLOSTERIC":
self.control_type = "nonallosteric_activation"
elif control_type == "ACTIVATION-ALLOSTERIC":
self.control_type = "allosteric_activation"
else:
raise ValueError("Control type %s not recognized" %
control_type)
BiopaxPhysicalInteraction.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CONTROLLER":
self.controller_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROLLED":
self.controlled_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROL-TYPE":
control_type = current_child.getValue()
if control_type == "ACTIVATION":
self.control_type = "activates"
elif control_type == "INHIBITION":
self.control_type = "inhibits"
elif control_type == "INHIBITION-ALLOSTERIC":
self.control_type = "allosteric_inhibition"
elif control_type == "INHIBITION-COMPETITIVE":
self.control_type = "competitive_inhibition"
elif control_type == "INHIBITION-IRREVERSIBLE":
self.control_type = "irreversible_inhibition"
elif control_type == "INHIBITION-NONCOMPETITIVE":
self.control_type = "non_competitive_inhibition"
elif control_type == "INHIBITION-OTHER":
self.control_type = "inhibits"
elif control_type == "INHIBITION-UNCOMPETITIVE":
self.control_type = "uncompetitive_inhibition"
elif control_type == "ACTIVATION-NONALLOSTERIC":
self.control_type = "nonallosteric_activation"
elif control_type == "ACTIVATION-ALLOSTERIC":
self.control_type = "allosteric_activation"
else:
raise ValueError("Control type %s not recognized" %control_type)
BiopaxPhysicalInteraction.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NEXT-STEP": # NOT USED FOR THE MOMENT...
self.next_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STEP-INTERACTIONS":
self.step_interactions_xref.append(current_child.attrs["rdf:resource"])
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:TAXON-XREF":
self.tax_ref = current_child.attrs["rdf:resource"]
else:
print current_child.name," not recognized"
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:TAXON-XREF":
self.tax_ref = current_child.attrs["rdf:resource"]
else:
print current_child.name, " not recognized"
def startElement(self, name, attrs):
if self.current_XMLNode is None:
self.current_XMLNode = XMLNode(name = name, attrs = attrs)
else:
t = XMLNode(name = name, attrs = attrs)
self.current_XMLNode.addChild(t)
self.xmlnode_hierarchylist.append(self.current_XMLNode)
self.current_XMLNode = t
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:LEFT":
self.left_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:RIGHT":
self.right_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:EC-NUMBER":
self.ec_number.append(current_child.getValue())
BiopaxEntity.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COFACTOR":
self.cofactor = current_child.attrs["rdf:resource"]
# NOT IMPLEMENTED YET!!!
elif current_child.name == "bp:DIRECTION":
self.direction = current_child.getValue()
# NOT IMPLEMENTED YET!!!
BiopaxControl.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:LEFT":
self.left_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:RIGHT":
self.right_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:EC-NUMBER":
self.ec_number.append(current_child.getValue())
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COFACTOR":
self.cofactor = current_child.attrs["rdf:resource"]
# NOT IMPLEMENTED YET!!!
elif current_child.name == "bp:DIRECTION":
self.direction = current_child.getValue()
# NOT IMPLEMENTED YET!!!
BiopaxControl.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CELLULAR-LOCATION":
self.cellular_location_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:PHYSICAL-ENTITY":
self.physical_entity_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STOICHIOMETRIC-COEFFICIENT":
self.stoichiometric_coefficient = current_child.getValue()
elif current_child.name == "bp:SEQUENCE-FEATURE-LIST":
# TO CHECK WHAT TO DO
pass
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CELLULAR-LOCATION":
self.cellular_location_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:PHYSICAL-ENTITY":
self.physical_entity_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STOICHIOMETRIC-COEFFICIENT":
self.stoichiometric_coefficient = current_child.getValue()
elif current_child.name == "bp:SEQUENCE-FEATURE-LIST":
# TO CHECK WHAT TO DO
pass
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
"""
"""
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:ORGANISM":
self.organism = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:XREF":
self.xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:SYNONYMS":
self.synonyms.append(current_child.getValue())
elif current_child.name == "bp:SHORT_NAME":
self.short_name = current_child.getValue()
elif current_child.name == "bp:COMMENT":
self.comments.append(current_child.getValue())
def set_attributes(self, XMLNode):
"""
"""
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:ORGANISM":
self.organism = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:XREF":
self.xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:SYNONYMS":
self.synonyms.append(current_child.getValue())
elif current_child.name == "bp:SHORT_NAME":
self.short_name = current_child.getValue()
elif current_child.name == "bp:COMMENT":
self.comments.append(current_child.getValue())
class BiopaxLevel2Handler(handler.ContentHandler):
"""
Class to handle content in Biopax Level2 XML files
"""
def _identity(a):
return a
def _entrez_funct(a):
return str(a).replace("gi|","")
datatype_operations = { "uniprot": _identity,
"ncbi_taxonomy": _identity,
"tigr": _identity,
"reactome": _identity,
"chebi": _identity,
"go": _identity,
"pubchem compound" : _identity,
"glycan" : _identity,
"compound" : _identity,
"entrez": _entrez_funct }
biopax_objects_dict = { "bp:unificationxref": BiopaxXREF,
"bp:relationshipxref": BiopaxXREF,
"bp:publicationxref": BiopaxXREF,
"bp:opencontrolledvocabulary": BiopaxOpenControlledVocabulary,
"bp:biosource": BiopaxBioSource,
"bp:protein": BiopaxProtein,
"bp:complex": BiopaxComplex,
"bp:dna": BiopaxDNA,
"bp:rna": BiopaxRNA,
"bp:smallmolecule": BiopaxSmallMolecule,
"bp:physicalentity": BiopaxSmallMolecule,
"bp:pathway": BiopaxPathway,
"bp:interaction": BiopaxInteraction,
"bp:physcialinteraction": BiopaxPhysicalInteraction,
"bp:conversion": BiopaxConversion,
"bp:control": BiopaxControl,
"bp:biochemicalreaction": BiopaxBiochemicalReaction,
"bp:complexassembly": BiopaxComplexAssembly,
"bp:transport": BiopaxTransport,
"bp:catalysis": BiopaxCatalysis,
"bp:modulation": BiopaxModulation,
"bp:sequenceparticipant": BiopaxPhysicalEntityParticipant,
"bp:physicalentityparticipant": BiopaxPhysicalEntityParticipant,
"bp:pathwaystep": BiopaxPathwayStep }
#"bp:transportwithbiochemicalreaction":,
# "bp:physicalentityparticipant":,
# "bp:proteinparticipant":,
# "bp:complexparticipant":,
# "bp:rnaparticipant":,
# "bp:dnaparticipant":,
# "bp:smallmoleculeparticipant": }
def get_biana_data_type(self, type):
return BiopaxLevel2Parser.BiopaxLevel2Handler.datatype_to_biana_type[type.lower()]
def __init__(self):
print "initalizing BiopaxLevel2Handler"
self.current_XMLNode = None
self.step = 0
self.xmlnode_hierarchylist = []
self.biopaxElements = {}
BiopaxEntity.resources = self.biopaxElements
BiopaxEntity.controlled_relations = {}
handler.ContentHandler.__init__(self)
def _get_cross_ref(self, xref_id):
if xref_id[0] == '#':
xref_id = xref_id[1:]
try:
return self.unification_xrefs[xref_id]
except:
return self._get_cross_ref( xref_id = self.recursive_xref[xref_id] )
def _get_link(self, xref_id):
if xref_id[0] == '#':
xref_id = xref_id[1:]
return self.links[ xref_id ]
# ContentHandler methods
def startDocument(self):
return
def endDocument(self):
self.step += 1
def startElement(self, name, attrs):
if self.current_XMLNode is None:
self.current_XMLNode = XMLNode(name = name, attrs = attrs)
else:
t = XMLNode(name = name, attrs = attrs)
self.current_XMLNode.addChild(t)
self.xmlnode_hierarchylist.append(self.current_XMLNode)
self.current_XMLNode = t
def endElement(self, name):
name = name.lower()
if name!=self.current_XMLNode.name.lower():
raise ValueError("ERROR IN XML FILE")
if BiopaxLevel2Parser.BiopaxLevel2Handler.biopax_objects_dict.has_key(name):
self.biopaxElements['#'+self.current_XMLNode.attrs["rdf:ID"]] = BiopaxLevel2Parser.BiopaxLevel2Handler.biopax_objects_dict[name](self.current_XMLNode)
# Sets the current object the parent
if len(self.xmlnode_hierarchylist)>0:
self.current_XMLNode = self.xmlnode_hierarchylist.pop()
else:
self.current_XMLNode = None
return
def characters(self, text):
#print text
self.current_XMLNode.addValue(text.replace('.<','<').replace('br>','>').encode("ascii","ignore"))
#self.current_XMLNode.addValue(text.replace('.<','<').replace('br>','>').decode("ascii","ignore"))
def toBiana(self):
for current_element in self.biopaxElements.values():
current_element.toBiana()
class BiopaxLevel2Handler(handler.ContentHandler):
"""
Class to handle content in Biopax Level2 XML files
"""
def _identity(a):
return a
def _entrez_funct(a):
return str(a).replace("gi|", "")
datatype_operations = {
"uniprot": _identity,
"ncbi_taxonomy": _identity,
"tigr": _identity,
"reactome": _identity,
"chebi": _identity,
"go": _identity,
"pubchem compound": _identity,
"glycan": _identity,
"compound": _identity,
"entrez": _entrez_funct
}
biopax_objects_dict = {
"bp:unificationxref": BiopaxXREF,
"bp:relationshipxref": BiopaxXREF,
"bp:publicationxref": BiopaxXREF,
"bp:opencontrolledvocabulary": BiopaxOpenControlledVocabulary,
"bp:biosource": BiopaxBioSource,
"bp:protein": BiopaxProtein,
"bp:complex": BiopaxComplex,
"bp:dna": BiopaxDNA,
"bp:rna": BiopaxRNA,
"bp:smallmolecule": BiopaxSmallMolecule,
"bp:physicalentity": BiopaxSmallMolecule,
"bp:pathway": BiopaxPathway,
"bp:interaction": BiopaxInteraction,
"bp:physcialinteraction": BiopaxPhysicalInteraction,
"bp:conversion": BiopaxConversion,
"bp:control": BiopaxControl,
"bp:biochemicalreaction": BiopaxBiochemicalReaction,
"bp:complexassembly": BiopaxComplexAssembly,
"bp:transport": BiopaxTransport,
"bp:catalysis": BiopaxCatalysis,
"bp:modulation": BiopaxModulation,
"bp:sequenceparticipant": BiopaxPhysicalEntityParticipant,
"bp:physicalentityparticipant": BiopaxPhysicalEntityParticipant,
"bp:pathwaystep": BiopaxPathwayStep
}
#"bp:transportwithbiochemicalreaction":,
# "bp:physicalentityparticipant":,
# "bp:proteinparticipant":,
# "bp:complexparticipant":,
# "bp:rnaparticipant":,
# "bp:dnaparticipant":,
# "bp:smallmoleculeparticipant": }
def get_biana_data_type(self, type):
return BiopaxLevel2Parser.BiopaxLevel2Handler.datatype_to_biana_type[
type.lower()]
def __init__(self):
print "initalizing BiopaxLevel2Handler"
self.current_XMLNode = None
self.step = 0
self.xmlnode_hierarchylist = []
self.biopaxElements = {}
BiopaxEntity.resources = self.biopaxElements
BiopaxEntity.controlled_relations = {}
handler.ContentHandler.__init__(self)
def _get_cross_ref(self, xref_id):
if xref_id[0] == '#':
xref_id = xref_id[1:]
try:
return self.unification_xrefs[xref_id]
except:
return self._get_cross_ref(
xref_id=self.recursive_xref[xref_id])
def _get_link(self, xref_id):
if xref_id[0] == '#':
xref_id = xref_id[1:]
return self.links[xref_id]
# ContentHandler methods
def startDocument(self):
return
def endDocument(self):
self.step += 1
def startElement(self, name, attrs):
if self.current_XMLNode is None:
self.current_XMLNode = XMLNode(name=name, attrs=attrs)
else:
t = XMLNode(name=name, attrs=attrs)
self.current_XMLNode.addChild(t)
self.xmlnode_hierarchylist.append(self.current_XMLNode)
self.current_XMLNode = t
def endElement(self, name):
name = name.lower()
if name != self.current_XMLNode.name.lower():
raise ValueError("ERROR IN XML FILE")
if BiopaxLevel2Parser.BiopaxLevel2Handler.biopax_objects_dict.has_key(
name):
self.biopaxElements['#' + self.current_XMLNode.attrs[
"rdf:ID"]] = BiopaxLevel2Parser.BiopaxLevel2Handler.biopax_objects_dict[
name](self.current_XMLNode)
# Sets the current object the parent
if len(self.xmlnode_hierarchylist) > 0:
self.current_XMLNode = self.xmlnode_hierarchylist.pop()
else:
self.current_XMLNode = None
return
def characters(self, text):
#print text
self.current_XMLNode.addValue(
text.replace('.<',
'<').replace('br>',
'>').encode("ascii", "ignore"))
#self.current_XMLNode.addValue(text.replace('.<','<').replace('br>','>').decode("ascii","ignore"))
def toBiana(self):
for current_element in self.biopaxElements.values():
current_element.toBiana()
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:TERM":
self.term = current_child.getValue()
elif current_child.name == "bp:XREF":
self.xref = current_child.attrs["rdf:resource"]
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:DB":
self.db = current_child.getValue()
elif current_child.name == "bp:ID":
self.id = current_child.getValue()
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COMPONENTS":
self.components.append(current_child.attrs["rdf:resource"])
BiopaxPhysicalEntity.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:PATHWAY-COMPONENTS":
#print "Adding component ",current_child.attrs["rdf:resource"]
self.pathway_components.append(current_child.attrs["rdf:resource"])
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COMPONENTS":
self.components.append( current_child.attrs["rdf:resource"] )
BiopaxPhysicalEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:DB":
self.db = current_child.getValue()
elif current_child.name == "bp:ID":
self.id = current_child.getValue()
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:TERM":
self.term = current_child.getValue()
elif current_child.name == "bp:XREF":
self.xref = current_child.attrs["rdf:resource"]
