def readFromString(inputString, reactionDefinitions, useID, speciesEquivalence=None, atomize=False): ''' one of the library's main entry methods. Process data from a string ''' try: reader = libsbml.SBMLReader() document = reader.readSBMLFromString(inputString) parser = SBML2BNGL(document.getModel(), useID) bioGrid = False if bioGrid: loadBioGrid() database = structures.Databases() namingConventions = resource_path('config/namingConventions.json') if atomize: translator, onlySynDec = mc.transformMolecules( parser, database, reactionDefinitions, namingConventions, speciesEquivalence, bioGrid) else: translator = {} return analyzeHelper(document, reactionDefinitions, useID, '', speciesEquivalence, atomize, translator)[-2] except: return -5
def analyzeFile(bioNumber,reactionDefinitions,useID,namingConventions,outputFile, speciesEquivalence=None,atomize=False,bioGrid=False): ''' one of the library's main entry methods. Process data from a string ''' reader = libsbml.SBMLReader() document = reader.readSBMLFromFile(bioNumber) parser =SBML2BNGL(document.getModel(),useID) database = structures.Databases() #call the atomizer (or not) bioGridDict = {} if bioGrid: bioGridDict = loadBioGrid() if atomize: translator = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid) else: translator={} returnArray= analyzeHelper(document,reactionDefinitions,useID,outputFile,speciesEquivalence,atomize,translator) with open(outputFile,'w') as f: f.write(returnArray[-2]) #with open('{0}.dict'.format(outputFile),'wb') as f: # pickle.dump(returnArray[-1],f) return returnArray[0:-2]
def readFromString(inputString,reactionDefinitions,useID,speciesEquivalence=None,atomize=False): ''' one of the library's main entry methods. Process data from a string ''' reader = libsbml.SBMLReader() document = reader.readSBMLFromString(inputString) parser =SBML2BNGL(document.getModel(),useID) bioGrid = False if bioGrid: loadBioGrid() database = structures.Databases() namingConventions = 'config/namingConventions.json' if atomize: translator = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid) else: translator={} return analyzeHelper(document,reactionDefinitions,useID,'',speciesEquivalence,atomize,translator)[-2]
def analyzeFile(bioNumber, reactionDefinitions, useID, namingConventions, outputFile, speciesEquivalence=None, atomize=False, bioGrid=False): ''' one of the library's main entry methods. Process data from a file ''' logMess.log = [] logMess.counter = -1 reader = libsbml.SBMLReader() document = reader.readSBMLFromFile(bioNumber) parser = SBML2BNGL(document.getModel(), useID) database = structures.Databases() database.forceModificationFlag = True bioGridDict = {} if bioGrid: bioGridDict = loadBioGrid() #call the atomizer (or not). structured molecules are contained in translator #onlysyndec is a boolean saying if a model is just synthesis of decay reactions if atomize: translator, onlySynDec = mc.transformMolecules(parser, database, reactionDefinitions, namingConventions, speciesEquivalence, bioGrid) else: translator = {} #process other sections of the sbml file (functions reactions etc.) returnArray = analyzeHelper(document, reactionDefinitions, useID, outputFile, speciesEquivalence, atomize, translator) with open(outputFile, 'w') as f: f.write(returnArray[-2]) #with open('{0}.dict'.format(outputFile),'wb') as f: # pickle.dump(returnArray[-1],f) if atomize and onlySynDec: returnArray = list(returnArray) returnArray[0] = -1 return tuple(returnArray[0:-2])
def analyzeFile(bioNumber,reactionDefinitions,useID,namingConventions,outputFile, speciesEquivalence=None,atomize=False,bioGrid=False): ''' one of the library's main entry methods. Process data from a file ''' logMess.log = [] logMess.counter = -1 reader = libsbml.SBMLReader() document = reader.readSBMLFromFile(bioNumber) parser =SBML2BNGL(document.getModel(),useID) database = structures.Databases() database.forceModificationFlag = True bioGridDict = {} if bioGrid: bioGridDict = loadBioGrid() #call the atomizer (or not). structured molecules are contained in translator #onlysyndec is a boolean saying if a model is just synthesis of decay reactions if atomize: translator,onlySynDec = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid) else: translator={} #process other sections of the sbml file (functions reactions etc.) returnArray= analyzeHelper(document,reactionDefinitions,useID,outputFile,speciesEquivalence,atomize,translator) with open(outputFile,'w') as f: f.write(returnArray[-2]) #with open('{0}.dict'.format(outputFile),'wb') as f: # pickle.dump(returnArray[-1],f) if atomize and onlySynDec: returnArray = list(returnArray) returnArray[0] = -1 return tuple(returnArray[0:-2])