def main(): parser = OptionParser() parser.add_option("-i","--input",dest="input", default='input.xml',type="string", help="The input SBML file in xml format. Default = 'input.xml'",metavar="FILE") parser.add_option("-o","--output",dest="output", default='output.bngl',type="string", help="the output file where we will store our matrix. Default = output.bngl",metavar="FILE") (options, args) = parser.parse_args() reader = SBMLReader() document = reader.readSBMLFromFile(options.input) print options.input parser =SBML2BNGL(document.getModel()) param2 = parser.getParameters() param,rules,functions = parser.getReactions() molecules,species,observables = parser.getSpecies() param += param2 print rules writer.finalText(param,molecules,species,observables,rules,functions,options.output)
def main(): if libsbml == None: return parser = OptionParser() parser.add_option( "-i", "--input", dest="input", default='', type="string", #default='/home/proto/Downloads/model.xml',type="string", help="The input SBML file in xml format. Default = 'input.xml'", metavar="FILE") parser.add_option("-o", "--output", dest="output", type="string", help="the output JSON file. Default = <input>.py", metavar="FILE") (options, args) = parser.parse_args() reader = libsbml.SBMLReader() nameStr = options.input if options.output == None: outputFile = nameStr + '.json' else: outputFile = options.output document = reader.readSBMLFromFile(nameStr) if document.getModel() == None: #logging.error('A model with path "{0}" could not be found'.format(nameStr)) return #logging.info('An SBML file was found at {0}.Attempting import'.format(nameStr)) parser = SBML2JSON(document.getModel()) parameters, observables = parser.getParameters() #compartments = parser.getRawCompartments() molecules, release = parser.getMolecules() reactions, release2, molecules2 = parser.getReactions(parameters) molecules.extend(molecules2) release.extend(release2) #release.extend(release2) definition = {} definition['par_list'] = parameters definition['mol_list'] = molecules definition['rxn_list'] = reactions definition['rel_list'] = release definition['obs_list'] = observables #definition['comp_list'] = compartments with open(outputFile, 'w') as f: json.dump(definition, f, sort_keys=True, indent=1, separators=(',', ': '))
def main(): # command line arguments parser = OptionParser() parser.add_option( "-i", "--input", dest="input", default="bngl2mcell/rec_dim_sbml.xml", type="string", help="The input SBML file in xml format. Default = 'input.xml'", metavar="FILE", ) parser.add_option( "-o", "--output", dest="output", type="string", help="the output JSON file. Default = <input>.py", metavar="FILE", ) (options, args) = parser.parse_args() reader = libsbml.SBMLReader() nameStr = options.input if options.output == None: outputFile = nameStr + ".py" else: outputFile = options.output # libsbml initialization stuff document = reader.readSBMLFromFile(nameStr) if document.getModel() == None: print("No such input file") return # get data parser = SBML2JSON(document.getModel()) parameters = parser.getParameters() molecules, release = parser.getMolecules() reactions = parser.getReactions(parameters) definition = {} definition["par_list"] = parameters definition["mol_list"] = molecules definition["rxn_list"] = reactions definition["rel_list"] = release print("Writing output to {0}".format(outputFile)) # output with open(outputFile, "w") as f: json.dump(definition, f, sort_keys=True, indent=1, separators=(",", ": "))
def main(): if libsbml == None: return parser = OptionParser() parser.add_option("-i","--input",dest="input", default='',type="string", #default='/home/proto/Downloads/model.xml',type="string", help="The input SBML file in xml format. Default = 'input.xml'",metavar="FILE") parser.add_option("-o","--output",dest="output", type="string", help="the output JSON file. Default = <input>.py",metavar="FILE") (options, args) = parser.parse_args() reader = libsbml.SBMLReader() nameStr = options.input if options.output == None: outputFile = nameStr + '.json' else: outputFile = options.output document = reader.readSBMLFromFile(nameStr) if document.getModel() == None: #logging.error('A model with path "{0}" could not be found'.format(nameStr)) return #logging.info('An SBML file was found at {0}.Attempting import'.format(nameStr)) parser = SBML2JSON(document.getModel()) parameters,observables = parser.getParameters() #compartments = parser.getRawCompartments() molecules,release = parser.getMolecules() reactions,release2,molecules2 = parser.getReactions(parameters) molecules.extend(molecules2) release.extend(release2) #release.extend(release2) definition = {} definition['par_list'] = parameters definition['mol_list'] = molecules definition['rxn_list'] = reactions definition['rel_list'] = release definition['obs_list'] = observables #definition['comp_list'] = compartments with open(outputFile,'w') as f: json.dump(definition,f,sort_keys=True,indent=1, separators=(',', ': '))
def main(): #command line arguments parser = OptionParser() parser.add_option("-i","--input",dest="input", default='bngl2mcell/rec_dim_sbml.xml',type="string", help="The input SBML file in xml format. Default = 'input.xml'",metavar="FILE") parser.add_option("-o","--output",dest="output", type="string", help="the output JSON file. Default = <input>.py",metavar="FILE") (options, args) = parser.parse_args() reader = libsbml.SBMLReader() nameStr = options.input if options.output == None: outputFile = nameStr + '.py' else: outputFile = options.output #libsbml initialization stuff document = reader.readSBMLFromFile(nameStr) if document.getModel() == None: print 'No such input file' return #get data parser = SBML2JSON(document.getModel()) parameters = parser.getParameters() molecules,release = parser.getMolecules() reactions = parser.getReactions(parameters) definition = {} definition['par_list'] = parameters definition['mol_list'] = molecules definition['rxn_list'] = reactions definition['rel_list'] = release print 'Writing output to {0}'.format(outputFile) #output with open(outputFile,'w') as f: json.dump(definition,f,sort_keys=True,indent=1, separators=(',', ': '))