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)
