Python parse_model_file_exit_on_error Examples

Example #1

File: biopepa_to_sbml.py Project: allanderek/prototype_sbsi

def convert_file(filename, arguments):
  """Parse in a Bio-PEPA file, translate to SBML and create an
     SBML file which should be the translated Bio-PEPA model.
  """
  model_file = open(filename, "r")
  parse_result = biopepa_parser.parse_model_file_exit_on_error(model_file)
  model_file.close()

  document = translate_biopepa_model(parse_result)
  sbml_ast.output_to_sbml_file(filename, arguments, document)

Example #2

File: biopepa_to_latex.py Project: allanderek/prototype_sbsi

def latexify_file(filename, arguments):
  """ Converts a file containing Bio-PEPA source into a file containing
      LaTeX source to format the same model.
  """
  model_file = open(filename, "r")
  parse_result = biopepa_parser.parse_model_file_exit_on_error(model_file)
  model_file.close()

  biopepa_model = parse_result

  out_filename = utils.get_output_filename(filename, arguments, ".tex")
  if out_filename == "stdout":
    translate_biopepa_model(biopepa_model, sys.stdout)
  else:
    out_file = open(out_filename, "w")
    translate_biopepa_model(biopepa_model, out_file)
    out_file.close()

Example #3

File: flatten_biopepa.py Project: allanderek/prototype_sbsi

def process_file(filename, arguments):
  """Parse in a Bio-PEPA file and convert to an equivalent Bio-PEPA
     file that is flattened in the sense that it uses no compartments
     and hence no compartment-related rules.
  """
  model_file = open(filename, "r")
  parse_result = biopepa_parser.parse_model_file_exit_on_error(model_file)
  model_file.close()

  output_filename = utils.get_output_filename(filename, arguments,
                                              "_flattened.biopepa") 
  if output_filename != "stdout":
    output_file = open(output_filename, "w")
  else:
    output_file = sys.stdout


  flatten_model(parse_result)
  parse_result.output_model(output_file)

  if output_filename != "stdout":
    output_file.close()