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)
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()
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()