Mercurial > repos > sybila > ebcsgen_sbml_export
diff ebcsgen_sbml_export.py @ 0:2f3f67415022 draft
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 74a375c33936106a892dafb042be953a943af026
author | sybila |
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date | Sat, 08 Oct 2022 12:55:26 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_sbml_export.py Sat Oct 08 12:55:26 2022 +0000 @@ -0,0 +1,30 @@ +import argparse + +from eBCSgen.Errors.ModelParsingError import ModelParsingError +from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError +from eBCSgen.Parsing.ParseBCSL import Parser + +import libsbml + + +args_parser = argparse.ArgumentParser(description='Export SBML model with usage of SBML-multi package') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') + +required.add_argument('--model', type=str, required=True) +required.add_argument('--output', type=str, required=True) + +args = args_parser.parse_args() + +model_parser = Parser("model") +model_str = open(args.model, "r").read() + +model = model_parser.parse(model_str) +if model.success: + document = model.data.export_sbml() + libsbml.writeSBMLToFile(document, args.output) +else: + if "error" in model.data: + raise UnspecifiedParsingError(model.data["error"]) + raise ModelParsingError(model.data, model_str)