Mercurial > repos > sybila > ebcsgen_simulation
view ebcsgen_simulate.py @ 0:179d32e79968 draft
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
author | sybila |
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date | Tue, 04 Oct 2022 13:15:48 +0000 |
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import argparse from eBCSgen.Errors import UnspecifiedParsingError from eBCSgen.Errors.InvalidInputError import InvalidInputError from eBCSgen.Errors.ModelParsingError import ModelParsingError from eBCSgen.Errors.RatesNotSpecifiedError import RatesNotSpecifiedError from eBCSgen.Parsing.ParseBCSL import Parser args_parser = argparse.ArgumentParser(description='Simulation') 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) required.add_argument('--deterministic', required=True) required.add_argument('--direct', required=True) required.add_argument('--runs', type=int, required=True) required.add_argument('--max_time', type=float, required=True) required.add_argument('--volume', type=float, required=True) required.add_argument('--step', type=float, 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: if len(model.data.params) != 0: raise InvalidInputError("Provided model is parametrised - simulation cannot be executed.") if not model.data.all_rates: raise RatesNotSpecifiedError("Some rules do not have rates specified - simulation cannot be executed.") if eval(args.deterministic): vm = model.data.to_vector_model() df = vm.deterministic_simulation(args.max_time, args.volume, args.step) else: if eval(args.direct): df = model.data.network_free_simulation(args.max_time) else: vm = model.data.to_vector_model() df = vm.stochastic_simulation(args.max_time, args.runs) df.to_csv(args.output, index=None, header=True) else: if "error" in model.data: raise UnspecifiedParsingError(model.data["error"]) raise ModelParsingError(model.data, model_str)