def run():
"""Do the simple task of generating a bunch of random parameters
for an sbml model. The input can either be the sbml model or
an initparams file
"""
description = "Create random parameters from an init params file"
parent_parser = guess_initparams.get_argument_parser()
parser = argparse.ArgumentParser(add_help=False,
parents=[parent_parser],
description=description)
arguments = parser.parse_args()
if len(arguments.filenames) < 1:
print ("Must provide an initial parameters file")
sys.exit(1)
filename = arguments.filenames[0]
if utils.has_xml_or_sbml_ext(filename):
params = guess_initparams.init_params_model_file(filename, arguments)
else:
params = parameters.get_init_param_parameters(filename)
for param in params:
print(param.name + "\t" + str(param.get_random_value_full_range()))
def run():
"""Perform the banalities of command-line argument processing
and then actually do the main work """
description = "Analyse SBML files for invariants"
parser = argparse.ArgumentParser(description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument("filenames", metavar="F", nargs="+", help="an sbml file to check invariants for")
parser.add_argument("--pretty", action="store_true", help="Pretty print the xml")
parser.add_argument("--column", action=utils.ListArgumentAction, help="Specify a column to be interpreted")
parser.add_argument("--mcolumn", action=utils.ListArgumentAction, help="Specify a column not to be interpreted")
arguments = parser.parse_args()
sbml_files = [x for x in arguments.filenames if utils.has_xml_or_sbml_ext(x)]
copasi_files = [x for x in arguments.filenames if utils.has_copasi_ext(x)]
timecourse_files = [x for x in arguments.filenames if not x in sbml_files and not x in copasi_files]
events = []
species = []
for filename in timecourse_files:
timecourse = timeseries.get_timecourse_from_file(filename)
species.extend(timecourse.get_column_names())
these_events = events_from_timecourse(timecourse, arguments)
events.extend(these_events)
if not events:
print("No events to add, doing nothing:")
sys.exit(1)
if not sbml_files and not copasi_files:
for event in events:
print(event.format_event())
else:
for filename in sbml_files:
add_events_sbml(filename, events, species, arguments)
for filename in copasi_files:
add_events_copasi(filename, events, arguments)
