def convert_file(filename, arguments):
"""Given an sbml file convert it into a corresponding facile model"""
model = outline_sbml.get_model_from_sbml_file(filename)
if arguments.output_file:
eqn_filename = arguments.output_file
else:
eqn_filename = utils.change_filename_ext(filename, ".eqn")
if eqn_filename == "stdout":
output_file = sys.stdout
else:
output_file = open(eqn_filename, "w")
# We also need to do the same for variables and parameters
parameters = outline_sbml.get_list_of_parameters(model)
for param in parameters:
output_file.write(" ".join(["variable", param.name, "=", param.value, ";\n"]))
# Reactions
reactions = outline_sbml.get_list_of_reactions(model)
for reaction in reactions:
output_reaction(output_file, reaction)
output_file.write("\nINIT\n")
species = outline_sbml.get_list_of_species(model)
init_assigns = outline_sbml.get_list_of_init_assigns(model)
for component in species:
init_string = component.initial_amount
for init_assign in init_assigns:
if init_assign.variable == component.name:
init_string = format_math_element(init_assign.expression)
output_file.write(component.name + " = " + init_string + " N;\n")
if eqn_filename != "stdout":
output_file.close()
def create_init_params_file(filename, arguments):
"""Get the parameters of an sbml file which we think are likely to
be 'optimisable' and based on that create an initparams file"""
output_filename = utils.change_filename_ext(filename, ".initparams")
output_file = open (output_filename, "w")
params = init_params_model_file(filename, arguments)
for param in params:
output_file.write (param.format_init(arguments.factor) + "\n")
output_file.close()
def run():
"""Perform the banalities of command line processing then get on
with the actual work"""
parser = create_arguments_parser(True)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="an sbml file to solve numerically")
parser.add_argument('--param-file', action='store',
help="Provide a parameter file to override parameters in the sbml file")
arguments = parser.parse_args()
# stop_time cannot have a default because the optimiser needs to know
# if the user has explicitly set the stop time or not, see the
# add_argument call for 'stop_time' in create_arguments_parser.
# So instead of a default value we check if it has been
# set and if not we set it:
if not arguments.stop_time:
arguments.stop_time = 1.0
initialise_logger(arguments)
configuration = arguments
for filename in arguments.filenames:
try:
if not os.path.exists(filename):
logging.error("Model file: " + filename + " does not exist")
continue
solver = get_solver(filename, arguments)
solver.initialise_solver()
solver.set_parameter_file(arguments.param_file)
timecourse = solver.solve_model(configuration)
all_columns = timecourse.get_column_names()
used_names = utils.get_non_ignored(all_columns,
arguments.column,
arguments.mcolumn)
if timecourse:
# First remove any columns which are going to be plotted.
for tc_column in all_columns:
if tc_column not in used_names:
timecourse.remove_column(tc_column)
results_filename = utils.change_filename_ext(filename, ".csv")
results_file = open(results_filename, "w")
timecourse.write_to_file(results_file)
results_file.close()
if arguments.plot_results:
plotcsv.run(argument_strings=[results_filename])
else:
logging.error ("solving the model failed, no timeseries to report")
continue
except SolverError:
# We should have already logged the error, now we just wish to
# allow ourselves to continue and solve the remaining models
continue
def translate_file(filename, arguments):
"""Given an sbml file convert it into a corresponding Bio-PEPA model"""
model = outline_sbml.get_model_from_sbml_file(filename)
if arguments.output_file:
biopepa_filename = arguments.output_file
else:
biopepa_filename = utils.change_filename_ext(filename, ".biopepa")
if biopepa_filename == "stdout":
output_file = sys.stdout
else:
output_file = open(biopepa_filename, "w")
output_file.write("\n\n// Parameters\n")
# We also need to do the same for variables and parameters
parameters = outline_sbml.get_list_of_parameters(model)
for param in parameters:
output_file.write(" ".join([param.name, "=", param.value, ";\n"]))
output_file.write("\n")
# Reactions
reactions = outline_sbml.get_list_of_reactions(model)
output_file.write("\n\n// Rate Definitions\n")
for reaction in reactions:
output_file.write(reaction.name + " = [ ")
output_file.write(format_math_element(reaction.kinetic_law))
output_file.write(" ] ;\n")
output_file.write("\n\n// Component Definitions\n")
component_defs = calculate_component_defs(reactions)
for component_def in component_defs:
output_file.write(component_def.show_definition())
output_file.write("\n")
output_file.write("\n// System Equation\n")
species = outline_sbml.get_list_of_species(model)
init_assigns = outline_sbml.get_list_of_init_assigns(model)
output_system_equation(output_file, species, init_assigns)
if biopepa_filename != "stdout":
output_file.close()
def __init__(self, model_file, cflags_prefix): self.model_file = model_file self.model_exec = utils.change_filename_ext(model_file, ".exe") self.param_filename = None self.cflags_prefix = cflags_prefix
def results_filename (self): """Return a suitable filename for the results contained here in""" model_file = self.model_data.model_file basename = os.path.basename(model_file) result_filename = utils.change_filename_ext(basename, ".csv") return result_filename
