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 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()
