def parameterise_model(self, param_file):
"""Given a parameter file modify the model (possibly in file)
to obtain a new model with the parameters as specified in the
param_file
"""
dom = xml.dom.minidom.parse(self.model_file)
model = dom.getElementsByTagName("model")[0]
parameter_dict = parameters.parse_param_file(param_file)
sbml_parametiser.parameterise_model(model, parameter_dict)
def run():
"""The main entry point, parameterise SBML model files given
on the command line
"""
description = "Parameterise an SBML model based on a given param file"
parser = argparse.ArgumentParser(description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="input files: parameters and sbml model files")
arguments = parser.parse_args()
sbml_extentions = [ ".xml", ".sbml" ]
param_files = [ x for x in arguments.filenames
if not utils.has_extension(x, sbml_extentions) ]
sbml_files = [ x for x in arguments.filenames
if utils.has_extension(x, sbml_extentions) ]
dictionary = dict()
for param_file in param_files:
parameters.parse_param_file(param_file, dictionary=dictionary)
for sbml_file in sbml_files:
parameterise_model_file(sbml_file, dictionary)
def run():
"""perform the banalities of command-line argument processing and
then get on with the proper work
"""
description = "Compare results of two separate optimisations"
parser = argparse.ArgumentParser(description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="the input files, should be exactly two")
arguments = parser.parse_args()
if len(arguments.filenames) != 2:
print ("Must provide at least two best params files")
sys.exit(1)
best_params_lists = [ parameters.parse_param_file(f)
for f in arguments.filenames ]
# We can do better than simply comparing every other file to the
# first parameter file but for now I'm going to do that.
first_best_params = best_params_lists[0]
for other_best_params in best_params_lists[1:]:
compare_parameters(first_best_params, other_best_params)
def run():
"""Perform the banalities of command-line argument processing and
and then get under way in parameterising the model"""
description = "Parameterise an SBML model based on a given param file"
parser = argparse.ArgumentParser(description=description)
# Might want to make the type of this 'FileType('r')'
parser.add_argument('filenames', metavar='F', nargs='+',
help="Bio-PEPA and parameter files")
arguments = parser.parse_args()
biopepa_extentions = [ ".biopepa" ]
param_files = [ x for x in arguments.filenames
if not utils.has_extension(x, biopepa_extentions) ]
biopepa_files = [ x for x in arguments.filenames
if utils.has_extension(x, biopepa_extentions) ]
dictionary = dict()
for param_file in param_files:
dictionary = parameters.parse_param_file(param_file, dictionary)
for biopepa_file in biopepa_files:
parameterise_model_file(dictionary, biopepa_file, "stdout")