def test_unnamed_parameters(self):
""" If there's a parameter without a name, we should use its id
as a name instead. """
model = SBML()
model.load_file("input/goodwin3.xml")
params = model.get_all_param()
self.assertEqual(len(params), 4)
def test_definition_of_sbml_parameters(self):
""" Tests if the priors have the correct parameter names of the
sbml model. """
model = SBML()
model.load_file("input/model1.xml")
theta = define_sbml_params_priors(model, 'input/model1.priors')
sbml_parameters = model.get_all_param()
for t in theta.get_model_parameters():
assert (t.name in sbml_parameters)
def test_with_sbml(self):
""" Tests if the module can define the prior of sbml parameters.
"""
model = SBML()
model.load_file("input/model1.xml")
theta = define_sbml_params_priors(model, 'input/model1.priors')
self.assertEqual(theta.get_size() - 1, len(model.get_all_param()))
sigma = theta.get_experimental_error()
assert (sigma > 0)
def test_get_original_name_with_id(self):
""" If there's a parameter without a name, when you call
get_original_param_name you should get the parameter's
id. """
model = SBML()
model.load_file("input/goodwin3.xml")
params = model.get_all_param()
names = []
for p in params:
original_name = model.get_original_param_name(p)
names.append(original_name)
assert ("m" in names)
assert ("k1" in names)
assert ("k2" in names)
assert ("k3" in names)
from lxml import etree
parser = argparse.ArgumentParser()
parser.add_argument("model", help="SBML file with model definition")
parser.add_argument ("output_file", help="A file to output the priors "\
+ "sketch file.")
args = parser.parse_args()
sbml_file = args.model
output_file = args.output_file
sbml = SBML()
sbml.load_file(sbml_file)
original_names = [sbml.get_original_param_name (p) for p in \
sbml.get_all_param ()]
priors_names = list(set(original_names))
priors_elm = etree.Element("priors")
for param_name in priors_names:
param_elm = etree.SubElement(priors_elm, "prior")
param_elm.set("distribution", "?")
param_elm.set("a", "?")
param_elm.set("b", "?")
param_elm.set("name", param_name)
exp_error_elm = etree.SubElement(priors_elm, "experimental_error")
exp_error_elm.set("distribution", "?")
exp_error_elm.set("a", "?")
exp_error_elm.set("b", "?")
exp_error_elm.set("name", "Noise")
tree = etree.ElementTree(priors_elm)
"experiment_file")
exit()
trace_file = sys.argv[1]
model_file = sys.argv[2]
experiment_file = sys.argv[3]
# define model
sbml = SBML ()
sbml.load_file (model_file)
ode = sbml_to_odes (sbml)
ode.print_equations ()
# get param names
param_names = []
for param in sbml.get_all_param ():
param_names.append (param)
# experiment info
exp_set = ExperimentSet (experiment_file)
experiment_times = exp_set[-1].times
experiment_measure = exp_set[-1].measure_expression
experiment_observations = []
for exp in exp_set:
obs = exp.values
experiment_observations.append (obs)
parameter_regex = re.compile (r"Current theta: \[(.*)\]")
f = open (trace_file)
theta = None