def __init__(self, **kwargs):
use_kappa = get_bool_arg('use_kappa', kwargs, default=False)
use_kappa_rest = get_bool_arg('use_kappa_rest', kwargs, default=False)
# Instantiate a singleton TRA agent
if not use_kappa:
logger.warning('You have chosen to not use Kappa.')
self.tra = tra.TRA(use_kappa, use_kappa_rest)
return super(TRA_Module, self).__init__(**kwargs)
def test_seq_hyp_test():
stmts = [Activation(Agent('BRAF'), Agent('KRAS'))]
model = tra_module.assemble_model(stmts)
entity = Agent('KRAS', activity=ActivityCondition('activity', True))
quantity = tra.MolecularQuantityReference('total', entity)
quant = tra.MolecularQuantity('qualitative', 'high')
pattern = tra.TemporalPattern('sometime_value', [entity],
None,
value=quant)
t = tra.TRA()
from bioagents.tra.model_checker import HypothesisTester
ht = HypothesisTester(alpha=0.1, beta=0.1, delta=0.05, prob=0.8)
res = t.check_property(model,
pattern,
conditions=None,
max_time=20000,
num_times=100,
hypothesis_tester=ht)
sat_rate, num_sim, kpat, pat_obj, fig_path = res
assert sat_rate == 1.0
assert num_sim == 18