def test_serialize(self):
""" The the serialization of the entire object. """
parameters = CancerSimulatorParameters()
cancer_sim = CancerSimulator(parameters, seed=2, outdir=mkdtemp())
# Cleanup.
self._test_files.append(cancer_sim.outdir)
# Dump.
cancer_sim.dump()
# Reload
loaded_simulation = load_cancer_simulation(cancer_sim.dumpfile)
self.assertIsInstance(loaded_simulation, CancerSimulator)
# Check parameters.
loaded_parameters = loaded_simulation.parameters
self.assertEqual(loaded_parameters.number_of_generations, parameters.number_of_generations)
self.assertEqual(loaded_parameters.matrix_size, parameters.matrix_size)
self.assertEqual(loaded_parameters.number_of_generations, parameters.number_of_generations)
self.assertEqual(loaded_parameters.division_probability, parameters.division_probability)
self.assertEqual(loaded_parameters.adv_mutant_division_probability, parameters.adv_mutant_division_probability)
self.assertEqual(loaded_parameters.death_probability, parameters.death_probability)
self.assertEqual(loaded_parameters.adv_mutant_death_probability, parameters.adv_mutant_death_probability)
self.assertEqual(loaded_parameters.mutation_probability, parameters.mutation_probability)
self.assertEqual(loaded_parameters.adv_mutant_mutation_probability, parameters.adv_mutant_mutation_probability)
self.assertEqual(loaded_parameters.number_of_mutations_per_division, parameters.number_of_mutations_per_division)
self.assertEqual(loaded_parameters.adv_mutation_wait_time, parameters.adv_mutation_wait_time)
self.assertEqual(loaded_parameters.number_of_initial_mutations, parameters.number_of_initial_mutations)
self.assertEqual(loaded_parameters.tumour_multiplicity, parameters.tumour_multiplicity)
self.assertEqual(loaded_parameters.read_depth, parameters.read_depth)
self.assertEqual(loaded_parameters.sampling_fraction, parameters.sampling_fraction)
# Check we can run.
loaded_simulation.run()
# dump again.
loaded_simulation.dump()
# Load again
loaded_again_simulation = load_cancer_simulation(loaded_simulation.dumpfile)
# Check that the internal state is the same as in the dump.
self.assertAlmostEqual(numpy.linalg.norm(loaded_simulation._CancerSimulator__mtx.toarray()
- loaded_again_simulation._CancerSimulator__mtx.toarray()), 0.0)
self.assertEqual(loaded_simulation._CancerSimulator__mut_container, loaded_again_simulation._CancerSimulator__mut_container)
self.assertEqual(loaded_simulation._CancerSimulator__xaxis_histogram, loaded_again_simulation._CancerSimulator__xaxis_histogram)
self.assertEqual(loaded_simulation._CancerSimulator__biopsy_timing, loaded_again_simulation._CancerSimulator__biopsy_timing)
self.assertEqual(loaded_simulation._CancerSimulator__beneficial_mutation, loaded_again_simulation._CancerSimulator__beneficial_mutation)
self.assertEqual(loaded_simulation._CancerSimulator__growth_plot_data, loaded_again_simulation._CancerSimulator__growth_plot_data)
self.assertEqual(loaded_simulation._CancerSimulator__mutation_counter, loaded_again_simulation._CancerSimulator__mutation_counter)
self.assertEqual(loaded_simulation._CancerSimulator__s, loaded_again_simulation._CancerSimulator__s)
self.assertEqual(loaded_simulation._CancerSimulator__ploidy, loaded_again_simulation._CancerSimulator__ploidy)
self.assertEqual(loaded_simulation._CancerSimulator__mut_multiplier, loaded_again_simulation._CancerSimulator__mut_multiplier)
self.assertEqual(loaded_simulation._CancerSimulator__pool, loaded_again_simulation._CancerSimulator__pool)
# Run once more.
loaded_again_simulation.run()
parameters = CancerSimulatorParameters(
matrix_size=4096,
number_of_generations=g, # vary
division_probability=dp, # 1 => exp. growth
adv_mutant_division_probability=0.3,
death_probability=0.0,
adv_mutant_death_probabilityability=0.0,
mutation_rate=1.0, # 1 =>
adv_mutant_mutation_probability=0.8,
mutations_per_division=
10, # if mutation event occurs, have this number of mutation
adv_mutation_interval=30000, # large to not kick in
number_of_initital_mutations=
2, # initial number of mutations in first cancer cell
tumour_multiplicity='single',
)
simulator = CancerSimulator(parameters,
seed=None,
outdir="%s" % (n_run))
t0 = time()
simulator.run()
T = time() - t0
with open(os.path.join(simulator.outdir, "log.txt"), 'a') as fp:
fp.write("%s\t%f\t%d\t%e\n" % (simulator.seed, dp, g, T))
simulator.dump()
sleep(1)