def test_last_states(self):
expected = {
'<nil>': 0.206,
'Apoptosis -- CellCycleArrest': 0.426,
'CellCycleArrest': 0.068,
'Migration -- Metastasis -- Invasion -- CellCycleArrest': 0.3
}
expected_nodes = {
'Metastasis': 0.3,
'Invasion': 0.3,
'Migration': 0.3,
'Apoptosis': 0.426,
'CellCycleArrest': 0.794
}
sim = cmaboss.MaBoSSSim(network="../examples/metastasis.bnd",
config="../examples/metastasis.cfg")
res = sim.run(only_last_state=False)
for key, value in res.get_last_states_probtraj().items():
self.assertAlmostEqual(value, expected[key])
for key, value in res.get_last_nodes_probtraj().items():
self.assertAlmostEqual(value, expected_nodes[key])
simfinal = cmaboss.MaBoSSSim(network="../examples/metastasis.bnd",
config="../examples/metastasis.cfg")
resfinal = simfinal.run(only_last_state=True)
for key, value in resfinal.get_last_states_probtraj().items():
self.assertAlmostEqual(value, expected[key])
for key, value in resfinal.get_last_nodes_probtraj().items():
self.assertAlmostEqual(value, expected_nodes[key])
def test_use_sbml_names(self):
sim = cmaboss.MaBoSSSim("../examples/sbml/Cohen.sbml")
self.assertEqual(sim.str_bnd().split("{")[0].split("node ")[1].strip(),
"S_26")
sim = cmaboss.MaBoSSSim("../examples/sbml/Cohen.sbml",
use_sbml_names=True)
self.assertEqual(sim.str_bnd().split("{")[0].split("node ")[1].strip(),
"CTNNB1")
def test_load_model_cellcycle(self):
net = cmaboss.MaBoSSNet(network="../tests/cellcycle/cellcycle.bnd")
cfg = cmaboss.MaBoSSCfg(
net, "../tests/cellcycle/cellcycle_runcfg.cfg",
"../tests/cellcycle/cellcycle_runcfg-thread_6.cfg")
sim = cmaboss.MaBoSSSim(net=net, cfg=cfg)
res = sim.run()
def test_simulate(self):
sim = cmaboss.MaBoSSSim(network="../examples/metastasis.bnd",
config="../examples/metastasis.cfg")
res = sim.run()
res.get_probtraj()
res.get_last_probtraj()
res.get_nodes_probtraj()
res.get_last_nodes_probtraj()
res.get_fp_table()
def test_load_model_str(self):
with open("../examples/metastasis.bnd",
"r") as bnd, open("../examples/metastasis.cfg", "r") as cfg:
sim = cmaboss.MaBoSSSim(network_str=bnd.read(),
config_str=cfg.read())
res = sim.run()
res.get_probtraj()
res.get_last_probtraj()
res.get_nodes_probtraj()
res.get_last_nodes_probtraj()
res.get_fp_table()
def test_last_states(self):
expected = {
'<nil>': 0.206,
'Apoptosis -- CellCycleArrest': 0.426,
'CellCycleArrest': 0.068,
'Migration -- Metastasis -- Invasion -- CellCycleArrest': 0.3
}
expected_nodes = {
'Metastasis': 0.3,
'Invasion': 0.3,
'Migration': 0.3,
'Apoptosis': 0.426,
'CellCycleArrest': 0.794
}
sim = cmaboss.MaBoSSSim(network="../examples/metastasis.bnd",
config="../examples/metastasis.cfg")
res = sim.run(only_last_state=False)
raw_res, states, _ = res.get_last_probtraj()
for i, value in enumerate(np.nditer(raw_res)):
self.assertAlmostEqual(value, expected[states[i]])
raw_nodes_res, nodes, _ = res.get_last_nodes_probtraj()
for i, value in enumerate(np.nditer(raw_nodes_res)):
self.assertAlmostEqual(value, expected_nodes[nodes[i]])
simfinal = cmaboss.MaBoSSSim(network="../examples/metastasis.bnd",
config="../examples/metastasis.cfg")
resfinal = simfinal.run(only_last_state=True)
raw_res, states, _ = res.get_last_probtraj()
for i, value in enumerate(np.nditer(raw_res)):
self.assertAlmostEqual(value, expected[states[i]])
raw_nodes_res, nodes, _ = res.get_last_nodes_probtraj()
for i, value in enumerate(np.nditer(raw_nodes_res)):
self.assertAlmostEqual(value, expected_nodes[nodes[i]])
def test_load_sbml_error(self):
with self.assertRaises(cmaboss.BNException):
sim = cmaboss.MaBoSSSim("../examples/sbml/BIOMD0000000562_url.xml")
def test_load_sbml(self):
sim = cmaboss.MaBoSSSim("../tests/sbml/cell_fate.sbml",
"../tests/sbml/cell_fate.cfg")
res = sim.run()
def test_load_model_str_error(self):
with open("../examples/metastasis-error.bnd",
"r") as bnd, open("../examples/metastasis.cfg", "r") as cfg:
with self.assertRaises(cmaboss.BNException):
cmaboss.MaBoSSSim(network_str=bnd.read(),
config_str=cfg.read())
def test_load_model(self):
net = cmaboss.MaBoSSNet(network="../examples/metastasis.bnd")
cfg = cmaboss.MaBoSSCfg(net, "../examples/metastasis.cfg")
sim = cmaboss.MaBoSSSim(net=net, cfg=cfg)
res = sim.run()
def test_load_model_error(self):
with self.assertRaises(cmaboss.BNException):
cmaboss.MaBoSSSim(network="../examples/metastasis-error.bnd",
config="../examples/metastasis.cfg")