def test_build_works(self, large):
opt = CORDA(*large)
opt.build()
include = [c for c in opt.conf if opt.conf[c] == 3]
assert len(include) > 3
rec = opt.cobra_model("reconstruction")
sol = rec.optimize()
assert sol.f > 1
def test_impossible_req(self, model):
mod, conf = model
D = Metabolite("D")
mod.add_metabolites([D])
opt = CORDA(mod, conf, met_prod=["D"])
need = opt.associated(["EX_CORDA_0"])
assert len(need) == 0
assert "EX_CORDA_0" in opt.impossible
def test_impossible_req(self, model):
mod, conf = model
D = Metabolite("D")
mod.add_metabolites([D])
opt = CORDA(mod, conf, met_prod=["D"])
need = opt.associated(["EX_CORDA_0"])
assert len(need) == 0
assert "EX_CORDA_0" in opt.impossible
def test_build_works(self, large):
opt = CORDA(*large)
opt.build()
include = [c for c in opt.conf if opt.conf[c] == 3]
assert len(include) > 3
rec = opt.cobra_model("reconstruction")
sol = rec.optimize()
assert sol.f > 1
def test_conf_vals(self, large):
mod, conf = large
for r in mod.reactions:
conf[r.id] = 1
conf["r60"] = 3
conf["r42"] = 0
conf["r12"] = 1
opt = CORDA(mod, conf)
opt.build()
include = [c for c in opt.conf if opt.conf[c] == 3]
assert len(include) > 3
def test_redundancy_works(self, model):
mod, conf = model
conf["r2"] = 2
opt = CORDA(mod, conf, met_prod="C ->")
need = opt.associated(["EX_CORDA_0"], conf)
assert len(need) == 4
assert opt.redundancies["EX_CORDA_0"] == 2
opt = CORDA(mod, conf, met_prod="C ->", n=1)
need = opt.associated(["EX_CORDA_0"], conf)
assert len(need) == 2
assert opt.redundancies["EX_CORDA_0"] == 1
def test_conf_vals(self, large):
mod, conf = large
for r in mod.reactions:
conf[r.id] = 1
conf["r60"] = 3
conf["r42"] = 0
conf["r12"] = 1
opt = CORDA(mod, conf)
opt.build()
include = [c for c in opt.conf if opt.conf[c] == 3]
assert len(include) > 3
def test_mock_add(self, model):
mod, conf = model
opt = CORDA(mod, conf, met_prod={"C": -1})
r = opt.model.reactions.get_by_id("EX_CORDA_0")
assert "mock" in r.notes
opt = CORDA(mod, conf, met_prod="C ->")
r = opt.model.reactions.get_by_id("EX_CORDA_0")
assert "mock" in r.notes
with pytest.raises(TypeError):
CORDA(mod, conf, met_prod=[["C"]])
opt.build()
mod = opt.cobra_model()
assert all(mr not in mod.reactions for mr in opt.mocks)
def test_mock_add(self, model):
mod, conf = model
opt = CORDA(mod, conf, met_prod={"C": -1})
r = opt.model.reactions.get_by_id("EX_CORDA_0")
assert "mock" in r.notes
opt = CORDA(mod, conf, met_prod="C ->")
r = opt.model.reactions.get_by_id("EX_CORDA_0")
assert "mock" in r.notes
with pytest.raises(TypeError):
CORDA(mod, conf, met_prod=[["C"]])
opt.build()
mod = opt.cobra_model()
assert all(mr not in mod.reactions for mr in opt.mocks)
def test_redundancy_works(self, model):
mod, conf = model
conf["r2"] = 2
opt = CORDA(mod, conf, met_prod="C ->")
need = opt.associated(["EX_CORDA_0"], conf)
assert len(need) == 4
assert opt.redundancies["EX_CORDA_0"] == 2
opt = CORDA(mod, conf, met_prod="C ->", n=1)
need = opt.associated(["EX_CORDA_0"], conf)
assert len(need) == 2
assert opt.redundancies["EX_CORDA_0"] == 1
def test_performance_metrics(self, model):
opt = CORDA(model[0], model[1])
assert "not built" in str(opt)
def test_performance_metrics(self, large):
opt = CORDA(*large)
opt.build()
assert "reconstruction complete" in str(opt)
assert "/60" in str(opt)
def test_conf_check(self, model):
mod, conf = model
co = conf.copy()
del co["EX_A"]
with pytest.raises(ValueError):
CORDA(mod, co)
def test_valid_conf(self, model):
mod, conf = model
co = conf.copy()
co["EX_A"] = 4
with pytest.raises(ValueError):
CORDA(mod, co)
elif rxns_mapped_expr[
r.id] <= lista_th_lower[th_l]:
rxns_conf[r.id] = -1
# Si no hay información de algún gen, como de los mitocondriales.
elif rxns_mapped_expr[r.id] == -1:
rxns_conf[r.id] = 0
else:
rxns_conf[r.id] = 1
else:
rxns_conf[r.id] = 0
rxns_conf[
"biomass_reaction"] = 3 # Esta el 'objetive funtion' del FBA.
print('------RECONSTRUYENDO EL MODELO-----')
# Reconstruyes el modelo celula_especifico
CORDA_builder = CORDA(reference_model, rxns_conf)
CORDA_builder.build()
csm2 = CORDA_builder.cobra_model()
write_sbml_model(
csm2, './thresholding/Th_upper_y_lower/' + cell_line +
'/csm2_%s_%s.sbml' % (th_l, th_u))
print('Numero de reacciones de modelo reconstruido:',
str(len(csm2.reactions)))
# Identificando los genes esenciales, como los genes cuya deleccion individual no producen crecimiento (Ecuación biomasa < 0.01).
print('------SINGLE GENE DELETION-----')
resultado_knocked_out = single_gene_deletion(
csm2, proprocesses=1)
rename_dict = {
i: list(i)[0]
def _():
opt = CORDA(mod, conf)
opt.build()
def test_association_works(self, model):
mod, conf = model
opt = CORDA(mod, conf, met_prod="C ->")
need = opt.associated(["EX_CORDA_0"])
solutions = (["EX_A", "r1"], ["EX_B", "r2"])
assert list(need) in solutions
def test_init_works(self, large):
opt = CORDA(*large)
assert len(opt.conf) > 0
def test_association_work(self, large):
opt = CORDA(*large)
need = opt.associated(["r60"])
assert len(need) > 0
def test_performance_metrics(self, large):
opt = CORDA(*large)
opt.build()
assert "reconstruction complete" in str(opt)
assert "/60" in str(opt)
def test_association_works(self, model):
mod, conf = model
opt = CORDA(mod, conf, met_prod="C ->")
need = opt.associated(["EX_CORDA_0"])
solutions = (["EX_A", "r1"], ["EX_B", "r2"])
assert list(need) in solutions
def _():
opt = CORDA(mod, conf)
opt.build()
def test_association_work(self, large):
opt = CORDA(*large)
need = opt.associated(["r60"])
assert len(need) > 0