def ko_etfl(model):
growth = dict()
gene_ko_config(model)
model.solver.configuration.timeout = 14400
model.growth_reaction.lower_bound = 0.1 * max_growth
# Gene essentiality is a feasibility problem
# /!\ Also, integer 0 will get the reaction number 0 !
# We need to use optlang's symbolic 0
model.objective = optlang.symbolics.Zero
for g in tqdm(model.genes):
with model as model:
if gene_has_associated_enzyme(model, g):
ret = ko_gene(model, g.id)
if ret is None:
# There is no translation associated to this gene
model.logger.warning('There is no translation associated '
'to this gene: {}'.format(g.id))
continue
else:
# default to GPR KO
model.genes.get_by_id(g.id).knock_out()
ret = safe_optim(model)
growth[g.id] = ret
model.growth_reaction.lower_bound = 0
return growth
def ko_etfl(model):
growth = dict()
gene_ko_config(model)
model.growth_reaction.lower_bound = 0.1 * max_growth
model.objective = 0 # Gene essentiality is a feasibility problem
for g in tqdm(model.genes):
with model as model:
ret = ko_gene(model, g.id)
if ret is None:
# There is no translation associated to this gene
model.logger.warning('There is no translation associated '
'to this gene: {}'.format(g.id))
continue
growth[g.id] = ret
model.growth_reaction.lower_bound = 0
return growth
def test_configs(request):
model = json_loads_model(request.config.cache.get('small_etfl', None))
standard_solver_config(model)
gene_ko_config(model)
growth_uptake_config(model)