def test_dict_with_predecessors(self):
model = map_iJR904()
solver = RepresentationRedundantCaseSolver(model, "BiGG")
res = solver.get_targets_to_replace_by_type(300374)
print()
def test_identification_of_biosynthesis_pathway_ecoli(self):
model = map_iJR904()
solver = RepresentationRedundantCaseSolver(model, "BiGG")
reactions, other = solver.identify_biosynthesis_pathway(12)
assert len(reactions) == 10
def redundant_granulator_ecoli():
model = map_iJR904()
components = ["cpd00214", "cpd01080", "cpd03847", "cpd05274"]
solver = RepresentationRedundantCaseSolver(model, "BiGG")
solver.swap_from_generic(["cpd22513", "cpd15649"], components, True, True)
cobra.io.write_sbml_model(solver.model,
"enhanced_model_ecoli_latest_version.xml")
cobra.io.save_json_model(solver.model, "enhanced_model_ecoli.json")
def redundant_granulator_ecoli_all():
start = time.time()
model = map_iJR904()
components = ["cpd00214", "cpd01080", "cpd03847", "cpd05274"]
solver = RepresentationRedundantCaseSolver(model, "BiGG")
solver.swap_from_generic(["cpd22513", "cpd15649"], components, False, True)
cobra.io.write_sbml_model(solver.model, "enhanced_model_ecoli_all.xml")
cobra.io.save_json_model(solver.model, "enhanced_model_ecoli_all.json")
end = time.time()
print("time")
print(end - start)
def test_algae_model(self):
model = cobra.io.read_sbml_model("../models/cvulgaris.xml")
model.objective = model.reactions.get_by_id("e_Biomass__cytop")
r_acyl = model.reactions.get_by_id("e_Fatty_acid__cytop")
reactants = r_acyl.reactants
components_list = []
for reactant in reactants:
if "kegg.compound" in reactant.annotation:
compound = reactant.annotation.get("kegg.compound")
components_list.append(compound)
### confirmar se há alguma reação com fatty acid
solver = RepresentationRedundantCaseSolver(model, "KEGG")
# components = ["lgnc","arach","C06427","clpnd"]
solver.swap_from_generic(["C00422", "C06037"], components_list, True)
cobra.io.write_sbml_model(model, "very_nice_algae_model.xml")
def redundant_granulator_ecoli_without_components_isa_reactions_for_all():
model = map_iJR904()
components = ["cpd00214", "cpd03847", "cpd05274", "cpd25615", "cpd05237"]
solver = RepresentationRedundantCaseSolver(model, "BiGG")
solver.swap_from_generic(["cpd22513", "cpd15649"], components, True)
solver.generateTestISAreactions()
cobra.io.write_sbml_model(
solver.model,
"enhanced_model_ecoli_without_components_isa_reactions_for_all.xml")
cobra.io.save_json_model(solver.model, "enhanced_model_ecoli.json")
def test_components_reactions_solver(self):
model = map_iJR904()
solver = RepresentationRedundantCaseSolver(model, "BiGG")
solver.solve_components_reactions(True)