Unverified Commit 4c3b1f3c authored by St. Elmo's avatar St. Elmo
Browse files

community tests done

parent f1444f5d
@testset "Small model join" begin
model_path = download_data_file(
"http://bigg.ucsd.edu/static/models/e_coli_core.json",
joinpath("data", "e_coli_core.json"),
......@@ -46,36 +45,39 @@ end
"7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
)
m1 = load_model(CoreModel, core_json)
m2 = load_model(CoreModel, iJO1366_mat)
m1 = load_model(core_json)
m2 = load_model(iJO1366_mat)
boundary_rxn_ids, boundary_met_ids = all_boundaries(m2)
exchange_rxn_ids = filter(startswith("EX_"), boundary_rxn_ids)
exchange_met_ids = filter(endswith("_e"), boundary_met_ids)
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ec_iML1515_core_75p37M"]
community = COBREXA.join([m1, m2], exchange_rxn_ids, exchange_met_ids; add_biomass_objective=true, biomass_ids=biomass_ids)
exchange_rxn_ids, exchange_met_ids = all_boundaries(community)
exchange_rxn_ids = filter(startswith("EX_"), exchange_rxn_ids)
exchange_met_ids = filter(endswith("_e"), exchange_met_ids)
boundary_rxn_ids, boundary_met_ids = all_boundaries(m2)
exchange_rxn_ids = filter(startswith("EX_"), boundary_rxn_ids)
exchange_met_ids = filter(endswith("_e"), boundary_met_ids)
env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
m2_ex_inds = indexin(exchange_rxn_ids, reactions(m2))
community.xl[env_ex_inds] .= m2.xl[m2_ex_inds]
community.xu[env_ex_inds] .= m2.xu[m2_ex_inds]
biomass_ids = ["BIOMASS_Ecoli_core_w_GAM", "BIOMASS_Ec_iJO1366_core_53p95M"]
biomass_metabolite_inds = indexin(["Core1_BIOMASS_Ecoli_core_w_GAM", "Core2_BIOMASS_Ecoli_core_w_GAM"], metabolites(community))
biomass_metabolite_inds = indexin(["species_1_BIOMASS_Ecoli_core_w_GAM", "species_2_BIOMASS_Ec_iML1515_core_75p37M"], metabolites(community))
community.S[biomass_metabolite_inds, end] .= -1.0
community.c[end] = 1.0
community.xl[end] = 0.0
community.xu[end] = 1000.0
community = COBREXA.join([m1, m2], exchange_rxn_ids, exchange_met_ids; add_biomass_objective=true, biomass_ids=biomass_ids)
d = flux_balance_analysis_dict(community, Tulip.Optimizer)#; modifications=[change_optimizer_attribute("OutputFlag", 0)])
d["community_biomass"]
env_ex_inds = indexin(exchange_rxn_ids, reactions(community))
m2_ex_inds = indexin(exchange_rxn_ids, reactions(m2))
m1_ex_inds = indexin(exchange_rxn_ids, reactions(m1))
for (env_ex, m2_ex, m1_ex) in zip(env_ex_inds, m2_ex_inds, m1_ex_inds)
m2lb = isnothing(m2_ex) ? 0.0 : m2.xl[m2_ex]
m2ub = isnothing(m2_ex) ? 0.0 : m2.xu[m2_ex]
m1lb = isnothing(m1_ex) ? 0.0 : m1.xl[m1_ex]
m1ub = isnothing(m1_ex) ? 0.0 : m1.xu[m1_ex]
community.xl[env_ex] = m1lb + m2lb # give less overall
community.xu[env_ex] = m1ub + m2ub # give less overall
end
biomass_metabolite_inds = indexin(["species_1_BIOMASS_Ecoli_core_w_GAM", "species_2_BIOMASS_Ec_iJO1366_core_53p95M"], metabolites(community))
community.S[biomass_metabolite_inds, end] .= -1.0
community.c[end] = 1.0
community.xl[end] = 0.0
community.xu[end] = 1000.0
@test size(stoichiometry(community)) == (2203, 3003)
@test isapprox(d["community_biomass"], 0.8, atol = TEST_TOLERANCE,)
end
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