From a36f397c34b114fbbaff8f3a371e0cd109ec54c5 Mon Sep 17 00:00:00 2001
From: st elmo <stelmozors@gmail.com>
Date: Wed, 31 Mar 2021 08:40:15 +0200
Subject: [PATCH] implement suggestions
---
src/io/{matlab_reader.jl => m_reader.jl} | 0
src/io/{matlab_writer.jl => m_writer.jl} | 0
.../{cobraModel.jl => metabolicModel.jl} | 0
test/analysis/fba.jl | 52 +++++++++++++++++++
test/analysis/fba2.jl | 51 ------------------
test/analysis/fva.jl | 33 ++++++++++++
test/analysis/fva2.jl | 32 ------------
7 files changed, 85 insertions(+), 83 deletions(-)
rename src/io/{matlab_reader.jl => m_reader.jl} (100%)
rename src/io/{matlab_writer.jl => m_writer.jl} (100%)
rename src/types/{cobraModel.jl => metabolicModel.jl} (100%)
delete mode 100644 test/analysis/fba2.jl
delete mode 100644 test/analysis/fva2.jl
diff --git a/src/io/matlab_reader.jl b/src/io/m_reader.jl
similarity index 100%
rename from src/io/matlab_reader.jl
rename to src/io/m_reader.jl
diff --git a/src/io/matlab_writer.jl b/src/io/m_writer.jl
similarity index 100%
rename from src/io/matlab_writer.jl
rename to src/io/m_writer.jl
diff --git a/src/types/cobraModel.jl b/src/types/metabolicModel.jl
similarity index 100%
rename from src/types/cobraModel.jl
rename to src/types/metabolicModel.jl
diff --git a/test/analysis/fba.jl b/test/analysis/fba.jl
index f4904c029..ccf7c5163 100644
--- a/test/analysis/fba.jl
+++ b/test/analysis/fba.jl
@@ -38,3 +38,55 @@
# rxns = reactions(cp)
# @test all([fluxesDict[rxns[i]] == sol[i] for i in eachindex(rxns)])
end
+
+@testset "Flux balance analysis with CobraModel" begin
+ model = read_model(
+ Downloads.download(
+ "http://bigg.ucsd.edu/static/models/e_coli_core.json",
+ joinpath("data", "e_coli_core.json"),
+ ),
+ )
+ @test length(model.reactions) == 95 # read in correctly
+
+ # FBA
+ biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
+ cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
+ optimizer = Tulip.Optimizer # quiet by default
+ sol = fba(model, optimizer; objective_func = biomass, constraints = cons)
+ pfl = findfirst(model.reactions, "PFL")
+ solmulti = fba(model, optimizer; objective_func = [biomass, pfl], weights = [0.8, 0.2]) # classic flux balance analysis
+
+
+ flux_vec = [sol[rxn.id] for rxn in model.reactions]
+ sol_mapped = map_fluxes(flux_vec, model)
+ @test isapprox(sol_mapped["BIOMASS_Ecoli_core_w_GAM"], 1.0572509997013568, atol = 1e-6)
+ @test isapprox(sol["BIOMASS_Ecoli_core_w_GAM"], 1.0572509997013568, atol = 1e-6)
+ @test !isempty(solmulti)
+
+ sol = fba(model, optimizer; objective_func = biomass)
+
+ # atom tracker
+ atom_fluxes = atom_exchange(sol, model)
+ @test isapprox(atom_fluxes["C"], -37.1902, atol = 1e-3)
+
+ # exchange trackers
+ consuming, producing = exchange_reactions(sol; verbose = false)
+ @test isapprox(consuming["EX_nh4_e"], -4.76532, atol = 1e-3)
+
+ # metabolite trackers
+ consuming, producing = metabolite_fluxes(sol, model)
+ @test isapprox(consuming["atp_c"]["PFK"], -7.47738, atol = 1e-3)
+ @test isapprox(producing["atp_c"]["PYK"], 1.75818, atol = 1e-3)
+
+ # set bounds
+ cbm, v, mb, lbs, ubs = makeOptimizationModel(model, optimizer)
+ glucose_index = model[findfirst(model.reactions, "EX_glc__D_e")]
+ o2_index = model[findfirst(model.reactions, "EX_o2_e")]
+ atpm_index = model[findfirst(model.reactions, "ATPM")]
+ set_bound(glucose_index, lbs, ubs; ub = -1.0, lb = -1.0)
+ @test normalized_rhs(ubs[glucose_index]) == -1.0
+ @test normalized_rhs(lbs[glucose_index]) == 1.0
+ set_bound(o2_index, lbs, ubs; ub = 1.0, lb = 1.0)
+ @test normalized_rhs(ubs[o2_index]) == 1.0
+ @test normalized_rhs(lbs[o2_index]) == -1.0
+end
diff --git a/test/analysis/fba2.jl b/test/analysis/fba2.jl
deleted file mode 100644
index 8d71e752d..000000000
--- a/test/analysis/fba2.jl
+++ /dev/null
@@ -1,51 +0,0 @@
-@testset "Flux balance analysis with CobraModel" begin
- model = read_model(
- Downloads.download(
- "http://bigg.ucsd.edu/static/models/e_coli_core.json",
- joinpath("data", "e_coli_core.json"),
- ),
- )
- @test length(model.reactions) == 95 # read in correctly
-
- # FBA
- biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
- cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
- optimizer = Tulip.Optimizer # quiet by default
- sol = fba(model, optimizer; objective_func = biomass, constraints = cons)
- pfl = findfirst(model.reactions, "PFL")
- solmulti = fba(model, optimizer; objective_func = [biomass, pfl], weights = [0.8, 0.2]) # classic flux balance analysis
-
-
- flux_vec = [sol[rxn.id] for rxn in model.reactions]
- sol_mapped = map_fluxes(flux_vec, model)
- @test isapprox(sol_mapped["BIOMASS_Ecoli_core_w_GAM"], 1.0572509997013568, atol = 1e-6)
- @test isapprox(sol["BIOMASS_Ecoli_core_w_GAM"], 1.0572509997013568, atol = 1e-6)
- @test !isempty(solmulti)
-
- sol = fba(model, optimizer; objective_func = biomass)
-
- # atom tracker
- atom_fluxes = atom_exchange(sol, model)
- @test isapprox(atom_fluxes["C"], -37.1902, atol = 1e-3)
-
- # exchange trackers
- consuming, producing = exchange_reactions(sol; verbose = false)
- @test isapprox(consuming["EX_nh4_e"], -4.76532, atol = 1e-3)
-
- # metabolite trackers
- consuming, producing = metabolite_fluxes(sol, model)
- @test isapprox(consuming["atp_c"]["PFK"], -7.47738, atol = 1e-3)
- @test isapprox(producing["atp_c"]["PYK"], 1.75818, atol = 1e-3)
-
- # set bounds
- cbm, v, mb, lbs, ubs = makeOptimizationModel(model, optimizer)
- glucose_index = model[findfirst(model.reactions, "EX_glc__D_e")]
- o2_index = model[findfirst(model.reactions, "EX_o2_e")]
- atpm_index = model[findfirst(model.reactions, "ATPM")]
- set_bound(glucose_index, lbs, ubs; ub = -1.0, lb = -1.0)
- @test normalized_rhs(ubs[glucose_index]) == -1.0
- @test normalized_rhs(lbs[glucose_index]) == 1.0
- set_bound(o2_index, lbs, ubs; ub = 1.0, lb = 1.0)
- @test normalized_rhs(ubs[o2_index]) == 1.0
- @test normalized_rhs(lbs[o2_index]) == -1.0
-end
diff --git a/test/analysis/fva.jl b/test/analysis/fva.jl
index 142e5f9b4..1bb309d43 100644
--- a/test/analysis/fva.jl
+++ b/test/analysis/fva.jl
@@ -59,3 +59,36 @@ end
]
rmprocs(pids)
end
+
+@testset "Flux variability analysis with CobraModel" begin
+ model = read_model(
+ Downloads.download(
+ "http://bigg.ucsd.edu/static/models/e_coli_core.json",
+ joinpath("data", "e_coli_core.json"),
+ ),
+ )
+ @test length(model.reactions) == 95 # read in correctly
+
+ biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
+ pfl = findfirst(model.reactions, "PFL")
+
+ # FVA
+ optimizer = Tulip.Optimizer
+ atts = Dict("IPM_IterationsLimit" => 500)
+ cons = Dict("EX_glc__D_e" => (-10.0, -10.0))
+ fva_max, fva_min =
+ fva(model, optimizer; objective_func = biomass, solver_attributes = atts)
+ fva_max2, fva_min2 = fva(
+ model,
+ optimizer;
+ objective_func = [biomass, pfl],
+ weights = [0.5, 0.5],
+ constraints = cons,
+ )
+ @testset "FVA" begin
+ @test isapprox(fva_max["PDH"]["PDH"], 9.338922420065819, atol = 1e-6)
+ @test isapprox(fva_min["PDH"]["PDH"], 9.270274952732315, atol = 1e-6)
+ @test !isempty(fva_max2)
+ @test !isempty(fva_min2)
+ end
+end
diff --git a/test/analysis/fva2.jl b/test/analysis/fva2.jl
deleted file mode 100644
index b55acf46e..000000000
--- a/test/analysis/fva2.jl
+++ /dev/null
@@ -1,32 +0,0 @@
-@testset "Flux variability analysis with CobraModel" begin
- model = read_model(
- Downloads.download(
- "http://bigg.ucsd.edu/static/models/e_coli_core.json",
- joinpath("data", "e_coli_core.json"),
- ),
- )
- @test length(model.reactions) == 95 # read in correctly
-
- biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
- pfl = findfirst(model.reactions, "PFL")
-
- # FVA
- optimizer = Tulip.Optimizer
- atts = Dict("IPM_IterationsLimit" => 500)
- cons = Dict("EX_glc__D_e" => (-10.0, -10.0))
- fva_max, fva_min =
- fva(model, optimizer; objective_func = biomass, solver_attributes = atts)
- fva_max2, fva_min2 = fva(
- model,
- optimizer;
- objective_func = [biomass, pfl],
- weights = [0.5, 0.5],
- constraints = cons,
- )
- @testset "FVA" begin
- @test isapprox(fva_max["PDH"]["PDH"], 9.338922420065819, atol = 1e-6)
- @test isapprox(fva_min["PDH"]["PDH"], 9.270274952732315, atol = 1e-6)
- @test !isempty(fva_max2)
- @test !isempty(fva_min2)
- end
-end
--
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