Merge pull request LCSB-BioCore#299 from LCSB-BioCore/mo-rm-verbose-u…

…tilities 🪓 Remove `exchange_reactions` Former-commit-id: 75cecb4
laurentheirendt · Jun 6, 2021 · 344aa50 · 344aa50
2 parents a936edd + 5b09ec2
commit 344aa50
Show file tree

Hide file tree

Showing 2 changed files with 0 additions and 73 deletions.
diff --git a/src/base/utils/StandardModel.jl b/src/base/utils/StandardModel.jl
@@ -19,75 +19,6 @@ function atom_exchange(flux_dict::Dict{String,Float64}, model::StandardModel)
     return atom_flux
 end
 
-"""
-    get_exchanges(flux_dict::Dict{String, Float64}; top_n=Inf, ignorebound=_constants.default_reaction_bound, verbose=true)
-
-Display the `top_n` producing and consuming exchange fluxes.
-If `top_n` is not specified (by an integer), then all are displayed.
-Ignores infinite (problem upper/lower bound) fluxes (set with ignorebound).
-When `verbose` is false, the output is not printed out.
-Return these reactions (id => ) in two dictionaries: `consuming`, `producing`
-"""
-function exchange_reactions(
-    flux_dict::Dict{String,Float64},
-    model::StandardModel;
-    top_n = Inf,
-    ignorebound = _constants.default_reaction_bound,
-    verbose = true,
-)
-    consuming = Dict{String,Float64}()
-    producing = Dict{String,Float64}()
-
-    for (k, v) in flux_dict
-        if is_boundary(model.reactions[k])
-            if v < 0 # consuming
-                consuming[k] = v
-            elseif v > 0 # producing
-                producing[k] = v
-            else # no flux
-                continue
-            end
-        end
-    end
-
-    if verbose
-        # Do consuming
-        ks = collect(keys(consuming))
-        vs = [consuming[k] for k in ks]
-        inds = sortperm(vs)
-        n_max = length(ks)
-        println("Consuming fluxes: ")
-        ii = 0 # counter
-        for i in inds
-            if vs[i] > -ignorebound
-                println(ks[i], " = ", round(vs[i], digits = 6))
-                ii += 1
-            end
-            if ii > top_n
-                break
-            end
-        end
-        # Do producing
-        ks = collect(keys(producing))
-        vs = [producing[k] for k in ks]
-        inds = sortperm(vs, rev = true)
-        n_max = length(ks)
-        println("Producing fluxes: ")
-        ii = 0 # counter
-        for i in inds
-            if vs[i] < ignorebound
-                println(ks[i], " = ", round(vs[i], digits = 6))
-                ii += 1
-            end
-            if ii > top_n
-                break
-            end
-        end
-    end
-
-    return consuming, producing
-end
-
 """
     metabolite_fluxes(flux_dict::Dict{String, Float64}, model::StandardModel)
 

diff --git a/test/base/utils/StandardModel.jl b/test/base/utils/StandardModel.jl
@@ -15,10 +15,6 @@
     atom_fluxes = atom_exchange(sol, model)
     @test isapprox(atom_fluxes["C"], -37.1902, atol = 1e-3)
 
-    # exchange trackers
-    consuming, producing = exchange_reactions(sol, model; 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)