finish the remove reactions/metabolites for core+std models

src/reconstruction/CoreModel.jl

@@ -305,110 +305,6 @@ function verify_consistency(
     return (new_reactions, new_metabolites)
 end
 
-"""
-    remove_metabolites(model::CoreModel, mets)
-
-Removes a set of `metabolites` from the `model` of type `CoreModel` and returns
-a new `CoreModel` without those metabolites. Here, `metabolites` can be either a
-string, a vector of strings, an index or a vector of indices. Also removes any
-reactions that have no associated metabolites after the metabolites have been
-removed.
-
-# Example
-```
-model = load_model(CoreModel, "e_coli_core.json")
-
-m1 = remove_metabolites(model, ["glc__D_e", "for_c"])
-m2 = remove_metabolites(model, "glc__D_e")
-m3 = remove_metabolites(model, indexin(["glc__D_e", "for_c"], metabolites(model)))
-m4 = remove_metabolites(model, first(indexin(["glc__D_e"], metabolites(model))))
-```
-"""
-function remove_metabolites(model::CoreModel, mets)
-    mets_to_keep = filter(!in(mets), 1:n_metabolites(model))
-    temp_S = model.S[mets_to_keep, :]
-
-    (I, rxns_to_keep, val) = findnz(temp_S)
-    sort!(rxns_to_keep)
-    unique!(rxns_to_keep)
-    new_S = model.S[mets_to_keep, rxns_to_keep]
-    new_b = model.b[mets_to_keep]
-    new_c = model.c[rxns_to_keep]
-    new_lbs = model.xl[rxns_to_keep]
-    new_ubs = model.xu[rxns_to_keep]
-    new_rxns = model.rxns[rxns_to_keep]
-    new_mets = model.mets[mets_to_keep]
-
-    return CoreModel(new_S, new_b, new_c, new_lbs, new_ubs, new_rxns, new_mets)
-end
-
-function remove_metabolites(model::CoreModel, met::Int)
-    return remove_metabolites(model, [met])
-end
-
-function remove_metabolites(model::CoreModel, met::String)
-    return remove_metabolites(model, [met])
-end
-
-function remove_metabolites(model::CoreModel, mets::Vector{String})
-    met_indices = filter(!isnothing, indexin(mets, metabolites(model)))
-    if isempty(met_indices)
-        return model
-    else
-        return remove_metabolites(model, met_indices)
-    end
-end
-
-"""
-    remove_reactions(m::CoreModel, rxns::Vector{Int})
-
-Removes a set of reactions from a CoreModel.
-Also removes the metabolites not involved in any reaction.
-"""
-function remove_reactions(m::CoreModel, rxns::Vector{Int})
-    rxns_to_keep = filter(!in(rxns), 1:n_reactions(m))
-    temp_s = m.S[:, rxns_to_keep]
-
-    (mets_to_keep, J, val) = findnz(temp_s)
-    sort!(mets_to_keep)
-    unique!(mets_to_keep)
-    new_s = m.S[mets_to_keep, rxns_to_keep]
-    newb = m.b[mets_to_keep]
-    newc = m.c[rxns_to_keep]
-    newxl = m.xl[rxns_to_keep]
-    newxu = m.xu[rxns_to_keep]
-    new_rxns = m.rxns[rxns_to_keep]
-    new_mets = m.mets[mets_to_keep]
-    new_model = CoreModel(new_s, newb, newc, newxl, newxu, new_rxns, new_mets)
-    return new_model
-end
-
-"""
-    remove_reactions(m::CoreModel, rxn::Int)
-"""
-function remove_reactions(m::CoreModel, rxn::Int)
-    return remove_reactions(m, [rxn])
-end
-
-"""
-    remove_reactions(m::CoreModel, rxn::String)
-"""
-function remove_reactions(m::CoreModel, rxn::String)
-    return remove_reactions(m, [rxn])
-end
-
-"""
-    remove_reactions(m::CoreModel, rxns::Vector{String})
-"""
-function remove_reactions(m::CoreModel, rxns::Vector{String})
-    rxn_indices = [findfirst(isequal(name), m.rxns) for name in intersect(rxns, m.rxns)]
-    if isempty(rxn_indices)
-        return m
-    else
-        return remove_reactions(m, rxn_indices)
-    end
-end
-
 @_change_bounds_fn CoreModel Int inplace begin
     isnothing(lower) || (model.xl[rxn_idx] = lower)
     isnothing(upper) || (model.xu[rxn_idx] = upper)
@@ -458,3 +354,89 @@ end
         upper = upper,
     )
 end
+
+@_remove_fn reaction CoreModel Int inplace begin
+    remove_reactions!(model, [reaction_idx])
+end
+
+@_remove_fn reaction CoreModel Int inplace plural begin
+    mask = .! in.(1:n_reactions(model), Ref(reaction_idxs))
+    model.S = model.S[:, mask]
+    model.c = model.c[mask]
+    model.xl = model.xl[mask]
+    model.xu = model.xu[mask]
+    model.rxns = model.rxns[mask]
+    nothing
+end
+
+@_remove_fn reaction CoreModel Int begin
+    remove_reactions(model, [reaction_idx])
+end
+
+@_remove_fn reaction CoreModel Int plural begin
+    n = copy(model)
+    n.S = copy(n.S)
+    n.c = copy(n.c)
+    n.xl = copy(n.xl)
+    n.xu = copy(n.xu)
+    n.rxns = copy(n.rxns)
+    remove_reactions!(model, reaction_idxs)
+    return n
+end
+
+@_remove_fn reaction CoreModel String inplace begin
+    remove_reactions!(model, [reaction_id])
+end
+
+@_remove_fn reaction CoreModel String inplace plural begin
+    remove_reactions!(model, Int.(indexin(reaction_ids, reactions(model))))
+end
+
+@_remove_fn reaction CoreModel String begin
+    remove_reactions(model, [reaction_id])
+end
+
+@_remove_fn reaction CoreModel String begin
+    remove_reactions(model, Int.(indexin(reaction_ids, reactions(model))))
+end
+
+@_remove_fn metabolite CoreModel Int inplace begin
+    remove_metabolites!(model, [metabolite_idx])
+end
+
+@_remove_fn metabolite CoreModel Int plural inplace begin
+    remove_reactions!(model,
+        [ridx for ridx in 1:n_reactions(model) if
+            any(in.(findnz(model.S[:,ridx])[2], Ref(metabolite_idxs)))])
+    mask = .! in.(1:n_metabolites(model), Ref(metabolite_idxs))
+    model.S = model.S[mask, :]
+    model.b = model.b[mask]
+    model.mets = model.mets[mask]
+    return nothing
+end
+
+@_remove_fn metabolite CoreModel Int begin
+    remove_metabolites(model, [metabolite_idx])
+end
+
+@_remove_fn metabolite CoreModel Int plural begin
+    n = deepcopy(model) #everything gets changed anyway
+    remove_metabolites!(model, metabolite_idxs)
+    return n
+end
+
+@_remove_fn metabolite CoreModel String inplace begin
+    remove_metabolites!(model, [metabolite_id])
+end
+
+@_remove_fn metabolite CoreModel String inplace plural begin
+    remove_metabolites!(model, Int.(indexin(metabolite_ids, metabolites(model))))
+end
+
+@_remove_fn metabolite CoreModel String begin
+    remove_metabolites(model, [metabolite_id])
+end
+
+@_remove_fn metabolite CoreModel String begin
+    remove_metabolites(model, Int.(indexin(metabolite_ids, metabolites(model))))
+end

src/reconstruction/StandardModel.jl

@@ -161,7 +161,7 @@ remove_gene!(model::StandardModel, gid::String; knockout_reactions::Bool = false
 @_change_bounds_fn StandardModel String inplace begin
     isnothing(lower) || (model.reactions[rxn_id].lb = lower)
     isnothing(upper) || (model.reactions[rxn_id].ub = upper)
-    nothing
+    return nothing
 end
 
 @_change_bounds_fn StandardModel String inplace plural begin
@@ -181,7 +181,7 @@ end
         n.reactions[i] = copy(n.reactions[i])
     end
     change_bounds!(n, rxn_ids, lower = lower, upper = upper)
-    n
+    return n
 end
 
 @_remove_fn reaction StandardModel String inplace begin
@@ -200,7 +200,7 @@ end
     n = copy(model)
     n.reactions = copy(model.reactions)
     remove_reactions!(n, reaction_ids)
-    n
+    return n
 end
 
 @_remove_fn metabolite StandardModel String inplace begin
@@ -216,6 +216,11 @@ end
         ],
     )
     delete!.(Ref(model.metabolites), metabolite_ids)
+    return nothing
+end
+
+@_remove_fn metabolite StandardModel String begin
+    remove_metabolites(model, [metabolite_id])
 end
 
 @_remove_fn metabolite StandardModel String plural begin
@@ -223,9 +228,5 @@ end
     n.reactions = copy(model.reactions)
     n.metabolites = copy(model.metabolites)
     remove_metabolites!(n, metabolite_ids)
-    n
-end
-
-@_remove_fn metabolite StandardModel String begin
-    remove_metabolites(model, [metabolite_id])
+    return n
 end

src/reconstruction/modifications/generic.jl

@@ -14,16 +14,24 @@ Specifies a model variant that has new bounds set. Forwards arguments to
 """
 with_changed_bounds(args...; kwargs...) = m -> change_bounds(m, args...; kwargs...)
 
+"""
+    with_removed_metabolite(args...; kwargs...)
+
+Specifies a model variant without a certain metabolite. Forwards arguments to
+[`remove_metabolite`](@ref). Intended to be used with [`screen`](@ref).
+"""
+with_removed_metabolite(args...; kwargs...) =
+    m -> remove_metabolite(m, args...; kwargs...)
+
 """
     with_removed_metabolites(args...; kwargs...)
 
-Specifies a model variant without specified metabolites. Forwards arguments to
-[`remove_metabolites`](@ref). Intended to be used with [`screen`](@ref).
+Plural version of [`with_removed_metabolite`](@ref), calls
+[`remove_metabolites`](@ref) internally.
 """
 with_removed_metabolites(args...; kwargs...) =
     m -> remove_metabolites(m, args...; kwargs...)
 
-
 """
     with_added_reactions(args...; kwargs...)
 
@@ -32,10 +40,18 @@ Specifies a model variant with reactions added. Forwards the arguments to
 """
 with_added_reactions(args...; kwargs...) = m -> add_reactions(m, args...; kwargs...)
 
+"""
+    with_removed_reaction(args...; kwargs...)
+
+Specifies a model variant without a certain reaction. Forwards arguments to
+[`remove_reaction`](@ref). Intended to be used with [`screen`](@ref).
+"""
+with_removed_reaction(args...; kwargs...) = m -> remove_reaction(m, args...; kwargs...)
+
 """
     with_removed_reactions(args...; kwargs...)
 
-Specifies a model variant with specified reactions removed. Forwards arguments
-to [`remove_reactions`](@ref). Intended to be used with [`screen`](@ref).
+Plural version of [`with_removed_reaction`](@ref), calls
+[`remove_reactions`](@ref) internally.
 """
 with_removed_reactions(args...; kwargs...) = m -> remove_reactions(m, args...; kwargs...)