Merge pull request #521 from LCSB-BioCore/tp-grr-coremodel

Gene-reaction rules for CoreModel and CoreModelCoupled #439
LCSB-BioCore · Nov 22, 2021 · 523c6eb · 523c6eb
2 parents 0cb74ae + 94c4361
commit 523c6eb
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Showing 4 changed files with 100 additions and 3 deletions.
diff --git a/src/base/types/CoreModel.jl b/src/base/types/CoreModel.jl
@@ -18,6 +18,7 @@ mutable struct CoreModel <: MetabolicModel
     xu::Vector{Float64}
     rxns::Vector{String}
     mets::Vector{String}
+    grrs::Vector{Maybe{GeneAssociation}}
 
     function CoreModel(
         S::MatType,
@@ -27,14 +28,19 @@ mutable struct CoreModel <: MetabolicModel
         xu::VecType,
         rxns::StringVecType,
         mets::StringVecType,
+        grrs::Vector{Maybe{GeneAssociation}} = Vector{Maybe{GeneAssociation}}(
+            nothing,
+            length(rxns),
+        ),
     )
         all([length(b), length(mets)] .== size(S, 1)) ||
             throw(DimensionMismatch("inconsistent number of metabolites"))
 
-        all([length(c), length(xl), length(xu), length(rxns)] .== size(S, 2)) ||
-            throw(DimensionMismatch("inconsistent number of reactions"))
+        all(
+            [length(c), length(xl), length(xu), length(rxns), length(grrs)] .== size(S, 2),
+        ) || throw(DimensionMismatch("inconsistent number of reactions"))
 
-        new(sparse(S), sparse(b), sparse(c), collect(xl), collect(xu), rxns, mets)
+        new(sparse(S), sparse(b), sparse(c), collect(xl), collect(xu), rxns, mets, grrs)
     end
 end
 
@@ -96,6 +102,31 @@ Return the stoichiometry of reaction at index `ridx`.
 reaction_stoichiometry(m::CoreModel, ridx)::Dict{String,Float64} =
     Dict(m.mets[k] => v for (k, v) in zip(findnz(m.S[:, ridx])...))
 
+"""
+    reaction_gene_association_vec(model::CoreModel)::Vector{Maybe{GeneAssociation}}
+
+Retrieve a vector of all gene associations in a [`CoreModel`](@ref), in the
+same order as `reactions(model)`.
+"""
+reaction_gene_association_vec(model::CoreModel)::Vector{Maybe{GeneAssociation}} = model.grrs
+
+"""
+    reaction_gene_association(model::CoreModel, ridx::Int)::Maybe{GeneAssociation}
+
+Retrieve the [`GeneAssociation`](@ref) from [`CoreModel`](@ref) by reaction
+index.
+"""
+reaction_gene_association(model::CoreModel, ridx::Int)::Maybe{GeneAssociation} =
+    model.grrs[ridx]
+
+"""
+    reaction_gene_association(model::CoreModel, rid::String)::Maybe{GeneAssociation}
+
+Retrieve the [`GeneAssociation`](@ref) from [`CoreModel`](@ref) by reaction ID.
+"""
+reaction_gene_association(model::CoreModel, rid::String)::Maybe{GeneAssociation} =
+    model.grrs[first(indexin([rid], model.rxns))]
+
 """
     Base.convert(::Type{CoreModel}, m::M) where {M <: MetabolicModel}
 
@@ -115,5 +146,8 @@ function Base.convert(::Type{CoreModel}, m::M) where {M<:MetabolicModel}
         xu,
         reactions(m),
         metabolites(m),
+        Vector{Maybe{GeneAssociation}}([
+            reaction_gene_association(m, id) for id in reactions(m)
+        ]),
     )
 end
diff --git a/src/base/types/CoreModelCoupled.jl b/src/base/types/CoreModelCoupled.jl
@@ -108,6 +108,32 @@ function reaction_stoichiometry(m::CoreModelCoupled, ridx)::Dict{String,Float64}
     reaction_stoichiometry(m.lm, ridx)
 end
 
+"""
+    reaction_gene_association_vec(model::CoreModelCoupled)::Vector{Maybe{GeneAssociation}}
+
+Retrieve a vector of gene associations in a [`CoreModelCoupled`](@ref), in the
+same order as `reactions(model)`.
+"""
+reaction_gene_association_vec(model::CoreModelCoupled)::Vector{Maybe{GeneAssociation}} =
+    reaction_gene_association_vec(model.lm)
+
+"""
+    reaction_gene_association(model::CoreModelCoupled, ridx::Int)::Maybe{GeneAssociation}
+
+Retrieve the [`GeneAssociation`](@ref) from [`CoreModelCoupled`](@ref) by reaction
+index.
+"""
+reaction_gene_association(model::CoreModelCoupled, ridx::Int)::Maybe{GeneAssociation} =
+    reaction_gene_association(model.lm, ridx)
+
+"""
+    reaction_gene_association(model::CoreModelCoupled, rid::String)::Maybe{GeneAssociation}
+
+Retrieve the [`GeneAssociation`](@ref) from [`CoreModelCoupled`](@ref) by reaction ID.
+"""
+reaction_gene_association(model::CoreModelCoupled, rid::String)::Maybe{GeneAssociation} =
+    reaction_gene_association(model.lm, rid)
+
 """
     Base.convert(::Type{CoreModelCoupled}, mm::MetabolicModel)
 

diff --git a/test/base/types/CoreModel.jl b/test/base/types/CoreModel.jl
@@ -4,3 +4,16 @@
     @test reaction_stoichiometry(model, "EX_ac_e") == Dict("ac_e" => -1)
     @test reaction_stoichiometry(model, 44) == Dict("ac_e" => -1)
 end
+
+@testset "Conversion from and to StandardModel" begin
+    cm = load_model(CoreModel, model_paths["e_coli_core.mat"])
+
+    sm = convert(StandardModel, cm)
+    cm2 = convert(CoreModel, sm)
+
+    @test Set(reactions(cm)) == Set(reactions(sm))
+    @test Set(reactions(cm)) == Set(reactions(cm2))
+
+    @test reaction_gene_association(sm, reactions(sm)[1]) ==
+          reaction_gene_association(cm, reactions(sm)[1])
+end
diff --git a/test/base/types/CoreModelCoupled.jl b/test/base/types/CoreModelCoupled.jl
@@ -5,3 +5,27 @@
     @test reaction_stoichiometry(model, 44) == Dict("ac_e" => -1)
 
 end
+
+@testset "Conversion from and to StandardModel" begin
+    cm = load_model(CoreModelCoupled, model_paths["e_coli_core.mat"])
+
+    sm = convert(StandardModel, cm)
+    cm2 = convert(CoreModelCoupled, sm)
+
+    @test Set(reactions(cm)) == Set(reactions(sm))
+    @test Set(reactions(cm)) == Set(reactions(cm2))
+
+    @test reaction_gene_association(sm, reactions(sm)[1]) ==
+          reaction_gene_association(cm, reactions(sm)[1])
+
+    @test reaction_gene_association_vec(cm)[1:3] == [
+        [["b3916"], ["b1723"]],
+        [
+            ["b0902", "b0903", "b2579"],
+            ["b0902", "b0903"],
+            ["b0902", "b3114"],
+            ["b3951", "b3952"],
+        ],
+        [["b4025"]],
+    ]
+end