-
Notifications
You must be signed in to change notification settings - Fork 8
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #60 from LCSB-BioCore/mva-loopless-fba
Added loopless fba
- Loading branch information
Showing
9 changed files
with
275 additions
and
44 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,158 @@ | ||
| # TODO | ||
| function _get_boundary_reaction_ids(model::StandardModel)::Array{String,1} | ||
| return [i.id for i in model.reactions if length(i.metabolites) == 1] | ||
| end | ||
|
|
||
| function add_cycle_free(fluxes::Dict{String,Float64}) | ||
| return (model, opt_model) -> begin | ||
| v = opt_model[:x] | ||
| old_objective = objective_function(opt_model) | ||
| boundary_ids = _get_boundary_reaction_ids(model) | ||
| min_objectives = zeros(Int64, 1, length(v)) | ||
| for (i, reaction) in enumerate(model.reactions) | ||
| id = reaction.id | ||
| if v[i] in old_objective.terms.keys | ||
| continue | ||
| end | ||
| flux = fluxes[id] | ||
| if id in boundary_ids | ||
| lb = flux | ||
| ub = flux | ||
| elseif flux >= 0 | ||
| lb = max(0, reaction.lb) | ||
| ub = max(flux, reaction.ub) | ||
| min_objectives[i] = 1 | ||
| else | ||
| lb = min(flux, reaction.lb) | ||
| ub = min(0, reaction.ub) | ||
| min_objectives[i] = -1 | ||
| end | ||
| set_bound(i, opt_model; ub=ub, lb=lb) | ||
| end | ||
| @objective(opt_model, Min, dot(min_objectives, v)) | ||
| end | ||
| end | ||
|
|
||
|
|
||
| """ | ||
| add_loopless(args...)::Union{COBREXA.JuMP.Model,Nothing} | ||
| Convert an existing FBA solution to a loopless one. Removes as many loops as possible using the method from [1] | ||
| References: | ||
| [1] CycleFreeFlux: efficient removal of thermodynamically infeasible | ||
| loops from flux distributions. Desouki AA, Jarre F, Gelius-Dietrich | ||
| G, Lercher MJ. Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: | ||
| 10.1093/bioinformatics/btv096. | ||
| """ | ||
| function add_loopless(model::M, opt_model, fluxes::Dict{String,Float64})::Union{COBREXA.JuMP.Model,Nothing} where {M <: MetabolicModel} | ||
| constrain_objective_value(1)(model, opt_model) | ||
| add_cycle_free(fluxes)(model, opt_model) | ||
| COBREXA.JuMP.optimize!(opt_model) | ||
| termination_status(opt_model) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] || return nothing | ||
| return opt_model | ||
| end | ||
|
|
||
| """ | ||
| add_loopless_vec(args...)::Union{Array{Float64,1},Nothing} | ||
| Convert an existing FBA solution to a loopless one. Removes as many loops as possible using the method from [1] | ||
| References: | ||
| [1] CycleFreeFlux: efficient removal of thermodynamically infeasible | ||
| loops from flux distributions. Desouki AA, Jarre F, Gelius-Dietrich | ||
| G, Lercher MJ. Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: | ||
| 10.1093/bioinformatics/btv096. | ||
| """ | ||
| function add_loopless_vec(model::M, opt_model, fluxes::Dict{String,Float64})::Union{Array{Float64,1},Nothing} where {M <: MetabolicModel} | ||
| opt_model = add_loopless(model, opt_model, fluxes) | ||
| termination_status(opt_model) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] || return nothing | ||
| return value.(opt_model[:x]) | ||
| end | ||
|
|
||
| """ | ||
| add_loopless_dict(args...)::Union{Dict{String,Float64},Nothing} | ||
| Convert an existing FBA solution to a loopless one. Removes as many loops as possible using the method from [1] | ||
| References: | ||
| [1] CycleFreeFlux: efficient removal of thermodynamically infeasible | ||
| loops from flux distributions. Desouki AA, Jarre F, Gelius-Dietrich | ||
| G, Lercher MJ. Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: | ||
| 10.1093/bioinformatics/btv096. | ||
| """ | ||
| function add_loopless_dict(model::M, opt_model, fluxes::Dict{String,Float64})::Union{Dict{String,Float64},Nothing} where {M <: MetabolicModel} | ||
| v = add_loopless_vec(model, opt_model, fluxes) | ||
| isnothing(v) && return nothing | ||
| return Dict(zip(reactions(model), v)) | ||
| end | ||
|
|
||
| """ | ||
| loopless_flux_balance_analysis(args...)::Union{COBREXA.JuMP.Model,Nothing} | ||
| Run loopless FBA. Removes as many loops as possible using the method from [1] | ||
| References: | ||
| [1] CycleFreeFlux: efficient removal of thermodynamically infeasible | ||
| loops from flux distributions. Desouki AA, Jarre F, Gelius-Dietrich | ||
| G, Lercher MJ. Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: | ||
| 10.1093/bioinformatics/btv096. | ||
| """ | ||
| function loopless_flux_balance_analysis( | ||
| model::M, | ||
| optimizer; | ||
| modifications=[(model, opt_model) -> nothing], | ||
|
|
||
| )::Union{COBREXA.JuMP.Model,Nothing} where {M <: MetabolicModel} | ||
| opt_model = flux_balance_analysis(model, optimizer, modifications=modifications) | ||
| termination_status(opt_model) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] || return nothing | ||
| fluxes = Dict(zip(reactions(model), value.(opt_model[:x]))) | ||
| return add_loopless( | ||
| model, | ||
| opt_model, | ||
| fluxes, | ||
| ) | ||
| end | ||
|
|
||
| """ | ||
| loopless_flux_balance_analysis_vec(args...)::Union{Array{Float64,1},Nothing} | ||
| Run loopless FBA. Removes as many loops as possible using the method from [1] | ||
| References: | ||
| [1] CycleFreeFlux: efficient removal of thermodynamically infeasible | ||
| loops from flux distributions. Desouki AA, Jarre F, Gelius-Dietrich | ||
| G, Lercher MJ. Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: | ||
| 10.1093/bioinformatics/btv096. | ||
| """ | ||
| function loopless_flux_balance_analysis_vec( | ||
| model::M, | ||
| optimizer; | ||
| modifications=[(model, opt_model) -> nothing], | ||
|
|
||
| )::Union{Array{Float64,1},Nothing} where {M <: MetabolicModel} | ||
| opt_model = loopless_flux_balance_analysis(model, optimizer, modifications=modifications) | ||
| termination_status(opt_model) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] || return nothing | ||
| return value.(opt_model[:x]) | ||
| end | ||
|
|
||
| """ | ||
| loopless_flux_balance_analysis_dict(args...)::Union{Dict{String,Float64},Nothing} | ||
| Run loopless FBA. Removes as many loops as possible using the method from [1] | ||
| References: | ||
| [1] CycleFreeFlux: efficient removal of thermodynamically infeasible | ||
| loops from flux distributions. Desouki AA, Jarre F, Gelius-Dietrich | ||
| G, Lercher MJ. Bioinformatics. 2015 Jul 1;31(13):2159-65. doi: | ||
| 10.1093/bioinformatics/btv096. | ||
| """ | ||
| function loopless_flux_balance_analysis_dict( | ||
| model::M, | ||
| optimizer; | ||
| modifications=[(model, opt_model) -> nothing], | ||
|
|
||
| )::Union{Dict{String,Float64},Nothing} where {M <: MetabolicModel} | ||
| v = loopless_flux_balance_analysis_vec(model, optimizer, modifications=modifications) | ||
| isnothing(v) && return nothing | ||
| return Dict(zip(reactions(model), v)) | ||
| end |
Oops, something went wrong.