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Merge pull request SysBioChalmers#364 from SysBioChalmers/feat/sortIt…
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feat: sort model alphabetically by identifiers
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@edkerk
edkerk authored Dec 5, 2021
2 parents 2187f7b + 34f8816 commit 96c0c33
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Showing 23 changed files with 2,475 additions and 2,088 deletions.
240 changes: 142 additions & 98 deletions core/permuteModel.m
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Original file line number Diff line number Diff line change
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% permuteModel
% Changes the order of the reactions or metabolites in a model
%
% Input:
% model a model structure
% indexes a vector with the same length as the number of reactions in the
% model which gives the new order of reactions
% type 'rxns' for reactions and 'mets' for metabolites
% indexes a vector with the same length as the number of items in the
% model, which gives the new order of items
% type 'rxns' for reactions, 'mets' for metabolites, 'genes' for
% genes, 'comps' for compartments
%
% newModel an updated model structure
% Output:
% newModel an updated model structure
%
% Usage: newModel=permuteModel(model, indexes, type)

newModel=model;
indexes=indexes(:);

if strcmp(type,'rxns')
if isfield(newModel,'rxns')
newModel.rxns=newModel.rxns(indexes);
end
if isfield(newModel,'lb')
newModel.lb=newModel.lb(indexes);
end
if isfield(newModel,'ub')
newModel.ub=newModel.ub(indexes);
end
if isfield(newModel,'rev')
newModel.rev=newModel.rev(indexes);
end
if isfield(newModel,'c')
newModel.c=newModel.c(indexes);
end
if isfield(newModel,'S')
newModel.S=newModel.S(:,indexes);
end
if isfield(newModel,'rxnNames')
newModel.rxnNames=newModel.rxnNames(indexes);
end
if isfield(newModel,'rxnGeneMat')
newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:);
end
if isfield(newModel,'grRules')
newModel.grRules=newModel.grRules(indexes);
end
if isfield(newModel,'subSystems')
newModel.subSystems=newModel.subSystems(indexes);
end
if isfield(newModel,'eccodes')
newModel.eccodes=newModel.eccodes(indexes);
end
if isfield(newModel,'equations')
newModel.equations=newModel.equations(indexes);
end
if isfield(newModel,'rxnMiriams')
newModel.rxnMiriams=newModel.rxnMiriams(indexes);
end
if isfield(newModel,'rxnComps')
newModel.rxnComps=newModel.rxnComps(indexes);
end
if isfield(newModel,'rxnFrom')
newModel.rxnFrom=newModel.rxnFrom(indexes);
end
if isfield(newModel,'rxnScores')
newModel.rxnScores=newModel.rxnScores(indexes);
end
if isfield(newModel,'rxnNotes')
newModel.rxnNotes=newModel.rxnNotes(indexes);
end
if isfield(newModel,'rxnReferences')
newModel.rxnReferences=newModel.rxnReferences(indexes);
end
if isfield(newModel,'rxnConfidenceScores')
newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes);
end
end

if strcmp(type,'mets')
if isfield(newModel,'mets')
newModel.mets=newModel.mets(indexes);
end
if isfield(newModel,'metNames')
newModel.metNames=newModel.metNames(indexes);
end
if isfield(newModel,'b')
newModel.b=newModel.b(indexes,:);
end
if isfield(newModel,'metComps')
newModel.metComps=newModel.metComps(indexes);
end
if isfield(newModel,'S')
newModel.S=newModel.S(indexes,:);
end
if isfield(newModel,'unconstrained')
newModel.unconstrained=newModel.unconstrained(indexes);
end
if isfield(newModel,'metMiriams')
newModel.metMiriams=newModel.metMiriams(indexes,:);
end
if isfield(newModel,'inchis')
newModel.inchis=newModel.inchis(indexes);
end
if isfield(newModel,'metFormulas')
newModel.metFormulas=newModel.metFormulas(indexes);
end
if isfield(newModel,'metFrom')
newModel.metFrom=newModel.metFrom(indexes);
end
if isfield(newModel,'metCharges')
newModel.metCharges=newModel.metCharges(indexes);
end
switch type
case 'rxns'
if isfield(newModel,'rxns')
newModel.rxns=newModel.rxns(indexes);
end
if isfield(newModel,'lb')
newModel.lb=newModel.lb(indexes);
end
if isfield(newModel,'ub')
newModel.ub=newModel.ub(indexes);
end
if isfield(newModel,'rev')
newModel.rev=newModel.rev(indexes);
end
if isfield(newModel,'c')
newModel.c=newModel.c(indexes);
end
if isfield(newModel,'S')
newModel.S=newModel.S(:,indexes);
end
if isfield(newModel,'rxnNames')
newModel.rxnNames=newModel.rxnNames(indexes);
end
if isfield(newModel,'rxnGeneMat')
newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:);
end
if isfield(newModel,'grRules')
newModel.grRules=newModel.grRules(indexes);
end
if isfield(newModel,'subSystems')
newModel.subSystems=newModel.subSystems(indexes);
end
if isfield(newModel,'eccodes')
newModel.eccodes=newModel.eccodes(indexes);
end
if isfield(newModel,'equations')
newModel.equations=newModel.equations(indexes);
end
if isfield(newModel,'rxnMiriams')
newModel.rxnMiriams=newModel.rxnMiriams(indexes);
end
if isfield(newModel,'rxnComps')
newModel.rxnComps=newModel.rxnComps(indexes);
end
if isfield(newModel,'rxnFrom')
newModel.rxnFrom=newModel.rxnFrom(indexes);
end
if isfield(newModel,'rxnScores')
newModel.rxnScores=newModel.rxnScores(indexes);
end
if isfield(newModel,'rxnNotes')
newModel.rxnNotes=newModel.rxnNotes(indexes);
end
if isfield(newModel,'rxnReferences')
newModel.rxnReferences=newModel.rxnReferences(indexes);
end
if isfield(newModel,'rxnConfidenceScores')
newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes);
end
case 'mets'
if isfield(newModel,'mets')
newModel.mets=newModel.mets(indexes);
end
if isfield(newModel,'metNames')
newModel.metNames=newModel.metNames(indexes);
end
if isfield(newModel,'b')
newModel.b=newModel.b(indexes,:);
end
if isfield(newModel,'metComps')
newModel.metComps=newModel.metComps(indexes);
end
if isfield(newModel,'S')
newModel.S=newModel.S(indexes,:);
end
if isfield(newModel,'unconstrained')
newModel.unconstrained=newModel.unconstrained(indexes);
end
if isfield(newModel,'metMiriams')
newModel.metMiriams=newModel.metMiriams(indexes,:);
end
if isfield(newModel,'inchis')
newModel.inchis=newModel.inchis(indexes);
end
if isfield(newModel,'metFormulas')
newModel.metFormulas=newModel.metFormulas(indexes);
end
if isfield(newModel,'metFrom')
newModel.metFrom=newModel.metFrom(indexes);
end
if isfield(newModel,'metCharges')
newModel.metCharges=newModel.metCharges(indexes);
end
case 'genes'
if isfield(newModel,'genes')
newModel.genes=newModel.genes(indexes);
end
if isfield(newModel,'geneComps')
newModel.geneComps=newModel.geneComps(indexes);
end
if isfield(newModel,'geneMiriams')
newModel.geneMiriams=newModel.geneMiriams(indexes);
end
if isfield(newModel,'geneShortNames')
newModel.geneShortNames=newModel.geneShortNames(indexes);
end
if isfield(newModel,'rxnGeneMat')
newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes);
end
case 'comps'
if isfield(newModel,'comps')
newModel.comps=newModel.comps(indexes);
end
if isfield(newModel,'compNames')
newModel.compNames=newModel.compNames(indexes);
end
if isfield(newModel,'compOutside')
newModel.compOutside=newModel.compOutside(indexes);
end
if isfield(newModel,'compMiriams')
newModel.compMiriams=newModel.compMiriams(indexes);
end
[~,J]=sort(indexes); % The *index* of compartment is used in next fields
if isfield(newModel,'metComps')
[toreplace, bywhat] = ismember(newModel.metComps,1:length(J));
newModel.metComps(toreplace) = J(bywhat(toreplace));
end
if isfield(model,'rxnComps')
[toreplace, bywhat] = ismember(model.rxnComps,1:length(J));
model.rxnComps(toreplace) = J(bywhat(toreplace));
end
if isfield(model,'geneComps')
[toreplace, bywhat] = ismember(model.geneComps,1:length(J));
model.geneComps(toreplace) = J(bywhat(toreplace));
end
end
end
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