getSubsetEcModel

 getSubset_ecModel
   Generate a context-specific ecModel (strain/cell-line/tissue) by
   mapping reactions and genes from a conventional context-specific GEM to
   a general ecModel (bigEcModel), to yield a context-specific ecModel.

   Both models (bigEcModel and the smallGEM) should have derived from the
   same starting model. If an ecModel with human-GEM 1.15.0 is made
   (yielding the bigEcModel), then human-GEM 1.15.0 should also be the
   basis from which the context-specific GEM (smallGEM) was generated by
   for instance tINIT.
 
 Input:
   bigEcModel  enzyme-constrained version of conventional model of
                  metabolism for a given species
   smallGEM       Reduced model (subset of the general model) for a
                  specific strain (microbes) or cell-line/tissues (mammals)
 
 Output:
   smallEcModel  Enzyme-constrained version of the context-specific model
 
 Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel)

0001 function smallEcModel = getSubsetEcModel(bigEcModel,smallGEM)
0002 % getSubset_ecModel
0003 %   Generate a context-specific ecModel (strain/cell-line/tissue) by
0004 %   mapping reactions and genes from a conventional context-specific GEM to
0005 %   a general ecModel (bigEcModel), to yield a context-specific ecModel.
0006 %
0007 %   Both models (bigEcModel and the smallGEM) should have derived from the
0008 %   same starting model. If an ecModel with human-GEM 1.15.0 is made
0009 %   (yielding the bigEcModel), then human-GEM 1.15.0 should also be the
0010 %   basis from which the context-specific GEM (smallGEM) was generated by
0011 %   for instance tINIT.
0012 %
0013 % Input:
0014 %   bigEcModel  enzyme-constrained version of conventional model of
0015 %                  metabolism for a given species
0016 %   smallGEM       Reduced model (subset of the general model) for a
0017 %                  specific strain (microbes) or cell-line/tissues (mammals)
0018 %
0019 % Output:
0020 %   smallEcModel  Enzyme-constrained version of the context-specific model
0021 %
0022 % Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel)
0023 
0024 % Check if models were derived from the same starting GEM
0025 Rxn_format = regexprep(bigEcModel.rxns,'_REV|_EXP_\d+','');
0026 rxnsDiff = find(~ismember(smallGEM.rxns,Rxn_format));
0027 if numel(rxnsDiff) > 0
0028     dispEM(['While both models should have derived from the same starting ',...
0029             'GEM, the following reactions from smallGEM could not be found ',...
0030             'in bigEcModel:'],true,smallGEM.rxns(rxnsDiff),false);
0031 end
0032 
0033 % Check if original bigEcModel contains context-dependent protein constraints
0034 if any(bigEcModel.lb(startsWith(bigEcModel.rxns,'usage_prot_')) ~= -1000)
0035     printOrange(['WARNING: The bigEcModel is constraint by protein concentrations that are\n' ...
0036                  'likely not relevant in the constructed smallEcModel.\n']);
0037 end
0038 
0039 % Remove genes (and associated reactions) that are absent in smallGEM
0040 genesToRemove  = setdiff(bigEcModel.genes,smallGEM.genes);
0041 % If genesToRemove contains "standard", then remove this entry
0042 if ismember('standard', genesToRemove)
0043     genesToRemove(strcmp(genesToRemove, 'standard')) = [];
0044 end
0045 smallEcModel = removeGenes(bigEcModel,genesToRemove,true,true,false);
0046 
0047 % Remove genes from ec-structure
0048 enzToRemove = ismember(smallEcModel.ec.genes,genesToRemove);
0049 smallEcModel.ec.genes(enzToRemove)       = [];
0050 smallEcModel.ec.enzymes(enzToRemove)     = [];
0051 smallEcModel.ec.concs(enzToRemove)       = [];
0052 smallEcModel.ec.mw(enzToRemove)          = [];
0053 smallEcModel.ec.sequence(enzToRemove)    = [];
0054 smallEcModel.ec.rxnEnzMat(:,enzToRemove) = [];
0055 
0056 % Remove any reaction (except prot_ associated) that is absent from smallGEM
0057 trimRxns = regexprep(smallEcModel.rxns,'_REV|_EXP_\d+','');
0058 protRxns = startsWith(smallEcModel.rxns,{'usage_prot_','prot_pool_exchange'});
0059 keepRxns = ismember(trimRxns,smallGEM.rxns) | protRxns;
0060 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
0061 
0062 % Remove reactions from ec-structure
0063 ecRxnsToRemove = ~ismember(smallEcModel.ec.rxns,smallEcModel.rxns);
0064 
0065 smallEcModel.ec.rxns(ecRxnsToRemove)        = [];
0066 smallEcModel.ec.kcat(ecRxnsToRemove)        = [];
0067 smallEcModel.ec.source(ecRxnsToRemove)      = [];
0068 smallEcModel.ec.notes(ecRxnsToRemove)       = [];
0069 smallEcModel.ec.eccodes(ecRxnsToRemove)     = [];
0070 smallEcModel.ec.rxnEnzMat(ecRxnsToRemove,:) = [];
0071 end
0072