SOURCE CODE ![^]()
end
0035
-0036 rxnIdxs = getIndexes(model,rxnNames,'rxns');
+0036 [~,rxnIdxs] = ismember(rxnNames,model.rxns);
0037
0038 % Check if eccodes are valid
0039 eccodes = model.eccodes;
diff --git a/doc/src/geckomat/utilities/getSubsetEcModel.html b/doc/src/geckomat/utilities/getSubsetEcModel.html
new file mode 100644
index 000000000..86aa614ad
--- /dev/null
+++ b/doc/src/geckomat/utilities/getSubsetEcModel.html
@@ -0,0 +1,116 @@
+
+
+
+ Description of getSubsetEcModel
+
+
+
+
+
+
+
+
+
+
+
+
+
+getSubsetEcModel
+
+
+PURPOSE 
+getSubset_ecModel
+
+SYNOPSIS
+function smallEcModel = getSubsetEcModel(bigEcModel,smallGEM)
+
+DESCRIPTION
+ 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.
+
+ 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)
+
+
+CROSS-REFERENCE INFORMATION
+This function calls:
+
+
+This function is called by:
+
+
+
+
+
+
+SOURCE CODE
+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 % Input:
+0008 % bigEcModel enzyme-constrained version of conventional model of
+0009 % metabolism for a given species
+0010 % smallGEM Reduced model (subset of the general model) for a
+0011 % specific strain (microbes) or cell-line/tissues (mammals)
+0012 %
+0013 % Output:
+0014 % smallEcModel Enzyme-constrained version of the context-specific model
+0015 %
+0016 % Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel)
+0017
+0018 % Check if original bigEcModel contains context-dependent protein constraints
+0019 if any(bigEcModel.lb(startsWith(bigEcModel.rxns,'usage_prot_')) ~= -1000)
+0020 disp(['The bigEcModel is constraint by protein concentrations that are ' ...
+0021 'likely not relevant in the constructed smallEcModel.'])
+0022 end
+0023
+0024 % Remove genes (and associated reactions) that are absent in smallGEM
+0025 genesToRemove = setdiff(bigEcModel.genes,smallGEM.genes);
+0026 smallEcModel = removeGenes(bigEcModel,genesToRemove,true,true,false);
+0027
+0028 % Remove genes from ec-structure
+0029 enzToRemove = ismember(smallEcModel.ec.genes,genesToRemove);
+0030 smallEcModel.ec.genes(enzToRemove) = [];
+0031 smallEcModel.ec.enzymes(enzToRemove) = [];
+0032 smallEcModel.ec.concs(enzToRemove) = [];
+0033 smallEcModel.ec.mw(enzToRemove) = [];
+0034 smallEcModel.ec.sequence(enzToRemove) = [];
+0035 smallEcModel.ec.rxnEnzMat(:,enzToRemove) = [];
+0036
+0037 % Remove any reaction (except prot_ associated) that is absent from smallGEM
+0038 trimRxns = regexprep(smallEcModel.rxns,'_REV|_EXP_\d+','');
+0039 protRxns = startsWith(smallEcModel.rxns,{'usage_prot_','prot_pool_exchange'});
+0040 keepRxns = ismember(trimRxns,smallGEM.rxns) | protRxns;
+0041 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
+0042
+0043 % Remove reactions from ec-structure
+0044 ecRxnsToRemove = ~ismember(smallEcModel.ec.rxns,smallEcModel.rxns);
+0045
+0046 smallEcModel.ec.rxns(ecRxnsToRemove) = [];
+0047 smallEcModel.ec.kcat(ecRxnsToRemove) = [];
+0048 smallEcModel.ec.source(ecRxnsToRemove) = [];
+0049 smallEcModel.ec.notes(ecRxnsToRemove) = [];
+0050 smallEcModel.ec.eccodes(ecRxnsToRemove) = [];
+0051 smallEcModel.ec.rxnEnzMat(ecRxnsToRemove,:) = [];
+0052
+0053 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);
+0054 end
+0055
+
Generated by m2html © 2005
+
+
\ No newline at end of file
diff --git a/doc/src/geckomat/utilities/index.html b/doc/src/geckomat/utilities/index.html
index de2fe64d4..fe07e76dc 100644
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+++ b/doc/src/geckomat/utilities/index.html
@@ -19,7 +19,7 @@ Index for src\geckomat\utilities
Matlab files in this directory:
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. + + 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 % Input: +0008 % bigEcModel enzyme-constrained version of conventional model of +0009 % metabolism for a given species +0010 % smallGEM Reduced model (subset of the general model) for a +0011 % specific strain (microbes) or cell-line/tissues (mammals) +0012 % +0013 % Output: +0014 % smallEcModel Enzyme-constrained version of the context-specific model +0015 % +0016 % Usage: smallEcModel = getSubsetEcModel(smallGEM,bigEcModel) +0017 +0018 % Check if original bigEcModel contains context-dependent protein constraints +0019 if any(bigEcModel.lb(startsWith(bigEcModel.rxns,'usage_prot_')) ~= -1000) +0020 disp(['The bigEcModel is constraint by protein concentrations that are ' ... +0021 'likely not relevant in the constructed smallEcModel.']) +0022 end +0023 +0024 % Remove genes (and associated reactions) that are absent in smallGEM +0025 genesToRemove = setdiff(bigEcModel.genes,smallGEM.genes); +0026 smallEcModel = removeGenes(bigEcModel,genesToRemove,true,true,false); +0027 +0028 % Remove genes from ec-structure +0029 enzToRemove = ismember(smallEcModel.ec.genes,genesToRemove); +0030 smallEcModel.ec.genes(enzToRemove) = []; +0031 smallEcModel.ec.enzymes(enzToRemove) = []; +0032 smallEcModel.ec.concs(enzToRemove) = []; +0033 smallEcModel.ec.mw(enzToRemove) = []; +0034 smallEcModel.ec.sequence(enzToRemove) = []; +0035 smallEcModel.ec.rxnEnzMat(:,enzToRemove) = []; +0036 +0037 % Remove any reaction (except prot_ associated) that is absent from smallGEM +0038 trimRxns = regexprep(smallEcModel.rxns,'_REV|_EXP_\d+',''); +0039 protRxns = startsWith(smallEcModel.rxns,{'usage_prot_','prot_pool_exchange'}); +0040 keepRxns = ismember(trimRxns,smallGEM.rxns) | protRxns; +0041 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true); +0042 +0043 % Remove reactions from ec-structure +0044 ecRxnsToRemove = ~ismember(smallEcModel.ec.rxns,smallEcModel.rxns); +0045 +0046 smallEcModel.ec.rxns(ecRxnsToRemove) = []; +0047 smallEcModel.ec.kcat(ecRxnsToRemove) = []; +0048 smallEcModel.ec.source(ecRxnsToRemove) = []; +0049 smallEcModel.ec.notes(ecRxnsToRemove) = []; +0050 smallEcModel.ec.eccodes(ecRxnsToRemove) = []; +0051 smallEcModel.ec.rxnEnzMat(ecRxnsToRemove,:) = []; +0052 +0053 smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true); +0054 end +0055
