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fix: refine animal GEM updating pipeline #692

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merged 4 commits into from
Aug 21, 2023
Merged

fix: refine animal GEM updating pipeline #692

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82b322d
fix: sync geneShortNames field with genes field
haowang-bioinfo Aug 16, 2023
880813a
feat: enable the option to reset biomass equation or not
haowang-bioinfo Aug 16, 2023
80e1a18
Update code/updateAnimalGEM.m
haowang-bioinfo Aug 17, 2023
bb4cc9f
fix: ensure b field in single column
haowang-bioinfo Aug 18, 2023
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5 changes: 4 additions & 1 deletion code/addMetabolicNetwork.m
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Original file line number Diff line number Diff line change
Expand Up @@ -144,8 +144,11 @@
newGenes = setdiff(newGenes, newModel.genes);
end

% append new genes to list of model genes
% append new genes and their names to model
newModel.genes = [newModel.genes; newGenes];
emptyGeneNames = newGenes;
emptyGeneNames(:) = {''};
newModel.geneShortNames = [newModel.geneShortNames; emptyGeneNames];

% add new columns to rxnGeneMat will be updated after the new reactions are added below.
newModel.rxnGeneMat(:, end+1:end+numel(newGenes)) = 0;
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8 changes: 5 additions & 3 deletions code/updateAnimalGEM.m
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@@ -1,4 +1,4 @@
function [animalGEM, speciesSpecNetwork, gapfillNetwork]=updateAnimalGEM(orthologPairs,rxnsToAdd,metsToAdd,modelId)
function [animalGEM, speciesSpecNetwork, gapfillNetwork]=updateAnimalGEM(orthologPairs,rxnsToAdd,metsToAdd,modelId,resetBiomass)
% updateAnimalGEM
% Generate a model by using the Human-GEM as a template and taking into
% account species-specific pathways/reactions
Expand All @@ -11,7 +11,9 @@
% rxnsToAdd the structure of species-specific reactions
% metsToAdd the structure of species-specific metabolites
% modelId model id
%
% resetBiomass reset biomass objective function to "biomass_componenets"
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% which is constituted by generic componenets that
% suppose to occur in a eukaryotic cell (opt, default TRUE)
%
% Output:
% animalGEM an updated animal GEM
Expand Down Expand Up @@ -81,7 +83,7 @@


%% Gap-filling
[animalGEM, gapfillNetwork]=gapfill4EssentialTasks(animalGEM,ihuman);
[animalGEM, gapfillNetwork]=gapfill4EssentialTasks(animalGEM,ihuman,resetBiomass);


%% post-gapfilling procedures
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