feat: add UniProt identifiers

README.md

@@ -33,7 +33,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
 |:-------|:--------------|:------|:------|:----------|:-----|
-| _Saccharomyces cerevisiae_ | 15-Jul-2023 | develop | 4131 | 2806 | 1163 |
+| _Saccharomyces cerevisiae_ | 19-Aug-2023 | develop | 4131 | 2806 | 1163 |
 
 # Installation & usage
 

code/modelCuration/v8_7_1.m

@@ -0,0 +1,49 @@
+% This scripts applies curations to be applied on yeast-GEM release 8.7.0, to
+% get to yeast-GEM release 8.7.1.
+% Indicate which Issue/PR are addressed. If multiple curations are performed
+% before a new release is made, just add the required code to this script. If
+% more extensive coding is required, you can write a separate (generic) function
+% that can be kept in the /code/modelCuration folder. Otherwise, try to use
+% existing functions whenever possible. In particular /code/curateMetsRxnsGenes
+% can do many types of curation.
+
+%% Load yeast-GEM 8.7.0 (requires local yeast-GEM git repository)
+cd ..
+codeDir=pwd();
+model = getEarlierModelVersion('8.7.0');
+model.id='yeastGEM_develop';
+dataDir=fullfile(pwd(),'..','data','modelCuration','v8_7_1');
+cd modelCuration
+
+%% Add Uniprot IDs (PR #349)
+% Gather Uniprot IDs with get_uniprot_id.py that is in dataDir.
+uniprotFile = fullfile(dataDir,'SGD_with_Uniprot.csv');
+fid = fopen(uniprotFile);
+uniprot = textscan(fid,'%q %q %q','Delimiter',',','HeaderLines',1);
+fclose(fid);
+
+% Only keep data for genes that are in the model
+uniprotGenes = uniprot{1,1};
+uniprotIDs   = uniprot{1,3};
+isInModel    = ismember(uniprotGenes,model.genes);
+model        = editMiriam(model,'gene',uniprotGenes(isInModel),'uniprot',uniprotIDs(isInModel),'add');
+
+%% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE.
+% Show some metrics:
+cd(fullfile(codeDir,'modelTests'))
+disp('Run gene essentiality analysis')
+[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model);
+fprintf('Genes in model: %d\n',numel(model.genes));
+fprintf('Gene essentiality accuracy: %.4f\n', new.accuracy);
+fprintf('True non-essential genes: %d\n', numel(new.tp));
+fprintf('True essential genes: %d\n', numel(new.tn));
+fprintf('False non-essential genes: %d\n', numel(new.fp));
+fprintf('False essential genes: %d\n', numel(new.fn));
+fprintf('\nRun growth analysis\n')
+R2=growth(model);
+fprintf('R2 of growth prediction: %.4f\n', R2);
+
+% Save model:
+cd ..
+saveYeastModel(model)
+cd modelCuration