Merge pull request #324 from SysBioChalmers/develop

yeast 8.6.2

README.md

@@ -33,21 +33,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
 |:-------|:--------------|:------|:------|:----------|:-----|
-| _Saccharomyces cerevisiae_ | 05-Sep-2022 | 8.6.1 | 4063 | 2744 | 1163 |
-
-### Gene essentiality prediction
-
-- Accuracy: 0.881
-- True non-essential genes: 929
-- True essential genes: 63
-- False non-essential genes: 96
-- False essential genes: 38
-
-### Growth prediction
-
-- Correlation coefficient R<sup>2</sup>: 0.865
-
-![Growth curve](growth.png)
+| _Saccharomyces cerevisiae_ | 05-Sep-2022 | develop | 4063 | 2744 | 1160 |
 
 # Installation & usage
 

code/increaseVersion.m

@@ -52,27 +52,29 @@ function increaseVersion(bumpType)
 %Run tests
 cd modelTests
 disp('Running gene essentiality analysis')
-[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(newModel);
+[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model);
 disp('Run growth analysis')
-new.R2=growth(newModel);
+new.R2=growth(model);
+
 saveas(gcf,'../../growth.png');
 
+cd ..
 copyfile('../README.md','backup.md')
 fin  = fopen('backup.md','r');
 fout = fopen('../README.md','w');
 searchStats1 = '^(- Accuracy\: )0\.\d+';
-searchStats2 = '^(- True positive genes\: )\d+';
-searchStats3 = '^(- True negative genes\: )\d+';
-searchStats4 = '^(- False positive genes\: )\d+';
-searchStats5 = '^(- False negative genes\: )\d+';
-newStats1 = ['$1' num2str(new.accuracy)];
+searchStats2 = '^(- True non-essential genes\: )\d+';
+searchStats3 = '^(- True essential genes\: )\d+';
+searchStats4 = '^(- False non-essential genes\: )\d+';
+searchStats5 = '^(- False essential genes\: )\d+';
+newStats1 = ['$1' num2str(new.accuracy,'%.3f')];
 newStats2 = ['$1' num2str(numel(new.tp))];
 newStats3 = ['$1' num2str(numel(new.tn))];
 newStats4 = ['$1' num2str(numel(new.fp))];
 newStats5 = ['$1' num2str(numel(new.fn))];
 
-searchStats6 = '^(- R<sup>2<\/sup>\: )0\.\d+';
-newStats6 = ['$1' num2str(new.R2)];
+searchStats6 = '^(- Correlation coefficient R<sup>2<\/sup>\: )0\.\d+';
+newStats6 = ['$1' num2str(new.R2,'%.3f')];
 
 while ~feof(fin)
     str = fgets(fin);
@@ -105,10 +107,11 @@ function increaseVersion(bumpType)
 delete('backup');
 
 %Include tag and save model:
+disp('Write model files')
 model.id = ['yeastGEM_v' newVersion];
 saveYeastModel(model,true,true,true)   %only save if model can grow
 
-%Check if any file changed (except for history.md and 1 line in yeast-GEM.xml):
+%Check for any unexpected file changes
 [~,diff]   = system('git diff --numstat');
 diff   = strsplit(diff,'\n');
 change = false;
@@ -117,18 +120,20 @@ function increaseVersion(bumpType)
     if length(diff_i) == 3
         switch diff_i{3}
             case 'model/yeast-GEM.xml'
-                %.xml file: 2 lines should be added & 2 lines should be deleted
-                if eval([diff_i{1} ' > 2']) || eval([diff_i{2} ' > 2'])
+                %.xml file: 4 lines should be added & 4 lines should be
+                %deleted (2 with version information, 2 with current date)
+                if eval([diff_i{1} ' > 4']) || eval([diff_i{2} ' > 4'])
                     disp(['NOTE: File ' diff_i{3} ' is changing more than expected'])
                     change = true;
                 end
             case 'model/yeast-GEM.yml'
                 %.yml file: 2 lines should be added & 2 lines should be deleted
+                %(1 with version information, 1 with current date)
                 if eval([diff_i{1} ' > 2']) || eval([diff_i{2} ' > 2'])
                     disp(['NOTE: File ' diff_i{3} ' is changing more than expected'])
                     change = true;
                 end                
-            case 'history.md'
+            case {'history.md','README.md','growth.png','model/yeast-GEM.mat'}
             otherwise
                 disp(['NOTE: File ' diff_i{3} ' is changing'])
                 change = true;                

code/modelCuration/TEMPLATEcuration.m

@@ -18,6 +18,7 @@
 cd ..
 model = getEarlierModelVersion('$VERSION');
 model.id='yeastGEM_develop';
+dataDir=fullfile(pwd(),'..','data','modelCuration','v8.6.1'); %Modify to the correct version
 cd modelCuration
 
 %% Brief description of curation to be performed (PR #xxx) [include correct PR or Issue number]
@@ -50,10 +51,10 @@
 [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('Gene essentiality TP: %d\n', numel(new.tp));
-fprintf('Gene essentiality TN: %d\n', numel(new.tn));
-fprintf('Gene essentiality FP: %d\n', numel(new.fp));
-fprintf('Gene essentiality FN: %d\n', numel(new.fn));
+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);

code/modelCuration/v8_6_1.m

@@ -0,0 +1,42 @@
+% This scripts applies curations to be applied on yeast-GEM release 8.6.1.
+% 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 8.6.1 (requires local yeast-GEM git repository)
+cd ..
+model = getEarlierModelVersion('8.6.1');
+model.id='yeastGEM_develop';
+dataDir=fullfile(pwd(),'..','data','modelCuration','v8.6.1');
+cd modelCuration
+
+%% Correct ATP synthase mitochondrial complex gene associations (PR #323)
+model = changeGrRules(model, 'r_0226', ['Q0080 and Q0085 and Q0130 and ' ...
+        'YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W ' ...
+        'and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and ' ...
+        'YDR322C-A and YPR020W and YOL077W-A'],true);
+model = deleteUnusedGenes(model);
+checkModelStruct(model,true,false)
+
+%% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE.
+% Show some metrics:
+cd ../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