Merge pull request #356 from SysBioChalmers/develop

yeast 8.7.1

.github/workflows/memote-history.yml

@@ -8,9 +8,11 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
+        # MEMOTE wants to fetch all branches
         with:
           fetch-depth: 0
 
+
       - name: Set up Python 3
         uses: actions/setup-python@v4
         with:
@@ -19,19 +21,12 @@ jobs:
       - name: Install memote
         run: pip install -r code/requirements/ci-requirements.txt
 
-      - name: Setup variables
-        id: setup
-        run: |
-          echo "::set-output name=history::history_report.html"
-          echo "::set-output name=deployment::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')"
-          echo "::set-output name=other-repo::gh-pages-repo"
-
       - name: Checkout repo for gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: ${{ github.repository }}
-          ref: ${{ steps.setup.outputs.deployment }}
-          path: ${{ steps.setup.outputs.other-repo }}
+          ref: gh-pages
+          path: gh-pages-repo
 
       # - name: Convert model
       #   run: |
@@ -40,21 +35,26 @@ jobs:
 
       - name: Memote short run
         run: |
-          git config --global user.name "memote-bot"
-          memote run --skip-unchanged --solver-timeout 30
+          memote run --ignore-git --skip-unchanged --solver-timeout 30
 
       - name: Compute Memote history on push
         run: |
           # Generate the history report on the deployment branch
-          memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}"
+          git config --global user.name "memote-bot"
+          memote report history --filename="gh-pages-repo/history_report.html"
+
+      - name: Fetch async changes in gh-pages
+        run: |
+          cd gh-pages-repo
+          git pull
 
       - name: Auto-commit results
         uses: stefanzweifel/git-auto-commit-action@v4
         with:
           commit_user_name: memote-bot
           commit_message: "chore: update memote history report"
-          file_pattern: ${{ steps.setup.outputs.history }}
-          branch: ${{ steps.setup.outputs.deployment }}
-          repository: ${{ steps.setup.outputs.other-repo }}
+          file_pattern: history_report.html
+          branch: gh-pages
+          repository: gh-pages-repo
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/memote-release.yml

@@ -24,13 +24,21 @@ jobs:
         with:
           python-version: "3.9"
 
+      - name: Create .env
+        run: touch .env
+
       - name: Install memote
         run: pip install -r code/requirements/requirements.txt
 
       - name: Memote run
         run: |
           memote report snapshot --solver-timeout 30 --filename="gh-pages-repo/release_report.html"
 
+      - name: Fetch async changes in gh-pages
+        run: |
+          cd gh-pages-repo
+          git pull
+
       - name: Auto-commit results
         uses: stefanzweifel/git-auto-commit-action@v4
         with:

.github/workflows/memote-run.yml

@@ -5,21 +5,20 @@ on: pull_request
 jobs:
   memote-run:
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/metabolicatlas/memote-docker:0.13
+      volumes:
+        - ${{ github.workspace }}:/project:rw
+      options: --user root --workdir /project
+
     steps:
       - name: Checkout
         uses: actions/checkout@v3
 
       - name: Create .env
-        run: touch .env
-
-      - name: Memote on PR
-        uses: addnab/docker-run-action@v3
-        with:
-          image: ghcr.io/metabolicatlas/memote-docker:0.13
-          options: -v ${{ github.workspace }}:/opt
-          shell: bash
-          run: |
-            cd /opt
-            pip install -r code/requirements/ci-requirements.txt
-            python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
-            memote run --ignore-git --solver-timeout 30
+        run: |
+          touch .env
+          cd /project
+          pip install -r code/requirements/ci-requirements.txt
+          python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+          memote run --ignore-git --solver-timeout 30

.gitignore

@@ -49,6 +49,7 @@ Thumbs.db
 *.mex*
 *.mlappinstall
 *.mltbx
+*.mat
 helpsearch*/
 
 # Python-related things #
@@ -59,6 +60,7 @@ helpsearch*/
 
 # Non-complying tables and files #
 ##################################
+*.xls*
 *.tab
 *.doc*
 *.ppt*

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_ | 21-Jul-2023 | 8.7.0 | 4131 | 2806 | 1163 |
-
-### Gene essentiality prediction
-
-- Accuracy: 0.881
-- True non-essential genes: 928
-- True essential genes: 63
-- False non-essential genes: 96
-- False essential genes: 38
-
-### Growth prediction
-
-- Correlation coefficient R<sup>2</sup>: 0.842
-
-![Growth curve](growth.png)
+| _Saccharomyces cerevisiae_ | 16-Oct-2023 | develop | 4131 | 2806 | 1163 |
 
 # Installation & usage
 

code/modelCuration/v8_7_1.m

@@ -0,0 +1,53 @@
+% 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');
+
+%% Corrent reaction name r_1024
+rxnIdx = getIndexes(model,'r_1024','rxns');
+model.rxnNames{rxnIdx} = 'sucrose hydrolyzing enzyme';
+
+%% 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