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| name: Test metabolic tasks | ||
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| on: [push, pull_request] | ||
| on: [push] | ||
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| jobs: | ||
| check-metabolictasks: | ||
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| This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the gene essentiality test: | ||
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| <pre> | ||
| {TEST_RESULTS} | ||
| </pre> | ||
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| > _Note: In the case of multiple test runs, this post will be edited._ |
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| This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the [MACAW](https://github.com/Devlin-Moyer/macaw) test: | ||
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| <pre> | ||
| {TEST_RESULTS} | ||
| </pre> | ||
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| This and a more detailed output from MACAW are also committed to `data/macawResults/`. | ||
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| > _Note: In the case of multiple test runs, this post will be edited._ |
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| Original file line number | Diff line number | Diff line change |
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| This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the gene essentiality test: | ||
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| <pre> | ||
| {TEST_RESULTS} | ||
| </pre> | ||
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| > _Note: In the case of multiple test runs, this post will be edited._ |
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| name: Check gene essentiality with Hart 2015 | ||
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| on: | ||
| pull_request: | ||
| branches: | ||
| - "main" | ||
| - "develop" | ||
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| jobs: | ||
| check-metabolictasks: | ||
| runs-on: self-hosted | ||
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| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
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| - name: Fetch RAVEN | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| repository: "SysBioChalmers/RAVEN" | ||
| path: "RAVEN" | ||
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| - name: Run gene essentiality | ||
| id: essentiality | ||
| run: > | ||
| TEST_RESULTS=$(/usr/local/bin/matlab -batch | ||
| "warning('off', 'MATLAB:rmpath:DirNotFound'); | ||
| rmpath(genpath('/home/m/ecModels-dependencies/RAVEN')); | ||
| rmpath(genpath('/home/m/actions-runner')); | ||
| addpath(genpath('.')); | ||
| setRavenSolver('gurobi'); | ||
| ihuman = readYAMLmodel('model/Human-GEM.yml'); | ||
| taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); | ||
| [~, eGenes] = evalc('estimateEssentialGenes(ihuman, ''Hart2015_RNAseq.txt'', taskStruct);'); | ||
| output = transpose(evaluateHart2015Essentiality(eGenes)); | ||
| fid = fopen('data/testResults/gene-essential.csv','w'); | ||
| fprintf(fid,[repmat('%s,',1,9) '%s\n'],output{:,1}); | ||
| fprintf(fid,['%s,%d,%d,%d,%d' repmat(',%.4g',1,5) '\n'],output{:,2:end}); | ||
| fclose(fid); | ||
| disp(cell2table(transpose(output(:,2:end)),'VariableNames',output(:,1)));") && | ||
| echo "$TEST_RESULTS" && | ||
| PARSED_RESULTS="${TEST_RESULTS//$'\n'/'<br>'}" && | ||
| PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}" && | ||
| echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT | ||
| - name: Mention PR# in README.md | ||
| env: | ||
| PR_NUMBER: ${{ github.event.number }} | ||
| run: sed -i -e "s/[[:digit:]]\{3,4\}\*\* (gene /$PR_NUMBER\*\* (gene /" data/testResults/README.md | ||
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| - name: Update local branch before committing changes | ||
| env: | ||
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | ||
| run: | | ||
| git stash | ||
| git fetch | ||
| git checkout $BRANCH_NAME | ||
| if git stash list | grep -q 'stash@{'; then | ||
| git stash pop | ||
| fi | ||
| - name: Auto-commit results | ||
| uses: stefanzweifel/git-auto-commit-action@v5 | ||
| with: | ||
| commit_user_name: memote-bot | ||
| commit_message: "chore: add gene essentiality test result" | ||
| file_pattern: data/testResults/* | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| PR_NUMBER: ${{ github.event.number }} | ||
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| - name: Post comment | ||
| uses: NejcZdovc/comment-pr@v2 | ||
| with: | ||
| file: "commentGeneEssential.md" | ||
| identifier: "GITHUB_COMMENT_GENE" | ||
| env: | ||
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | ||
| TEST_RESULTS: ${{steps.essentiality.outputs.results}} | ||
| GH_ACTION_RUN: ${{github.run_id}} |
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| name: Run macaw tests | ||
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| on: [pull_request] | ||
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| jobs: | ||
| macaw-tests: | ||
| runs-on: ubuntu-latest | ||
| timeout-minutes: 60 | ||
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| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
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| - name: Test checkout | ||
| run: ls -la && cd code && ls -la | ||
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| - name: Set up Python 3 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.10" | ||
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| - name: Install macaw | ||
| run: pip install git+https://github.com/Devlin-Moyer/macaw.git@main numpy==1.26.4 | ||
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| - name: Run macaw | ||
| id: macaw-run | ||
| run: | | ||
| TEST_RESULTS=$(python code/test/macawTests.py) | ||
| echo $TEST_RESULTS | ||
| PARSED_RESULTS="${TEST_RESULTS//$'\n'/'<br>'}" | ||
| PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}" | ||
| echo $PARSED_RESULTS | ||
| echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT | ||
| printf "$TEST_RESULTS" > data/testResults/macaw_summary.md | ||
| - name: Mention PR# in README.md | ||
| env: | ||
| PR_NUMBER: ${{ github.event.number }} | ||
| run: sed -i -e "s/[[:digit:]]\{3,4\}\*\* (MACAW)/$PR_NUMBER\*\* (MACAW)/" data/testResults/README.md | ||
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| - name: Update local branch before committing changes | ||
| env: | ||
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | ||
| run: | | ||
| git stash | ||
| git fetch | ||
| git checkout $BRANCH_NAME | ||
| if git stash list | grep -q 'stash@{'; then | ||
| git stash pop | ||
| fi | ||
| - name: Auto-commit results | ||
| uses: stefanzweifel/git-auto-commit-action@v4 | ||
| with: | ||
| commit_user_name: memote-bot | ||
| commit_message: "chore: add macaw test result" | ||
| file_pattern: data/testResults/* | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| PR_NUMBER: ${{ github.event.number }} | ||
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| - name: Post comment | ||
| uses: NejcZdovc/comment-pr@v2 | ||
| with: | ||
| file: "commentMacaw.md" | ||
| identifier: "GITHUB_COMMENT_MACAW" | ||
| env: | ||
| GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} | ||
| TEST_RESULTS: ${{steps.macaw-run.outputs.results}} | ||
| GH_ACTION_RUN: ${{github.run_id}} | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,6 +1,6 @@ | ||
| name: Test YAML conversion | ||
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| on: [push, pull_request] | ||
| on: [push] | ||
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| jobs: | ||
| yaml-conversion: | ||
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| name: YAML validation | ||
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| on: [push, pull_request] | ||
| on: [push] | ||
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| jobs: | ||
| yaml-validation: | ||
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| import cobra | ||
| from macaw.main import dead_end_test, duplicate_test | ||
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| model = cobra.io.load_yaml_model("model/Human-GEM.yml") | ||
| (dead_end_results, dead_end_edges) = dead_end_test(model) | ||
| (duplicate_results, duplicate_edges) = duplicate_test(model) | ||
| output = dead_end_results.merge(duplicate_results) | ||
| output.to_csv('data/testResults/macaw_results.csv', index = False) |
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| # Test results | ||
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| The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. | ||
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| The test results shown here were obtained by the GitHub Actions run in **PR #675** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. | ||
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| ### MACAW: `dead_end_test` | ||
| Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. | ||
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| ### MACAW: `duplicate_test` | ||
| Identifies sets of reactions that may be duplicates of each other because they: | ||
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| - Involve exactly the same metabolites with exactly the same stoichiometric coefficients (but potentially different associated genes). | ||
| - Involve exactly the same metabolites, but go in different directions and/or some are reversible and some are not. | ||
| - Involve exactly the same metabolites, but with different stoichiometric coefficients. | ||
| - Represent the oxidation and/or reduction of the same metabolite, but use different electron acceptors/donors from the given list of pairs of oxidized and reduced forms of various electron carriers (e.g. NAD(H), NADP(H), FAD(H2), ubiquinone/ubiquinol, cytochromes). | ||
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| It is possible for a single reaction to fit in multiple of the above categories. There are sometimes cases where sets of reactions that fall into one of the above categories are completely legitimate representations of real biochemistry (e.g. separate irreversible reactions for importing vs exporting the same metabolite because two different transporters encoded by different genes are each responsible for transporting that metabolite in only one direction, enzymes that can use NAD(H) or NADP(H) interchangeably to catalyze the same redox reaction), but reactions that meet these criteria are generally worth close examination to ensure that they should actually all exist as separate reactions. | ||
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| ### Cell-line specific gene essentiality | ||
| Evaluate gene essentiality predictions in 5 cell-line specific GEMs with experimental fitness data gathered from the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015). | ||
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| Cell-line specific GEMs are constructed with tINIT2 for DLD1, GBM, HCT116, HeLa and RPE1 cell lines. Then, the `metabolicTasks_Essential.txt` list of tasks is used to identify essential genes in each of these models. The predicted gene essentiality is compared to results from a high-throughput CRISPR-Cas9 screen for identifying genes that affect fitness. Only the summary statistics of this comparison are kept. |
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| cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC | ||
| DLD1,36,2185,59,279,0.8679,0.1143,0.9737,0.1756,0.1529 | ||
| GBM,34,2165,61,298,0.8597,0.1024,0.9726,0.1593,0.1333 | ||
| HCT116,46,2207,53,309,0.8616,0.1296,0.9765,0.2026,0.1905 | ||
| HELA,30,2263,69,254,0.8765,0.1056,0.9704,0.1567,0.124 | ||
| RPE1,14,2204,81,259,0.8671,0.05128,0.9646,0.07609,0.02585 | ||
| all,7,2408,92,109,0.9232,0.06034,0.9632,0.06512,0.0254 |
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