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* fix: remove non-metabolic genes * fix: remove the actual genes from the model
* Wrong subsystems > Peptide metabolism * Set all rxns irreversible in Peptide metabolism
fix: heneicosanoic acid in metabolicTasks_Full.txt
* feat: PR template specify merge type * feat: clarify location of deprecated IDs lists
* feat: first macaw test scripts * fix: set python version to 3.10 * fix: path to human-GEM repo * fix: correct path to macaw-tests.py * feat: store macaw results * fix: prepare output for comment post * test: storing of output file in new commit * chore: add macaw test result * fix: reorganize macaw output file * fix: write macaw results to correct location * chore: add macaw test result * fix: reset when different workflow are run * chore: add macaw test result * test: reset macaw_results to test workflow commit * chore: add macaw test result * fix: no need to specify action on PR, as push already has the same effect * fix: but run macaw only in PR as output is tracked with PR number, which would not exist with every push * fix: remove link to macaw_results in comment * fix: reference to PR # in README.md --------- Co-authored-by: edkerk <edkerk@users.noreply.github.com>
* fix: removed MAR07799 for being a less-accurate version of MAR00080 * fix: added ATP6AP1 to GPR of MAR00080 so it was still associated with at least one reaction * feat: adds new reference for MAR00080 * chore: add macaw test result * fix: stoichiometry of V-ATPase * chore: add macaw test result --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se> Co-authored-by: edkerk <edkerk@users.noreply.github.com>
* feat: gene essentiality workflow with pr comment * chore: expand workflow targets * fix: add to matlab path * fix: style of macaw summary output * feat: post and store gene essentiality results * fix: model path and allow 2 workflow comments * chore: add macaw test result * fix: use recent RAVEN and gurobi * fix: avoid Penr statistic calculation * fix: missing ) in gene-essentiality.yml * chore: add gene essentiality test result * fix: gene-essentiality.yml output format * fix: location of data/testResults/README.md * chore: add macaw test result * fix: test workflow including branch update * fix: correct git-auto-commit-action@v5 * chore: add gene essentiality test result * fix: run all Hart et al. 2015 tests * fix: missing ) * chore: add gene essentiality test result * fix: only git stash pop if stash exist * fix gene-essentiality ' not " --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se> Co-authored-by: edkerk <edkerk@users.noreply.github.com>
# Conflicts: # .github/workflows/macaw-tests.yml # data/testResults/README.md
feat: store summary macaw results
fix-GPR curation for Xenobiotics metabolism
Fix: GPR curation for Sulfur metabolism
…amino_acid Fix: GPR curation for subsystems related with amino acid
…tabolism Fix: GPR curation for starch and sucrose metabolism
…of_MAR02041_MAR02036 Fix: change the reversibility of MAR02041 and MAR02036
…of-MAR04644 Fix: change the bounds of MAR04644
…for_FN_FP_genes Fix: Curate the GPRs for FN and FP genes
…nsistent_compartments- Fix: curate GPRs with inconsistent compartments
…4387_MAR04386 Fix: curate GPRs of MAR09802, MAR04387 and MAR04386
Fix: curate the GPR of MAR06474
…ene_associated Fix remove rxns without gene associated with them
mihai-sysbio
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Jul 4, 2025
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All looks good, very minor formatting issue in the TSV files.
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@edkerk I guess this is expected to be propagated to Metabolic Atlas (via https://github.com/MetabolicAtlas/data-files)? |
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Main improvements in this PR:
MAR07799and changes the GPR ofMAR00080as discussed in A few reactions that look fishy #348Peptide metabolismto irreversible;Peptide metabolism: MAR11413, MAR11414, MAR11411, MAR06898, MAR06861, MAR06915, MAR07149, MAR07193, MAR08979metabolicTasks_Full.txtas discussed in Update name of heneicosanoic acid in full metabolic task file #828ENSG00000175592) and EGFR (ENSG00000146648)data/macawResults/macawSummary.mdreadYAMLmodel,writeYAMLmodelandexportForGitto load and export Human-GEM;increaseHumanGEMVersionHuman-GEM.txtto showmetNames[comps];getGenesFromGrRulesfunction;README.mdto reflect changes in model I/O functions.developbranch #938developbranch #963MAR05769,MAR05891,MAR05856,MAR05821,MAR05756,MAR05757,MAR05818,MAR05813,MAR05816,MAR05758,MAR05805, MAR05759, MAR05761, MAR05804, MAR05770, MAR05771, MAR05773, MAR05774, MAR05775, MAR05786, MAR05789, MAR05467, MAR06383, MAR06379, MAR05901, MAR05886, MAR05831, MAR05811, MAR05809, MAR05806, MAR05803, MAR05802, MAR05801, MAR05799, MAR05798, MAR05794
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developas a target branch