diff --git a/data/testResults/README.md b/data/testResults/README.md index def0df92..d969776e 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -4,9 +4,9 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: -- **PR #1027** (model QC checks) -- **PR #1027** (MEMOTE) -- **PR #1027** (MACAW and mass/charge balance) +- **PR #1060** (model QC checks) +- **PR #1060** (MEMOTE) +- **PR #1060** (MACAW and mass/charge balance) - **PR #1027** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index 5b8d58da..8aef992a 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -632,7 +632,7 @@ MAR08607,MAM01016c + MAM01975c + 2 MAM02039c --> MAM01974c + MAM02471c,ok,ok,ok, MAR08608,MAM01742c + MAM02630c --> MAM00558c + MAM02039c + MAM02041c,MAM00558c,ok,ok,ok,N/A MAR08609,MAM00559m + 2 MAM02039m + MAM02555m --> MAM02554m + MAM02770m,ok,ok,ok,ok,N/A MAR08610,MAM01802c + MAM02770c --> MAM00559c + MAM01803c + MAM02039c,ok,ok,ok,ok,N/A -MAR08611,MAM01802m + MAM02770m --> MAM00559m + MAM01803m + MAM02039m,ok,ok,ok,ok,N/A +MAR08611,MAM02770m + MAM03103m --> MAM00559m + MAM02039m + MAM03102m,ok,ok,ok,ok,N/A MAR04285,MAM02040m + MAM02552m + MAM02942m --> 2 MAM02039m + MAM02553m + MAM02943m,ok,ok,ok,ok,N/A MAR00457,MAM01371c + MAM01982c --> MAM00913c + MAM01285c + MAM02039c,ok,ok,ok,ok,N/A MAR00460,MAM01371m + MAM01982m --> MAM00913m + MAM01285m + MAM02039m,ok,ok,ok,ok,N/A @@ -2474,7 +2474,7 @@ MAR00001,MAM01570e --> MAM01569e + 77243 MAM02956e,ok,ok,ok,ok,N/A MAR00002,MAM02040e + MAM02956e --> MAM00234e + MAM01807e,ok,ok,ok,ok,N/A MAR00003,MAM00234e + MAM02040e --> MAM00503e + MAM01807e,ok,ok,ok,ok,N/A MAR00005,MAM00503c + MAM02040c --> MAM01807c + MAM01983c,ok,ok,ok,ok,N/A -MAR00449,MAM01802m + MAM02914m --> MAM01690m + MAM01803m,ok,ok,ok,ok,N/A +MAR00449,MAM02914m + MAM03103m --> MAM01690m + MAM03102m,ok,ok,ok,ok,N/A MAR00604,MAM00240c + MAM01371c --> MAM01285c + MAM02039c + MAM02733c,ok,ok,ok,ok,N/A MAR00605,MAM00240c + MAM10007c --> MAM01597c + MAM02958c,ok,ok,ok,ok,N/A MAR00665,MAM02040c + MAM02958c --> MAM00240c + MAM02039c + MAM10005c,ok,ok,ok,ok,N/A @@ -8198,7 +8198,7 @@ MAR01078,MAM03578g <=> MAM03578c,only when going backwards,ok,ok,ok,N/A MAR01083,2 MAM01950g + MAM03584g --> MAM01856g + 2 MAM01948g + 2 MAM02039g,ok,ok,ok,ok,N/A MAR01118,MAM01950g + MAM03092g --> MAM01948g + MAM02039g + MAM03578g,ok,ok,ok,ok,N/A MAR01141,MAM01950g + MAM03095g --> MAM01948g + MAM02039g + MAM03577g,ok,ok,ok,ok,N/A -MAR01169,MAM01802m + MAM02914c --> MAM01690c + MAM01803m,ok,ok,ok,ok,N/A +MAR01169,MAM02914c + MAM03103m --> MAM01690c + MAM03102m,ok,ok,ok,ok,N/A MAR01314,MAM00970c + MAM01371c + MAM02040c --> MAM00970e + MAM01285c + MAM02039c + MAM02751c,ok,ok,ok,MAR07738,N/A MAR01340,MAM01915g <=> MAM01884c,ok,ok,ok,ok,N/A MAR01348,MAM03586c <=> MAM03586g,only when going backwards,ok,ok,ok,N/A diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index 281a485e..5a08959f 100644 --- a/data/testResults/model_qc_summary.md +++ b/data/testResults/model_qc_summary.md @@ -23,17 +23,17 @@ _Duplicate keys (model unloadable) and no growth block the merge; the other rows | Unused metabolites | 0 | 0 | :white_check_mark: | | Unused genes | 0 | 0 | :white_check_mark: | | Malformed cross-references | 0 | 0 | :white_check_mark: | -| Cross-refs inconsistent across compartments | [3](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/qc_annotation_issues.csv) | 0 | :warning: | +| Cross-refs inconsistent across compartments | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/qc_annotation_issues.csv) | 0 | :warning: | ### MACAW and mass/charge balance | Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| Reactions flagged by MACAW dead-end test | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/macaw_results.csv) | 0 | :warning: | -| Reactions flagged as MACAW duplicates | [377](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/macaw_results.csv) | 0 | :warning: | -| Mass-imbalanced reactions | [87](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/balance_results.csv) | 0 | :warning: | -| Charge-imbalanced reactions | [234](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/balance_results.csv) | 0 | :warning: | -| Structure vs formula/charge inconsistencies | [397](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/qc_structure_consistency.csv) | 0 | :warning: | +| Reactions flagged by MACAW dead-end test | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/macaw_results.csv) | 0 | :warning: | +| Reactions flagged as MACAW duplicates | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/macaw_results.csv) | 0 | :warning: | +| Mass-imbalanced reactions | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/balance_results.csv) | 0 | :warning: | +| Charge-imbalanced reactions | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/balance_results.csv) | 0 | :warning: | +| Structure vs formula/charge inconsistencies | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/qc_structure_consistency.csv) | 0 | :warning: | ### Model file and metabolic tasks diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5dc46667..9a80bc1c 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -70454,13 +70454,13 @@ - confidence_score: 0 - !!omap - id: "MAR08611" - - name: "L-proline:(acceptor) oxidoreductase" + - name: "L-proline:ubiquinone oxidoreductase" - metabolites: !!omap - MAM00559m: 1 - - MAM01802m: -1 - - MAM01803m: 1 - MAM02039m: 1 - MAM02770m: -1 + - MAM03102m: 1 + - MAM03103m: -1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000100033 or ENSG00000250799" @@ -101769,12 +101769,12 @@ - confidence_score: 0 - !!omap - id: "MAR00449" - - name: "sn-Glycerol-3-phosphate:(acceptor) 2-oxidoreductase" + - name: "sn-glycerol-3-phosphate:ubiquinone oxidoreductase" - metabolites: !!omap - MAM01690m: 1 - - MAM01802m: -1 - - MAM01803m: 1 - MAM02914m: -1 + - MAM03102m: 1 + - MAM03103m: -1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000115159" @@ -187814,12 +187814,12 @@ - confidence_score: 0 - !!omap - id: "MAR01169" - - name: "Glycerol-3-Phosphate Dehydrogenase (FAD), Mitochondrial" + - name: "Glycerol-3-Phosphate Dehydrogenase (ubiquinone), Mitochondrial" - metabolites: !!omap - MAM01690c: 1 - - MAM01802m: -1 - - MAM01803m: 1 - MAM02914c: -1 + - MAM03102m: 1 + - MAM03103m: -1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000115159"