feat: export model.ec to Excel (ENZYMES and ENZRXNS sheets)#641
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Function test results202 tests 178 ✅ 36s ⏱️ Results for commit dc92276. ♻️ This comment has been updated with latest results. |
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exportToExcelFormat now writes the contents of the model.ec structure of enzyme-constrained (GECKO) models to two additional sheets: ENZYMES (one row per enzyme: ID, GENE, MW, SEQUENCE, CONC) and ENZRXNS (one row per ec-reaction: ID, KCAT, SOURCE, NOTE, EC-NUMBER, ENZYMES). The ENZRXNS ENZYMES column encodes the subunit stoichiometry from model.ec.rxnEnzMat as 'enzyme:count' pairs (e.g. 'P12345:1;P67890:2'). Export-only: importExcelModel does not read these sheets back; the YAML format remains the round-trippable format for ecModels. NaN molecular weights/concentrations are written as empty cells. writeSheet gains column widths for the two new sheets.
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Main improvements in this PR:
exportToExcelFormatnow writes the contents of themodel.ecstructure of enzyme-constrained (GECKO) models to two additional sheets:ID(UniProt),GENE,MW,SEQUENCE,CONCID,KCAT,SOURCE,NOTE,EC-NUMBER,ENZYMESwriteSheetgains column widths for the two new sheets.The ENZRXNS ENZYMES column encodes the subunit stoichiometry from
model.ec.rxnEnzMatasenzyme:countpairs (e.g.P12345:1;P67890:2), capturing the enzyme-reaction coupling in readable per-row form rather than as a separate matrix.These sheets are export-only:
importExcelModeldoes not read them back. The YAML format (writeYAMLmodel/readYAMLmodel) remains the round-trippable format for ecModels.NaNmolecular weights / concentrations are written as empty cells; thekcat == 0"unassigned" sentinel is kept.A test (
tIO/exportToExcelFormatWritesEcSheets) attaches a minimalmodel.ecto the e. coli test model, exports it, and verifies the two sheets exist and carry the expected content (including theenzyme:countENZYMES column).The Python counterpart (raven-toolbox
export_to_excel) is SysBioChalmers/raven-toolbox#38, and the ecModel-build fix that motivated this is SysBioChalmers/geckopy#32.Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.