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fix: prefix whole gene ids in grRules in addIdentifierPrefix - #758
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Gene ids with a dash, dot or colon (5-HT1A) got a prefix at every word start in grRules but one prefix in model.genes, so exportModel failed on models with such genes.
Function test results393 tests 354 ✅ 1m 38s ⏱️ Results for commit 3477970. ♻️ This comment has been updated with latest results. |
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Main improvements in this PR:
addIdentifierPrefix: a gene id containing a dash, dot or colon (for example the fly gene5-HT1A) got aG_prefix at every word start ingrRules(G_5-G_HT1A) but one prefix inmodel.genes(G_5-HT1A).exportModelthen failed incheckModelStructbecause the grRules named genes that were not inmodel.genes. Genes are now prefixed as whole tokens, leavingand,orand brackets alone.tConversion: a gene with a dash and one with a colon keep one prefix and still matchmodel.genes.Found when exporting the regenerated Fruitfly-GEM to SBML (SysBioChalmers/Human-GEM#1141). The full
testing/function_testssuite passes (MATLAB R2024b, Gurobi).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.