fix: gene field alignment in removeLowScoreGenes#670
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removeLowScoreGenes regenerated model.genes from getGenesFromGrRules, which returns a sorted list, but trimmed the gene-associated fields (geneShortNames, proteins, geneMiriams, geneFrom, geneComps) using a mask in the original gene order. When model.genes was not already sorted, this left every annotation field shifted relative to model.genes, corrupting the gene ID to gene symbol mapping in ftINIT-reconstructed models (removeGenes=true). Retain the remaining genes in their original order and reorder the rxnGeneMat columns to match, so the trimmed annotation fields stay aligned. Fixes #669
edkerk
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Hi, Thank you very much for the quick fix. I tested the latest version from the develop branch, and the gene ID-gene symbol mapping are now correct. The issue seems to be resolved on my end. Kind regards, |
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Main improvements in this PR:
removeLowScoreGenesmisaligned the gene-associated fields (geneShortNames,proteins,geneMiriams,geneFrom,geneComps) relative tomodel.genes, corrupting the gene ID → gene symbol mapping in ftINIT-reconstructed models whenremoveGenes = true(solves Possible gene ID–gene symbol mismatch in ftINIT-reconstructed models #669).Background
removeLowScoreGenesregeneratedmodel.genesfromgetGenesFromGrRules, which returns a sorted list (uniquewithout'stable'), but trimmed the gene-associated annotation fields usingremInd, a logical mask in the originalmodel.genesorder. Whenmodel.geneswas not already sorted (as for Human-GEM–derived models), the annotation fields ended up shifted relative tomodel.genes— exactly the "systematic shift of gene symbols after a certain point" reported in #669. GPRs andrxnGeneMatstayed internally consistent, so only the ID↔symbol mapping was affected.The defect has been present since
removeLowScoreGenes.mwas first moved into RAVEN (May 2022, commit d7b8ba2).Fix
Gene removal never introduces new genes, so the retained set is
model.genes(~remInd). Keep that original order fornewModel.genesand reorder therxnGeneMatcolumns to match, so theremInd-trimmed annotation fields stay aligned.Instructions on merging this PR:
developas target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved as descriped here.