GECKO 3.2.0 #381
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GECKO 3.2.0 #381
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…g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.
…g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.
- use fluxes from usageData - give protein pool in usageReport instead of printing to command window
Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes
* fix: loadDatabases error when uniprot dl fails * chore: updateDocumentation * chore: update Actions dependency and trying to fix an issue: https://stackoverflow.com/questions/70435286/resource-not-accessible-by-integration-on-github-post-repos-owner-repo-ac * fix: calculateFfactor read header in paxDB.tsv sometimes, the first # in the file is missed * chore: updateGECKOdoc * fix: runDLKcat parse full paths * fix: applyKcatConstraints if all kcat are zero * fix: getStandardKcat also if enzyme is missing * feat: removeStandardKcat new function * chore: RAVEN release 2.9.1 as dependency
* fix: calculateFfactor can take protData input * feat: constrainEnzConcs keep prot pool draw addresses #375 * fix: updateProtPool obsolete * doc: update full_ecModel for prot_usage rxns * fix: enzymeUsage correct mention of output units solves #376 * doc: updateGECKOdoc * doc: update README.md with protocol change * fix: README.md link
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Main improvements in this PR:
loadDatabasesclarifies what to do if download from UniProt failscalculateFfactorsometimes failed to properly readpaxDB.tsvfilesrunDLKcatshould parseparams.pathas absolute paths to docker (solves runDLKcat() cannot find path to data #378applyKcatConstraintscan handle when all kcat are zerogetStandardKcatshould also assign standard kcat values for reactions that do have a non-emptygrRulesfield, but are not inmodel.ecdue to the genes not matching any of the enzymes in theuniprot.tsvfilecalculateFfactorcan take protData inputenzymeUsagecorrect mention of output units enzyme usage unit #376updateProtPoolis made obsolete new in GECKO 3.2.0: protein usage reactions always draw from protein pool, also when proteomics is integrated #375removeStandardKcatfunction removes all traces ofgetStandardKcathaving modified a modelInstructions on merging this PR:
developas target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved with a merge commit.