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feat: currencyMets and pseudoreactions handling #313
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ae-tafur
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May 17, 2023
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Looks good
edkerk
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Jul 3, 2023
* fix: getStandardKcat with multiple subSystems * Bug: Fix compatibility running ecFSEOF with GECKO3 models (#301) * reverse: simulateGrowth for ecFSEOF * fix: consistency in terminology * refactor: fluxes for a target * refactor: compatibility to GECKO3 ecFlux_scanning * refactor: add compatibility to GECKO3 * fix: typo * fix: save file type file * fix: filter tolerance * fix: if not carbon uptake have been defined * fix: add toleracne to protein pool * refactor: spaces instead of tabs * fix: function input description * Update src/geckomat/utilities/ecFSEOF/run_ecFSEOF.m --------- Co-authored-by: edkerk <eduardk@chalmers.se> * feat: user defined proteins to ignore in tunning kcats (#306) * fix: applyCustomKcats with customKcats structure input (#304) * fix: applyCustomKcats should allow struct as input * fix: applyCustomKcats correct parse default param * fix: applyCustomKcats * applyCustomKcats doc and tests * refactor: reduce command window output testss * Apply suggestions from code review Co-authored-by: Albert Tafur Rangel <39610893+ae-tafur@users.noreply.github.com> --------- Co-authored-by: Albert Tafur Rangel <39610893+ae-tafur@users.noreply.github.com> * doc: updateProtPool and flexibilizeProtConcs (#297) * fix: updateProtPool avoid correctinf for f twice * doc: flexibilizeProtConcs explain overconstraining * fix: loadProtData measuredProt if NaN exist * doc: protocol.m describe updateProtPool input * fix: updateProtPool simplified new pool calculation * chore: update protocol for updateProtPool --------- Co-authored-by: Mihail Anton <mihail.anton@chalmers.se> * feat: a function that creates a the project structure an adapter class (#312) * feat: create structure project * feat: include empty .keep files --------- Co-authored-by: edkerk <eduardk@chalmers.se> * feat: currencyMets and pseudoreactions handling (#313) * fix: writeDLKcatInput currencyMets handling * fix: filter out pseudoreactions makeEcModel * fix: makeEcModel find pseudoreactions * chore: restructure tutorials (#310) * chore: rename userData to tutorials * chore: move protocol and adapters * chore: keep original in full under blankExample * chore: compact adapters for human and yeast * chore: cleanup protocol for yeast * feat: add a model adapter under blankExample * chore: rename adapter * feat: copy protocol from yeast to human * fix: typo * fix: new folder names in adapters * fix: update paths to tutorials * refactor: model adapter expects full adapter path and extension * fix: file paths for yeast-GEM tutorial * style: protocol in tutorial prints step * chore: rm doc * feat: compress outputs about downloading complexes * fix: full path to adapter in test * fix: full paths for adapters in tests * fix: undo bad path change * chore: remove blankExample, use startGECKOproject * chore: restore yeast-GEM protocol.m content * chore: run through yeast-GEM protocol * feat: simplify ModelAdapterManager commands * fix: allow to set empty default adapter * fix: tests refer to test adapter --------- Co-authored-by: edkerk <eduardk@chalmers.se> * feat: add manually-generated doc for online use * feat: updateGECKOdoc function * chore: update documentation by running updateGECKOdoc() * fix: getStandardKcat and applyKcatConstraints (#320) * fix: getStandardKcat light model standard enzyme In light ecModels, even if standard enzyme is not a pseudo-substrate (it will always use prot_pool instesad), standard enzyme should still be in ecModel.ec.enzyme (and .rxnEnzMat etc.), to calculate MW/kcat. * refactor: applyKcatConstraints simplify light * refactor: getStandardKcat * fix: applyKcatConstraints zero-kcats light ecModel * feat: copyECtoGEM function * fix: minor bugs identified (#316) * fix: use logical vector to construct equations * fix: increase default tolerance * style: typo * style: use standard input names * fix: adaptar default method name * fix: set values under solver tol to zero * feat: run_ecFSEOF check alphaLims parameter --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se> * feat: updates related to tutorials (#319) * feat: new/updated functions around enzyme usage * feat: install and adapter manager * feat: Crabtree plot and data * feat: updated protocol and model file * refactor: rename tutorials full_ and light_ecModel * feat: loadConventionalGEM can load YAML * feat: use progressbar to give time estimates * fix: ecFVA correct number of simulations * feat: sensitivityTuning reports eccodes * feat: fillProtConcs select column from protData * feat: flexibilizeProtConcs sort by highest ratio * feat: plotCrabtree plus graphs * feat: plot light vs full ecModel analysis * feat: GECKOInstaller checks RAVEN version * feat: update of full_ecModel protocol moved progressbar to RAVEN 2.8.2 * fix: getStandardKcat light model standard enzyme In light ecModels, even if standard enzyme is not a pseudo-substrate (it will always use prot_pool instesad), standard enzyme should still be in ecModel.ec.enzyme (and .rxnEnzMat etc.), to calculate MW/kcat. * refactor: applyKcatConstraints simplify light * refactor: getStandardKcat * feat: light_ecModel tutorial overhaul * fix: plot light vs full * fix: applyKcatConstraints zero-kcats light ecModel * feat: copyECtoGEM function * chore: updateDocumentation * fix: full_ecModel/protocol.m step 13 * full_ecModel misc small fixes * fix: full_ecModel/protocol.m step 15 * fix: full_ecModel/protocol.m install instructions * fix: findMetSmiles report success and handle prot_ * fix: full_ecModel customKcat non-funct. protein * fix: plotCrabtree avoid flux minimalization * fix: full_ecModel various minor changes * fix: GECKOInstaller RAVEN dep version bump * fix: full_ecModel and light_ecModel from review * fix: remove unused functions * feat: rerun light_ecModel pipeline * refactor: change vanHoek1998.csv to .tsv * fix: full_ecModel tutorial ecFVA (#321) * fix: remake ecFVA plot with generic plot function * fix: GECKOInstaller ignore doc subfolder * chore: updateGECKOdoc * fix: remove old ecFVA.tsv no purpose to write this file * refactor: speedup fuzzyKcatMatching & getECfromGEM * feat: saveEcModel more logical input * refactor: swap TIFF for PDF * refactor: applyComplexData (#323) * refactor: speed increase applyComplexData * feat: applyComplexData progressbar + code comments * feat: light_ecModel tutorial getSubsetEcModel (#322) * fix: remake ecFVA plot with generic plot function * fix: GECKOInstaller ignore doc subfolder * chore: updateGECKOdoc * fix: remove old ecFVA.tsv no purpose to write this file * fix: getStandardKcat no standard gene in light-ec * fix: light_ecModel until step 29 * feat: getSubsetEcModel + tutorial * feat: parameters format, phylDist.mat file and yeast-GEM.yml (#325) * refactor: rename KEGG params to param.kegg. to param.kegg.geneID * refactor: rename Complex params to param.complex * refactor: rename UniProt params to param.uniprot. * fix: remove unused obj.params entries remnants of GECKO2 * refactor: add _id to uniprot taxonomy * refactor: use taxonomicID from complex portal easier to find than precise species name * feat: use RAVEN's phylDist.mat from RAVEN 2.8.3 includes species names * feat: tutorial yeast-GEM as yaml * feat: yeast-GEM file is for tutorial only * fix: remove unused manualModifications * fix: small fixes * docs: add link to tutorials in README * docs: skip mentioning the required RAVEN version, since it is checked at installation * feat: compare light vs full ecModel (#328) * chore: rerun full_ecModel tutorial * feat: light vs full ecModel comparison * doc: swap step 29 and 30 * chore: rerun light_ecModel tutorial (#331) * chore: rerun full_ecModel tutorial * feat: light vs full ecModel comparison * doc: swap step 29 and 30 * chore: rerun light_ecModel tutorial * refactor: consistent use of isozyme In agreement with manuscript * chore: updateDocumentation * doc: format of warning messages * fix: plotlightVSfull.m handle use of alt solvers * fix: consistent cutoff for low fluxes --------- Co-authored-by: Albert Tafur Rangel <39610893+ae-tafur@users.noreply.github.com> Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
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Main improvements in this PR:
Based on reviewer's comments:
makeEcModel
can use pseudoRxns.tsv to identify pseudoreactionswriteDLKcatInput
only exclude currency metabolites if there are other reactants involved in the reactionI hereby confirm that I have:
develop
as a target branch (top left drop-down menu)