GECKO 3.2.2 #388
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GECKO 3.2.2 #388
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* doc: README.md MATLAB badge * fix: setKcatForReactions correct source field * feat: sensitivityTuning note of preTuneKcat * doc: adapterTemplate set reviewed to false by default allow for more uniprot protein matches * fix: update tutorial ecYeastGEM.yml * doc: clarify params.enzyme_comp in model adapter
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* fix: compatible with next RAVEN release * fix: rename anaerobicModel A yeast-GEM-specific script that ideally should be refactored. For now, just rename to avoid conflict with the function in yeast-GEM repository
* feat: alternative path of DLKcat in/output * fix: avoid double output with printOrange function * fix: remove mentions of Gitter * doc: makeEcModel informative error noUniprof * fix: check RAVEN version
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sensitivityTuningmodifies a kcat value, it will now be indicated inmodel.ec.sourceas 'sensitivityTuning', and the previous kcat value and source will be kept in themodel.ec.notesfield aspreTuneKcat=*value* | source:*original source*. If the kcat value had been subjected tosenstivityTuningbefore, then the notes field will remain unchanged, so repeated runs ofsensitivityTuningwill not overwrite the notes.runDLKcatsupport alternative paths and names of the DLKcat.tsv file (solves runDLKcat(): use DLKcat.tsv in a different directory #392) .obj.params.uniprot.reviewedparameter in theadapterTemplateis set tofalse, to increase the number of matching proteins.model.ec.sourceentry after runningsetKcatForReactionshas been corrected to 'setKcatForReactions'.README.md.obj.params.enzyme_compin model adapter (solves GECKO Model Adapter. Is it possible to define more than one compartment with the parameter 'obj.params.enzyme_comp' ? #386).Instructions 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.