Repository navigation
feat: complexPolicy, keepGeneFree and preserveNotes in getModelFromHomology, and no repeated genes - #757
Merged
Conversation
…mology, and no repeated genes complexPolicy decides what happens to an and-linked subunit without an ortholog (flag, keep, drop), keepGeneFree also transfers template reactions without a grRule, and preserveNotes keeps the template's rxnNotes, rxnReferences and rxnConfidenceScores. A gene that several template genes map to appears once in a grRule, and the draft no longer carries the templates' version, date and description. Matches get_model_from_homology in raven-toolbox.
Function test results392 tests 353 ✅ 1m 40s ⏱️ Results for commit 613428d. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Main improvements in this PR:
getModelFromHomology: new name-value options, matchingget_model_from_homologyin raven-toolbox (feat: keep gene-free reactions and template notes in get_model_from_homology, drop duplicate genes CompMetEng/raven-toolbox#166):complexPolicy: what happens to an and-linked subunit without an ortholog.flag(default, current behaviour) keeps it asOLD_MODELID_gene,keepdrops just that subunit,dropdrops the reaction.keepGeneFree(default false): also transfer template reactions without a grRule (spontaneous, transport, exchange, artificial).preserveNotes(default false): keep the template'srxnNotes,rxnReferencesandrxnConfidenceScoresinstead of overwriting them.getModelFromHomology: a gene that several template genes map to now appears once in a grRule (wasA or A or A), and redundant brackets are removed.getModelFromHomology: the draft no longer carries the templates'version,date,descriptionor descriptive annotation.tReconstruction: the three policies, gene-free reactions, kept notes, deduplication and the metadata; an unknown policy errors.Needed by the MATLAB animal GEM generator in Human-GEM (SysBioChalmers/Human-GEM#1141), which with these options gives the same Mouse, Rat, Worm, Fruitfly and Zebrafish models as the Python generator. 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.