GECKO 3.1.2 #358
Merged
GECKO 3.1.2 #358
Conversation
This file contains 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
* fix: FSEOF to 0.9 of teorethical max prod * refactor: switch force objetive to target * fix: remove unnecesary function * fix: update input arguments * fix: temporal solution k-score * refactor: FSEOF * feat: add gene essentiality to FSEOF * fix: file writing * feat: add cutoff based on quantile * feat: report target transport reactions * refactor: add cutoff for essentiality * fix: bug identifying gene essentiality
|
This PR has been automatically tested with GH Actions. Here is the output of the tests:
|
ae-tafur
approved these changes
Dec 1, 2023
* move installation instructions to wiki * GECKOInstaller checks for latest GECKO version * fix: prevent duplications in protein pseudometabolites * minor fixes * doc: update documentation * doc: swap gitter for GitHub Discussions * fix: correct link to upgrade instructions
|
I'll also resolve #348 and push to |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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:
makeEcModelprevent duplicated protein pseudometabolitesapplyKcatConstraintsoccassionally fills S-matrix with NaN in light ecModels (solves bug: applyKcatConstraints may give NaN in S-matrix of light ecModel #344)calculateFfactorhandle data from PAXdb if the taxonomic ID is not 4 digits long (solves bug: correctly parse PaxDB if taxonomic ID > 4 digits #345)runDLKcatcorrectly handlesparam.pathif the folder name has spaces (solves error: DLKcat Docker invalid reference format error #351)loadDatabasesthrows error if duplicate protein IDs are foundgetSubsetEcModelrequires bothbigEcModelandsmallGEMto have derived from the same starting GEM, and will therefore check whether all reactions fromsmallGEMare also present inbigEcModel. (solves bug: full ecHumanGEM has multiple usage reactions for the same proteins #353)HumanGEMAdapter.mecFSEOFfollow the original implementation of FSEOF (PR refactor: FSEOF #356)startGECKOprojectInstructions 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.