Sco-GEM 1.3.1 #146
Merged
Sco-GEM 1.3.1 #146
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
- remove 3dmet, cas, kegg.drugs, kegg.orthology - correct metabetx to metanetx - correct a few CHEBI%3A to CHEBI:
- issue #62
- see issue #106, experimental prove
- see issue #104
- move /ComplementaryScripts to /scripts - move scripts specific for Sulheim et al. 2020 to /scripts/sulheim2020
- move /ComplementaryData to /data - move dataspecific for Sulheim et al. 2020 to /data/sulheim2020
- to follow standard-GEM, use /code
- rename /ModelFiles to /model to agree with standard-GEM - move ec-models to /data/sulheim2020/ecmodel/ecmodels as they are specific for Sulheim et al. 2020
- follow standard-GEM
refactor: modified file and folder structure
- not all reactions were properly sorted in previous model file - fix finding SBO terms - cobra 0.20 adds zero charge for metabolite without specified charge
chore: rerun model export
- solves #105 partially
- partial fixes #111
fix: annotations and minor reaction curations
- search for proteome:UP000001973 - edited file to separate genes with identical uniprot ID - gene name information supplemented from: - genome file: https://www.sanger.ac.uk/resources/downloads/bacteria/streptomyces-coelicolor.html - few manual searches in http://strepdb.streptomyces.org.uk/ - few references to papers
Added som space, comments, and rearranged some lines to increase readability of code resolving issue #89
Chore: Add model ID
fix: acetyl-CoA rewiring from iKS1317
* fix: remove remaining glucose anomer reactions * doc: increase readability Added som space, comments, and rearranged some lines to increase readability of code resolving issue #89 * feat: subroutine to load latest master model version * chore: all model changes tracked in code * feat: increaseVersion function - should be run on `master` branch to prepare for a new release * fix: bug in #129 * chore: model I/O Co-authored-by: Snorre Sulheim <[email protected]>
fix: remove remaining glucose anomers
- these pseudorxns are included to be able to activate reactions with unknown redox co-factor (donor or acceptor), but also has the risk to introduce unrealistic loops and unnaturally links NADPH and NADH pools. Reactions will remain in the model to allow enabling the reactions with unknown redox co-factor, while blocking it by default.
* feat: separate requirements.txt for sulheim2020 * doc: update folder-specific README.md
* doc: updated README.md - updated instructions on model usage and contribution * doc: new contributing guidelines - also, template for new curations, as referred to in contributing guidelines. * refactor: v1_3_0.py adjusted to template * fix: incorrect syntax export function * doc: text review Very minor textual changes. Co-authored-by: Snorre Sulheim <[email protected]>
* feat: subroutine to load latest master model version * chore: all model changes tracked in code * feat: increaseVersion function - should be run on `master` branch to prepare for a new release * chore: remove history.rst from devel branch - will be replaced with history.md in master branch only * fix: bug in #129 * chore: model I/O * feat: use dotenv to indicate root of repository * feat: load previous model from version tag e.g. `export.get_earlier_model_unversioned('v1.2.1')` * fix: remove unused gene SCO2529 Co-authored-by: Snorre Sulheim <[email protected]>
# Conflicts: # README.md
* fix: remove invalid refseq ids - starting with WP not valid according to identifiers.org * fix: legacy support get_earlier_model_unversioned - older versions of the model were stored with different folder structure * chore: update travis and memote scripts * chore: gitattributes text=auto for line-endings * refactor: basic_test and growth_test * feat: increaseVersion includes memote score * fix: remove boundary metabolites solves #136 * chore: travis bump python to 3.8
Must be merged with `devel` before Travis is using the changes..
should be mentioned in travis.yml, not travis_deploy.sh
refactor: travis prevent time-out
- travis_wait prevents showing memote output in realtime when running on Travis, making it more difficult to see what is happening. - just skip the test that is taking so long (other tests run in <3 mins, test_inconsistent_min_stoichiometry takes >1.5 h), it failed anyway
fix: revert travis time-out, skip memote test
and print memote output to log, handling of failed Memote run
in `devel`, model stats might not agree with the actual model in this branch. Do not report this in `devel`. NOTE: after next PR to `master`, locally revert this change in README.md before running increaseVersion.py
Curate selected ec-codes and KEGG reaction IDs, and remove unused metabolite g1p_B_c (solves #111)
|
I tried to resolve a merge conflict, and thereby already merged this PR with |
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:
README.mdI hereby confirm that I have:
masteras a target branch (top left drop-down menu)