Uniprot #62
Open
Uniprot #62
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
…es classified to species level
… processing and file output format
…d cmsearch outputs
Update infernal container
mberacochea
reviewed
Nov 6, 2024
mberacochea
reviewed
Nov 6, 2024
helpers/database-import-scripts/uniprot/uniprot_sanity_check.py
Outdated
Show resolved
Hide resolved
Adjusted pytest to include the required folders in the pythonpath
mberacochea
approved these changes
Nov 6, 2024
There was a problem hiding this comment.
Good stuff.. I think we should merge this one.
We should start migrating the UniProt, RNAcentral, and file_organizer bash scripts as subworkflows in the pipeline. They are becoming unwieldy. Or as prefect flows... not sure yet.
Another thing that is missing is running the linters, I ran the pre-commits and bumped into loads os warning and errors (we need to fix them). I would do this after the merge in another PR, and probably not now.
Cheers
…prot file generation process
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Outdated suggestions cannot be applied.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.
Added scripts to generate import files for Uniprot. Scripts are executed outside of the main pipeline from file_organisher.sh (to be folded into a future pipeline version). Scripts generate individual Uniprot import files for each species representative genome and one Uniprot metadata file per catalogue.