BUG: Add updated megares mappings #87
Merged
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
|
Can we have a check in the code that this doesn't happen again? |
…ed from argnorm's argannot and resfinder mappings
…nloading it for every test
|
Better, but can you (1) prefilter the CSV table that gets put into the test directory so that it only has the entries that actually get tested (5% of the total), (2) also add the code that generates this csv table as part of db construction, (3) add some comments to the test so that when it fails next time, the poor student has a chance to figure out what is going on? |
luispedro
reviewed
Feb 9, 2025
…_mappings` These mappings are aggregated in `construct_megares_mapping.py` and are initiatlly stored in './db_harmonisation/mapping/megares_resfinder_argannot_mapping.tsv`. This is then moved into `./tests/megaes_mappings/`
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Outdated suggestions cannot be applied.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.
These mappings were missed by #79. The
construct_megares_mapping.pyscript depends on other argNorm mappings for a large number of the mappings. While I was rerunningcrude_db_harmonisation.pyfor #79, theconstruct_megares_mapping.pymust have used the older mappings forresfinderandargannotfor ARGs that didn't have to be passed through RGI (which explains why some megares mappings changed but these didn't).