Support abricate outputs that use the CARD database#106
Merged
luispedro merged 5 commits intoBigDataBiology:mainfrom Jul 16, 2025
Merged
Support abricate outputs that use the CARD database#106luispedro merged 5 commits intoBigDataBiology:mainfrom
luispedro merged 5 commits intoBigDataBiology:mainfrom
Conversation
Abricate uses an older version of CARD (the March 2020 version). Hence, the CARD sequences used by abricate are directly downloaded from abricate's repository and a seperate mapping table is created for abricate's supported CARD.
…malizer. - get_aro_mapping_table() and map_to_aro() in lib.py have also been modified to support the `abricate-card` database
- Added integration tests as well as normalized ouptuts for abricate.card ARG annotation output files. - Added an abricate-card gene to test_map_to_aro() and test_get_aro_mapping_table_smoke() - Added tests for abricate-card in test_hamronization_normalizer(), test_abricate_normalizer() - Pass in `card` to test_abricate_validation to ensure that AbricateNormalizer doesn't accept any other database other than `abricate_card' or `abricate-card'
…d, and index.md in the docs directory
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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
No description provided.