Comments (1)
Aim is to end up with hAMRonization.parse("report.tsv", "abricate")
returning an iterator over hAMRonized formatted AMR result records.
Parser scripts will just use that common interface with CLI handling for ease-of-use afterwards
from hamronization.
Related Issues (20)
- Wrong Docker link HOT 2
- staramr issue HOT 1
- Implementing logging and debug flag to simplify exception messages HOT 2
- help understanding resfinder run HOT 1
- ORF_ID missing once RGI report hAMRonized HOT 1
- RgiIO.py: Typo in line 79 HOT 1
- Fix issue of very similar runs falsely combining results in summary
- Genetic_variation_type HOT 1
- hamronize summarize - local variable 'parsed_report' reference before assignment HOT 3
- Flag overlapping ranges in hAMRonization
- AMR Variant detection - Parsers to be updated HOT 1
- Obtain specification field data information from JSON schema HOT 1
- Update README
- Add xlsx output HOT 1
- Add CONTRIBUTING.md
- Add fARGene
- PyPi not updated, 1.0.4 tarball reports version 1.0.3 HOT 2
- [BUG] `KeyError: 'reference_database_name'` when running summarize HOT 9
- [BUG] Generated output does not follow CSP rules HOT 1
- Request for Zenodo archive
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from hamronization.