Comments (1)
Use hamronize resfinder4
for resfinder v4. The output file and format changed a lot between v3 and v4 so they are separate parsers within hamronization.
hamronize --help
(and the README) list examples of the input files used for each parser, if you are still unsure you can look at the test files: https://github.com/pha4ge/hAMRonization/tree/master/test/dummy to look at the exact output file format expected for each tool's parser.
To maximise utility of your output try and use accurate values in the additional metadata supplied e.g., the actual resfinder database version used in --reference_database_version
and the actual resfinder tool version in --analysis_software_version
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
- 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.