hAMRonization
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pha4ge
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
This is a suggestion to add the tool [fARGene](https://github.com/fannyhb/fargene/) to the hAMRonization tool list. fARGene detects AMR genes based on pre-defined HMM models (provided together with the tool). It would...
In the hAMRonizedResult class definition, the field terms for the parsers, and their value types, should be obtained from the schema JSON file and not be hardcoded into the tool....
If the exact same tool is run with different settings (but all the other metadata stays the same such as version) summarize falsely combines them e.g., running RGI on contigs...
Hi Finlay, when running ORFs through the RGI-hARMonization pipeline, the ORF_ID (important for final hAMR report) is skipped. Here https://github.com/SvetlanaUP/hAMRonization/blob/master/hAMRonization/RgiIO.py you can see that I fixed ORF_ID self.field_mapping manually (Fixed...
For the interactive report or tabular report possibly have an option to just summarise results (genome, gene, tool, versions, phenotype annotation) and the full genomics results (i.e., the whole spec...
https://github.com/github/docs/blob/main/CONTRIBUTING.md
- [ ] Improve installation instructions - [ ] Update parsers included - [ ] Add wiki with small tutorial
**Describe the bug** Summarize function failed when no genes were present in the input files. This should be caught and handled by summarize function.
To handle concerns raised by @cimendes in #39 and try and make issues with input selection clearer to users e.g., #54 we should add proper use of `logging` library, default...