Fast ARG normalization by mapping to the ARO ontology.
Project description
argNorm
Fast antibiotic resistance gene (ARG) normalization by mapping to the antibiotic resistance ontology (ARO) by CARD.
This is a very-first implementation (not ready for production), but you're welcomed to try it and provide feedback to make it better.
We welcome your feedback on the Issues Page.
Supported databases
Installation
pip install argnorm
Basic usage
Use argnorm -h
to see available options.
argnorm [database] -i [original_annotation.tsv] -o [annotation_result_with_aro.tsv]
Examples
Handling hamronized inputs.
argnorm deeparg -i examples/hamronized/deeparg.deeparg.orfs.tsv -o tmp
argnorm megares -i examples/hamronized/abricate.megares.tsv -o tmp
argnorm argannot -i examples/hamronized/abricate.argannot.tsv -o tmp
argnorm resfinder -i examples/hamronized/abricate.resfinder.tsv -o tmp
argnorm ncbi -i examples/hamronized/abricate.ncbi.tsv -o tmp
Handling raw inputs (not hamronized by hAMRonization)
argnorm deeparg -i examples/hamronized/deeparg.deeparg.orfs.tsv -o tmp
argnorm megares -i examples/hamronized/abricate.megares.tsv -o tmp # tested
argnorm argannot -i examples/hamronized/abricate.argannot.tsv -o tmp
argnorm resfinder -i examples/hamronized/abricate.resfinder.tsv -o tmp
argnorm ncbi -i examples/hamronized/abricate.ncbi.tsv -o tmp # tested
Maintainers
Name | Organization | |
---|---|---|
Hui Chong | huichong.me@gmail.com | Research Assistant, Big Data Biology Lab, Fudan University |
Svetlana Ugarcina Perovic | svetlana.ugarcina@gmail.com | Postdoc Researcher, Big Data Biology Lab, Fudan University |
Luis Pedro Coelho | luis@luispedro.org | Principle Investigator, Big Data Biology Lab, Fudan University |
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