argnorm 0.0.1rc2

Fast ARG normalization by mapping to the ARO ontology.

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

• deeparg
• sarg
• ncbi
• argannot
• megares
• resfinder

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	Email	Organization
Hui Chong	[e-mail]	Research Assistant, Big Data Biology Lab, Fudan University
Svetlana Ugarcina Perovic	[e-mail]	Postdoc Researcher, Big Data Biology Lab, Fudan University
Luis Pedro Coelho	[e-mail]	Principle Investigator, Big Data Biology Lab, Fudan University