argnorm 0.0.1rc3

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 tools

• DeepARG
• ARGs-OAP
• Abricate (work in progress)

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

argnorm argsoap --mode reads -i examples/raw/args-oap.sarg.reads.tsv -o tmp
argnorm argsoap --mode reads -i examples/hamronized/args-oap.sarg.reads.tsv -o tmp --hamronized
argnorm argsoap --mode orfs -i examples/raw/args-oap.sarg.orfs.tsv -o tmp
argnorm argsoap --mode orfs -i examples/hamronized/args-oap.sarg.orfs.tsv -o tmp --hamronized

argnorm deeparg -i examples/raw/deeparg.deeparg.orfs.tsv -o tmp
argnorm deeparg -i examples/hamronized/deeparg.deeparg.orfs.tsv -o tmp --hamronized

argnorm abricate --db ncbi -i examples/raw/abricate.ncbi.tsv -o tmp
argnorm abricate --db megares -i examples/raw/abricate.megares.tsv -o tmp
argnorm abricate --db argannot -i examples/raw/abricate.argannot.tsv -o tmp

argnorm abricate --db ncbi -i examples/hamronized/abricate.ncbi.tsv -o tmp --hamronized
argnorm abricate --db megares -i examples/hamronized/abricate.megares.tsv -o tmp --hamronized
argnorm abricate --db argannot -i examples/hamronized/abricate.argannot.tsv -o tmp --hamronized
argnorm abricate --db resfinder -i examples/hamronized/abricate.resfinder.tsv -o tmp --hamronized

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
Finlay Maguire	[e-mail]	Assistant Professor, Department of Community Health and Epidemiology, Dalhousie University