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 tools
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 | 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 |
Finlay Maguire | finlaymaguire@gmail.com | Assistant Professor, Department of Community Health and Epidemiology, Dalhousie University |
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