argnorm 0.1.0

Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD).

argNorm

Antibiotic resistance gene (ARG) normalization by mapping to the antibiotic resistance ontology (ARO) by CARD.

Right now, many tools exist for annotating ARGs in genomes and metagenomes. However, each tool will output in its own format. The hAMRonization package can normalize file formats, but each tool will use different names/identifiers (e.g., TetA or TETA or tet(A) or tet-A are all different ways to spell the same gene name). For a small number of isolate genomes, a human user can still quickly evaluate the outputs. However, for metagenomics, especially for large-scale projects, this becomes infeasible. Thus, argNorm normalizes the output vocabulary of these tools by mapping all tools to the same ontology (ARO).

This is a beta-quality implementation (subject to changes and some bugs may remain), but you're welcomed to try it and provide feedback.

We welcome your feedback on the Issues Page.

Supported tools

Note that CARD RGI already uses ARO, thus there is no need to use argNorm.

• DeepARG (v1.0.2)
• ARGs-OAP (v2.3)
• ABRicate (v1.0.1) with NCBI (v3.6), ResFinder (v4.1.11), MEGARes (v2.0), ARG-ANNOT (v5)
• ResFinder (v4.0)
• AMRFinderPlus (v3.10.30)

Installation

pip install argnorm

Basic usage

Use argnorm -h to see available options.

argnorm [tool] -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

argnorm resfinder -i examples/raw/resfinder.resfinder.orfs.tsv -o outputs/raw/resfinder.resfinder.orfs.tsv
argnorm resfinder -i examples/raw/resfinder.resfinder.reads.tsv -o outputs/raw/resfinder.resfinder.reads.tsv

argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.tsv

Authors

• Vedanth Ramji [e-mail]*
• Hui Chong [e-mail]
• Svetlana Ugarcina Perovic [e-mail]
• Finlay Maguire [e-mail]
• Luis Pedro Coelho [e-mail]

*: current maintainer