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Using argNorm as a command line tool

Quick example

Here is a quick demo of running argNorm on the command line.

Step 1: Install argNorm

Install argNorm and check installation

pip install argnorm
argnorm -h

argnorm -h or argnorm --help will display all the available options to run argNorm with.

> argnorm -h
usage: argnorm [-h] [--db {argannot,deeparg,megares,ncbi,resfinder,resfinderfg,sarg,groot-db,groot-core-db,groot-argannot,groot-resfinder,groot-card}] [-i INPUT] [--hamronization_skip_unsupported_tool]
               [-o OUTPUT]
               {argsoap,abricate,deeparg,resfinder,amrfinderplus,groot,hamronization}

argNorm normalizes ARG annotation results from different tools and databases to the same ontology, namely ARO (Antibiotic Resistance Ontology).

positional arguments:
  {argsoap,abricate,deeparg,resfinder,amrfinderplus,groot,hamronization}
                        tool (required): The bioinformatics tool used for ARG annotation.

options:
  -h, --help            show this help message and exit
  --db {argannot,deeparg,megares,ncbi,resfinder,resfinderfg,sarg,groot-db,groot-core-db,groot-argannot,groot-resfinder,groot-card}
                        --db (mostly optional): The database used alongside the ARG annotation tool. This is only required if abricate or groot is used as a tool. Please refer here for more information
                        on --db: https://github.com/BigDataBiology/argNorm?tab=readme-ov-file#--db-optional
  -i INPUT, --input INPUT
                        -i (required): The path to the ARG annotation result which needs to be normalized.
  --hamronization_skip_unsupported_tool
                        --hamronization_skip_unsupported_tool (optional): skip rows with unsupported tools for hamronization outputs. argNorm be default will raise an exception if unsupported tool is
                        found in hamronization. Use this if you only want argNorm to raise a warning.
  -o OUTPUT, --output OUTPUT
                        -o (required): The path to the output file where you would like to store argNorm's results

Step 2: Create working directory & download sample data

argNorm adds ARO mappings and drug categories as additional columns to the outputs of ARG annotation tools.

For this example, we will run argNorm on the ARG annotation output from the ResFinder tool (with the ResFinder database).

Create a folder called argNorm_tutorial and store the downloaded data file in it. Navigate into the argNorm_tutorial folder.

mkdir argNorm_tutorial
cd argNorm_tutorial

Click here to download the input data.

If you are on Linux:

wget https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/raw/resfinder.resfinder.orfs.tsv

Step 3: Running argNorm

Here is a basic outline of most argNorm commands:

argnorm [tool] -i [original_annotation.tsv] -o [argnorm_result.tsv] [--db]

Here, tool refers to the ARG annotation tool used (ResFinder in this case). original_annotation.tsv is the path to the input data and argnorm_result.tsv is the path to output file where the resulting table from argNorm will be stored. --db is the ARG databases used along with tool to perform annotation. ResFinder does not require a --db (argNorm will automatically load up the ResFinder database), however, --db is required for the ARG annotation tools groot and abricate.

To run argNorm on the input data, use this command in your terminal:

argnorm resfinder -i ./resfinder.resfinder.orfs.tsv -o ./resfinder.resfinder.orfs.normed.tsv

The argNorm result will be stored in the file resfinder.resfinder.orf.normed.tsv.

Examples for each tool

Create a folder called argnorm_cli_tutorial and download the sample data inside it.

mkdir argnorm_cli_tutorial
cd argnorm_cli_tutorial

Here is a basic outline of calling argNorm.

argnorm [tool] -i [original_annotation.tsv] -o [annotation_result_with_aro.tsv]

ARGs-OAP

argnorm argsoap -i examples/raw/args-oap.sarg.reads.tsv -o outputs/raw/args-oap.sarg.reads.tsv

DeepARG

argnorm deeparg -i examples/raw/deeparg.deeparg.orfs.tsv -o outputs/raw/deeparg.deeparg.orfs.tsv

ABRicate

When using abricate, it is necessary to specify the database used:

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

ResFinder

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

AMRFinderPlus

argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.v3.10.30.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.v3.10.30.tsv
argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.v4.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.v4.tsv

GROOT

argnorm groot -i examples/raw/groot.argannot.tsv -o outputs/raw/groot.argannot.tsv --db groot-argannot
argnorm groot -i examples/raw/groot.resfinder.tsv -o outputs/raw/groot.resfinder.tsv --db groot-resfinder
argnorm groot -i examples/raw/groot.card.tsv -o outputs/raw/groot.card.tsv --db groot-card
argnorm groot -i examples/raw/groot.groot-db.tsv -o outputs/raw/groot.groot-db.tsv --db groot-db
argnorm groot -i examples/raw/groot.groot-core-db.tsv -o ouptuts/raw/groot.groot-core-db.tsv --db groot-core-db

Hamronization

argnorm hamronization -i examples/hamronized/args-oap.sarg.reads.tsv -o outputs/hamronized/args-oap.sarg.reads.tsv
argnorm hamronization -i examples/hamronized/deeparg.deeparg.orfs.tsv -o outputs/hamronized/deeparg.deeparg.orfs.tsv
argnorm hamronization -i examples/hamronized/abricate.ncbi.tsv -o outputs/hamronized/abricate.ncbi.tsv 
argnorm hamronization -i examples/hamronized/abricate.megares.tsv -o outputs/hamronized/abricate.megares.tsv 
argnorm hamronization -i examples/hamronized/abricate.argannot.tsv -o outputs/hamronized/abricate.argannot.tsv 
argnorm hamronization -i examples/hamronized/abricate.resfinder.tsv -o outputs/hamronized/abricate.resfinder.tsv 
argnorm hamronization -i examples/hamronized/resfinder.resfinder.orfs.tsv -o outputs/hamronized/resfinder.resfinder.orfs.tsv 
argnorm hamronization -i examples/hamronized/resfinder.resfinder.reads.tsv -o outputs/hamronized/resfinder.resfinder.reads.tsv 
argnorm hamronization -i examples/hamronized/amrfinderplus.ncbi.orfs.tsv -o outputs/hamronized/amrfinderplus.ncbi.orfs.tsv
argnorm hamronization -i examples/hamronized/groot.argannot.tsv -o outputs/hamronized/groot.argannot.tsv 
argnorm hamronization -i examples/hamronized/groot.resfinder.tsv -o outputs/hamronized/groot.resfinder.tsv
argnorm hamronization -i examples/hamronized/groot.card.tsv -o outputs/hamronized/groot.card.tsv
argnorm hamronization -i examples/hamronized/groot.groot-db.tsv -o outputs/hamronized/groot.groot-db.tsv
argnorm hamronization -i examples/hamronized/groot.groot-core-db.tsv -o outputs/hamronized/groot.groot-core-db.tsv
argnorm hamronization -i examples/hamronized/combined_hamronization.tsv -o outputs/hamronized/combined_hamronization.tsv
argnorm hamronization -i examples/hamronized/combined_hamronization_full.tsv -o outputs/hamronized/combined_hamronization_full.tsv ----hamronization_skip_unsupported_tool