Bioawk

Introduction

Bioawk is an extension to Brian Kernighan’s awk, adding the support of several common biological data formats, including optionally gzip’ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

For more information, please check its website: https://biocontainers.pro/tools/bioawk and its home page on Github.

Versions

• 1.0

Commands

• bioawk

Module

You can load the modules by:

module load biocontainers
module load bioawk

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Bioawk on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bioawk
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bioawk

bioawk -c fastx '{print ">"$name;print revcomp($seq)}' seq.fa.gz