Csvkit

Introduction

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.

For more information, please check:
Docker hub: https://hub.docker.com/r/johnyaku/csvkit
Home page: https://csvkit.readthedocs.io/en/latest/

Versions

  • 1.1.1

Commands

  • csvclean

  • csvcut

  • csvformat

  • csvgrep

  • csvjoin

  • csvjson

  • csvlook

  • csvpy

  • csvsort

  • csvsql

  • csvstack

  • csvstat

  • in2csv

  • sql2csv

Module

You can load the modules by:

module load biocontainers
module load csvkit

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 csvkit on our clusters:

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

module --force purge
ml biocontainers csvkit