Improve your command line skills by learning a few words of Perl

Improve your command line skills by learning a few words of Perl (28/11/2023)

The GenoToul bioinformatics platform and Sigenae organize a series of training courses to familiarize yourself with the various resources it provides. These resources are currently: the hardware infrastructure, biological data banks and widely used bioinformatics softwares. This “Perl one-liners” training session is organized by the Sigenae platform. Perl one-liners are small and awesome Perl programs that fit in a single line of code and perform many operations such as replacing of text, spacing, deleting, calculation, manipulation in files and many more. This training will allow you to discover the power of Perl on the command line and learn how to use it to automate your file manipulations and command line generation with classical file formats such as tabulated text, fastq, sam/bam, and vcf.



This training lasts one day and is focused on practice. It consists of 3 parts with a large variety of exercises:

  • Introduction to Perl and its characteristics: Perl is a widely used programming language for data processing and task automation. We will introduce the main characteristics of Perl and discuss why it is particularly suited for biologists who want to manipulate files and generate command lines.
  • Perl on the command line: we will show how to use Perl on the command line to perform common tasks, such as searching and replacing strings, merging files, and loop over lists of files.
  • Concrete examples: we will present several concrete examples drawn from biology, such as extracting information from genomic sequence files, converting files between different formats, and generating command lines for data biology tools.


The session will take place in the room ‘salle de formation MIAT’ at INRAE center of Toulouse-Auzeville. 


Prerequisites: ability to use a Unix environment (see Unix training) and Cluster (see Cluster training).


Training materials is available here


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