Introduction to Perl: Programming for bioinformatics


Perl is a programming language for getting your job done. It is designed to make the easy jobs easy, without making the hard jobs impossible. Perl is also well known for BioPerl, a collection of modules which greatly simplify complicated bioinformatics tasks.

Learning outcomes

  • Process text files for the purpose of reformatting / sorting / selecting from them.
  • Run external programs and capture their output from within Perl.
  • Automate the repetitive running of other programs such as BLAST+.
  • Take advantage of pre-existing modules to make complicated tasks easy.
  • Understand the basics of using BioPerl modules for bioinformatics tasks. Full course syllabus -------------
  • Basics of programming.
  • Writing and running Perl scripts.
  • Accessing the Perl documentation.
  • Built-in data types.
  • References.
  • Data Structures.
  • Regular Expressions.
  • Using modules, including BioPerl modules.
  • Interacting with other programs.

Licence: Other (Not Open)

Keywords: perl, John Innes Centre, JIC

Target audience: Any students, postdocs or RAs who have an interest in programming and who intend to carry out computational analysis of their experimental data. Perl is often used for preparing input files for more specialized software such as R, and also to post-process the output from R and various other bioinformatics tools. It is a glue language allowing you to build pipelines of analyses of arbitrary complexity. This two day course is planned to be a gentle introduction to the basic concepts of Perl and will also introduce you to the BioPerl library of modules.

Authors: Govind Chandra

Scientific topics: Software engineering

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