Awk workshop

AWK is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool.

This two-days workshop aims to promote and demonstrate the flexibility of the tool, where the overhead of more sophisticated approaches and programming languages is not worth the bother.

Learn how to

  • use Awk as an advanced grep command, capable of arithmetic selection rules with control over the content of the matched lines
  • perform simple conversions, analysis or filter you data on the fly making it easy to plot or read in your favorite research tool
  • handle and take advantage on data split over multiple file data sets.
  • use Awk as simple function or data generator
  • perform simple sanity checks on your results

Awk for bioinformaticians

Use what you learn and dive into the basic concepts of bioinformatics with simple exercises on typical scientific problems and tasks.

Registration: 

Please apply via this form.

Schedule


1-st day 9:15 - 12:00

  • Seminar session
    • Examples of typical problems suitable for Awk “treatment”
    • Introduction to the basics of Awk scripting language
    • Solving interactively simple problems
  • Lunch break
  • Exercises 13:15 -16:00
    • Solving interactively the exercise problems

2-nd day 9:15 - 12:00

  • Awk for bioinformaticians - seminar
  • Case Study: Manipulating the output from a genome analysis - vcf and gff
    • Filtering and formatting raw data
    • Counting and piling features
    • Indexing and hashing to compare variants and annotations
  • Lunch break
  • Walk-through session on various topics:
    • Awk parsing “simultaneously” multiple input files
      Multiple input files - second approach scenario will be discussed.
    • How to trick awk to accept options on the command line like regular program i.e. $ script.awk filename parameter1 parameter2 link
    • Declaring and calling functions in awk - link
    • Input/output to/from an external programs
      Learn how to send input to an external program (might be based on your data) and read the result back - link
    • Handy tips: awk oneliners use with Vim, gnuplot…

Prerequisites

MacOS

The system provided awk version will work for most of the examples during the workshop with few exceptions, which are noted in the online material.

Tilda ~ sign on Mac with Swedish keyboard layout - Alt + ^

Linux

Several distributions have other awk flavors installed by default. The easiest fix is to install the gnu version gawk i.e. for Ubuntu: sudo apt install gawk

Windows 10

  • Ubuntu for Windows 10 - it is better to read from the source, despite it might not be the easiest tutorial. To my experience, this is the best Linux environment without virtualization.
  • MobaXterm use the internal package manager to install gawk. The default is provided by Busybox and is not enough for the purpose of the workshop.

Linux computer center

  • Just login to your account and use the provided awk - any version newer than 4 will work.
rackham3:[~] awk -V
GNU Awk 4.0.2
Copyright (C) 1989, 1991-2012 Free Software Foundation.

 Virtual Linux Machine

Just follow some tutorial on how to setup and use the virtual Linux environment.

singularity run shub://pmitev/Teoroo-singularity:gawk 'BEGIN{ for(i=1;i<=4;i++) print i}'
  • https://www.onworks.net/ - provides multiples Opeative systems to start up for free. Warning - sessions are disconnected in 5 minutes inactivity; overloaded by commercials.

Online meeting - Zoom 

The meeting will be active 30 minutes before the workshop, so we can help you with some trivial setup problems and general questions.

The workshop is intended to be interactive, which could be a challenging task on computers with small screens. The best is to leave space for the shared Zoom window and an active terminal. The material for the workshop is available online https://pmitev.github.io/to-awk-or-not/


Suggest topic for discussion or see recently suggested topics.


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Senast uppdaterad: 2022-05-24