Unix Primer for Biologists

Abel Vertesy

Transforming data throughout the analysis

pipeline {width=300px}

Learning the Unix essentials

(Thank goodness, no need for Perl anymore :-D )

Introduction

Advances in high-throughput methods have transformed modern biology into an incredibly data-rich science.

Biologists who never thought they needed computer programming skills are now finding that using an Excel spreadsheet is simply not enough.

Why Unix?

  • Runs behind Linux and Mac desktop computers and all HPCs (high performance computing clusters)
  • Free → most bioinfo software are written for it
  • Very fast at large data

Using the Terminal

  • Always pre-installed
  • Many software does not have GUI
  • Interact
    • by typing instead of clicking
  • Choose your terminal program if you use it a lot. I use iterm2 on OSX.

Your first Unix commands

  • ls
  • pwd
  • cd
    • cd ~
    • cd ./
  • ..
  • Relative and absolute path

Command options (arguments)

  • What are these?
  • ls
    • ls -a
    • ls -l
    • ls -lh
  • man help
    • Google is often faster…

Create …

  • mkdir create a dir
    • mkdir -p Temp1/Temp2 touch create a file cp copy mv move

… and destroy

  • rm is an atom bomb: it deletes forever, and does not ask for confirmation.
  • “It is possible to delete EVERY file you have ever created with the rm command. Are you scared yet? You should be.”
  • rm -i

Create your first .fasta file!

  • nano, less and more …
  • duplicate it
  • make a subfolder
  • Use the *.txt

Command overview

With some extra’s

The absolute basics File control Viewing, creating, or editing files Misc. useful commands Power commands Process-related commands
ls mv less man uniq top
cd cp head chmod sort ps
pwd mkdir tail source cut kill
rmdir touch wc tr
rm nano grep
| (pipe) sed
> (write to file)
< (read from file)

Pipe

“pipe-ing” | connects the output of one command to the input of the next command → Allows compressed programming.

head myfile | head | nano

Use cat to read the entire file’s content into another command

cat myfile | grep ">" | wc -l

Finding patterns

  • grep ">" your.fasta
  • grep -v ">"
  • wc :-D
  • head and tail
  • grep "^ATG.*ACACAC.*TGA$" chr1.fasta
    • This is a “regular expression”

Thanks for your attention

Edited from Keith Bradnam & Ian Korf’s excellent online book: Unix and Perl Primer for Biologists.