Unix Primer for Biologists

Transforming data throughout the analysis

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Learning the Unix essentials

• Based on Bradnam & Ian Korf’s excellent online book: Unix and Perl Primer for Biologists

(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

Navigate

• 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

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”

• Please take a look at Regular Expressions from the Text Processing lecture in the Exploratory Data Analysis course.

Thanks for your attention

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