User:Konrad U Foerstner/Introduction to the Unix shell

Reading recommendations

• Introduction to text manipulation on UNIX-based systems

Todo

• man
• apropos
• ls
• cd
• pwd
• mv
• rm
• cat
• cp
• wc
• cut
• head
• tail
• less
• top
• grep
• sort
• uniq
• du
• diff
• md5sum
• echo
• find
• tar, gzip, bz2, zip, bunzip, bzcat, zgrep ...
• tab completion
• globbing
• ssh
• screen
• pipes
• less
• parameter and arguments
• stdin, stout
• home dir ~/
• http://ss64.com/bash/

Useful commands

man

Maybe the most important command! Show the manual page of command.

man page

ls

list directory contents

man page

Text editors

• emacs
• vi
• gedit

Some examples

Retrieve a fasta file

$ wget ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Campylobacter_jejuni_81116_uid17953/CP000814.faa

Inspect it with a viewer (leave it with "q")

$ less CP000814.faa

List all fasta headers

$ grep ">" CP000814.faa

Count the number of protein names

$ grep -c ">" CP000814.faa

Get only the accessions

$ grep ">" CP000814.faa | cut -f 4 -d\|

Count the total number of amino acids

$ grep -v ">" CP000814.faa | wc -m

Tasks

• How many hypothetical protein are in the file?
• Generate a list of their accession numbers and a list of their IDs (e.g. C8J_1629)