http://creativecommons.org/licenses/by-sa/2.0/
Tutorial 2.1
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Unix Tutorial 2.1a
Mike Wilson
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Unix tutorial 2.1a
1. Review of some essential UNIX commands
1. Hands on demo of cat, grep and du
2. Getting into your shell
3. A few more commands
4. Using sim4 to align cDNA to genomic
sequence
5. Time to play!!!! Time to play: open up your
laptops
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A review of the essential
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cd
ls
cp
mv
rm
mkdir
rmdir
pwd
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– change directory
– list
– copy a file
– move or rename a file
– remove a file (use caution)
– make a directory
– remove a directory (must be empty)
– print working directory
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Redirecting and reading files
• cat can be used to display file contents
• cat is also used to concatenate files
1) Move to unixtutorial directory
2) Type: cat bka.txt unix.txt > both.txt
– Copies contents of bka.txt and unix.txt into one
file called both.txt
– Note that if you already had a file called both.txt
it would be overwritten!
– Type less both.txt to read the file
3) Type: cat unix2.txt >> both.txt
– Appends unix2.txt to both.txt
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Grep
• grep = global regular expression print
• grep is powerful for searching file names and contents
• grep [options] regexpression [files]
– grep –e [vfy][fyw].*[gstne][gstqcr][fyw].*p filename
• searches for this pattern in filename
• -e option indicates expression pattern;
• [ ] one of any of the character
• .* zero, one or more of any character
• Goal: use grep to look for fun in one of your files
1) Go to unixtutorial directory if you aren’t there already
2) Type: grep fun both.txt
• Looks for “fun” in the file “both.txt”
• Did you find fun?
• Are you having fun?
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Print disk usage: du
• du [options] directory
– du by itself prints current directory and all subdirectory names and sizes
– du –a prints information for all files as well
• Du you want to find a file?
– du –a | grep filename
– you can of course search for partial filenames with
your wild cards/arguments etc.
– go to home and look for unix.txt
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Shell files and aliases
• A buffer between you
and the operating
system
• Bourne-again shell
(BASH) is the standard
Linux shell (from GNU)
• The shell is interactive,
it allows you to
customize your Linux
session as well as
program
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Common Shell symbols
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>
>>
<
|
&
*
?
[]
\
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redirect output
append output
redirect input
pipe output
run process in background
match any characters in filename
match single character in filename
match any characters enclosed
quote following character
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Customizing your shell
• Special BASH files you will find in your home
directory
.bash_profile
executed at login
.bashrc
executed at shell startup
.bash_logout
executed at logout
.bash_history
contains your previous commands
• Type: ls –al to see all your files
• Customizing your shell usually will involve editing
the .bashrc file
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Aliases: making HOME feel like home
• aliases can make
your life easier
• typing alias will
reveal ‘default
aliases’
• you can add
temporary aliases
• alias lf=‘ls –F | less’
• unalias will remove
this: unalias lf
• you can add
permanent aliases
to your .bashrc file
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I don’t know much about history
• Scroll through your history with 
• Look at your history file by typing history
• history lists your previous commands next to a
number.
• you can rerun any given number by typing !n
• !55 would re-execute command 55 in my history
• It’s worth learning more about history
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Environment variables
• Environment variables are settings that control specific
aspects of the system
– each program has its own variables
– the shell (a program we spend a lot of time with) has variables
too
– you can look at all your shell environment variables by typing set
Some common environment variables for the shell
• HOME
– points to the home directory
• PATH
– places that the shell will look for your commands
• PS1
– determines what is displayed at the command prompt
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Customizing environment variables
• variables can be used in commands and
filenames by preceding them with a $ sign
– i.e. $HOME/unixtutorial/unix.txt
• you can use $PATH in a command to add a
new directory to your PATH
– export PATH=$PATH:$HOME/unixtutorial
export makes
shell variable
PATH global
$PATH
refers to
current path
: separates
current PATH
from new one
new PATH to be
added
– this appends the new PATH to the existing one
– to view your PATH: echo $PATH
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Editing .bashrc with emacs
– make your changes to the PATH memorable by editing
.bashrc
• open .bashrc in a text editor (emacs or gedit or vi)
• add PATH=$PATH:$HOME/unixtutorial
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Installing programs in Linux/Unix
• Unix and Linux comes with many applications preinstalled
• You will likely want to install more
• This can sometimes prove to be difficult for a few reasons some of
which inlcude:
– what flavour of unix/linux you are running
– what privledges you have as a user (i.e. root)
– the nature and quality of the program you want to install
• Much softwares builds upon previous work, programs, libraries etc.
• Sometimes you need to find and install these yourself.
• Depending on the nature of the program and implementation this
can become a really annoying scavenger hunt.
• The art of installation can take patience and practice
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Implementation energy
– situation A
• some energy needed to install
and learn new program
• energy is regained from the time
saved obtaining results
– situation B
• energy spent installing and
learning program is more than
time/energy saved
– Experience takes energy and time
(so everything may look like a B
when you start)
– Even experience may not make up
for time wasted implementing a
poorly written or compiled program
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Making and breaking tar files
• File is now filename.tar
– Tar is short for tape archive
– It is mostly used to bundle files and directories
• To untar a tar file
– Type: tar -xvf filename.tar directoryname
– When extracting make
c
Creates (a new tar file)
sure the directory you
x
Extracts (a tar file)
choose is where you
f
Files
want the files
(could be messy)
v
Verbose (lets you see files created)
z
Use (tar -xzvf) to uncompress and untar
in one step
• Create a tar file of everything inside of a directory
– Type: tar -cvf filename.tar directoryname
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Un/compressing files
• Most UNIX software you download will be
compressed and bundled.
• These files often look like: filename.tar.gz
– To uncompress type: gunzip filename.tar.gz
– File is now filename.tar
• To compress a file type: gzip filename
– You then get a smaller file named: filename.gz
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A process is a program in action
– To suspend a process type: control z
– Situation:You are working on a buffer in emacs and
want to get back to the command prompt without
closing emacs
– type: control z
• emacs is suspended and you are back at the command prompt
• You can type ps to see what processes are running
– Now type: fg
• You are back in emacs working on your buffer
– If you type bg it will run the process in the
background (as opposed to suspending it)
– somtimes you may want to run a process in the
background from the start. Use &
• mozilla &
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A process is a program in action
– To check out the action type: ps
– To put a stop to the action type:
kill processnumber
• You can also can use the command top to manage processes and
check memory usage etc. (more powerful than ps)
•In top
–Type u and then enter your username to see processes you
are running
–Type k and enter process ID to kill a program
–Type q to leave top
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Sim4- A Computer Program for Aligning a
cDNA Sequence with a Genomic DNA
Sequence. (Florea et al 1998)
• Align cDNA, EST data with genomic sequences
• Uses BLAST based technique finds “exon cores” of a given word size.
• Takes into account conventional splicing logic and possibility of
sequencing errors.
• Sim4 is a useful, efficient and commonly used bioinformatic program
• It’s also well documented and easy to install. Try it at home or work!
• Usage:
– sim4 seqfile1 seqfile2db {[WXKCRDAPNB]=value}
– sim4 my_genomic my_cDNA_list K=15 C=11 A=3 W=10
• For the rest of the lab you will use sim4 to do some bioinformatic work
and get to know your shell
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Sim4
•You can see the parameters of sim4 by typing:
sim4
•We will use default parameters but you will have to look
at the instructions (its important to do this for all
bioinformatic programs).
• A basic sim4 run will look like:
sim4 genomic_sequence list_of_cdnas A=3 > outfile
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A little aside about the Linux mascot
Tux
• Some people have told me
they don't think a fat penguin
really embodies the grace of
Linux, which just tells me
they have never seen a
angry penguin charging at
them in excess of 100mph.
They'd be a lot more careful
about what they say if they
had.
-- Linus Torvalds
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Unix Tutorial- when you have had
enough
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A few more
Resources
• http://www.gnu.org/software/bash/
manual/bash.html
– The official BASH manual from
GNU
• http://linux.org.mt/article/terminal
– excellent tour of the BASH
shell!
• http://www.tldp.org/
– the linux documentation
project. Great resource
• http://globin.cse.psu.edu/globin/ht
ml/docs/sim4.html
– info about and download sim4
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The last resources- have fun!
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