UNIX

Connect to the unix machine at CBS

On Windows

On Mac

Basic commands

pwd   This command returns the path to your current location (the current directory, as you can also see in your promt)

cp -R /usr/opt/www/pub/CBS/courses/27685.imm/exercise_unix/immu00   .

ls                      short listing of the content of the current directory (a directory is called a folder in Windows or Mac OS)
ls ..                   short listing of content of the directory above the current directory [".." means one directody up "../.." is two directories up]
ls immu00        short listing mail directory (equivalent to ls ./immu00  ["." means here])
ls -l immu00     detailed listing of projects directory
ls -ltr immu00   long listing sorted by time (t) and reversed (r): newest files last 
                        (essential for old bioinformaticians who can not remember what they just did)

mkdir testdir           Make a new directory (folder) with the name testdir in the directory (folder) where you are now.
mkdir mynewdir          Make a new directory (folder) with the name mynewdir in the directory where you are now

cd testdir              go to the testdir directory (relative address to where you are)
cd ..                   up one level
cd                      go to my home directory
cd immu00        go to immu00 directory (verify you are there by the pwd command)

touch myfile            Makes a new empty file
mv myfile mynewfile     Rename myfile to mynewfile
mv mynewfile testdir    Moves the file mynewfile into the directory named testdir (How can you check that this has actually happened?)

rm mynewfile         removes (deletes) mynewfile
rmdir mydirectory    remove an empty directory 
rmdir testdir        remove an empty directory (this directory is not empty thus this didn't succeed)
rm -rf testdir       remove a directory, including files and subdirectories - no questions asked - make sure this is what you want to do, 
                     there is no recycle bin on UNIX; once it is gone it is gone!

touch myfile          make file called "myfile"
cp myfile mynewfile   copy myfile to mynewfile

cat test.dat          write contents of file to screen
head test.dat         write top of file (default 10 lines)
head -30 test.dat     write top 30 lines of file
tail test.dat         write the last 10 lines of end of file
tail -25 test.dat     write the last 30 lines of the file
more test.dat         show test.dat pagewise, pres "space to go one page down, "q" to quit.
less test.dat         show test.dat pagewise, pres "space to go one page down, "j" to go one line down, "k" to go one line up, "q" to quit.

n test.dat   edit the file test.dat with nedit

cat test.dat | wc              pipe the contents of test.dat into the program called wc (word count) count number of lines, words and bytes in test.dat

head test.dat > tmp.dat        first ten lines of test.dat into tmp.dat

head test.dat >> tmp.dat       first ten lines of test.dat into tmp.dat (now it should contain 20 lines)

head < test.dat 

Bioinformatics using Unix commands

gawk '{print $1}' epitope2protein.HLA-D_m13.out                          Print first field in file
gawk '{print $1, $3}' epitope2protein.HLA-D_m13.out                      Print first and third field in file
cat epitope2protein.HLA-D_m13.out|gawk '{print $1}'                      Print first field in file getting data from standard input
cat epitope2protein.HLA-D_m13.out|gawk '{if (/NP/) {print $1}}'          Print first field in lines containing "NP"
cat epitope2protein.HLA-D_m13.out|gawk '{if (/^NP/) {print $1}}'         Print first field in lines starting with "NP"
gawk '{print substr($7,2,5)}' epitope2protein.HLA-D_m13.out              Print five characters of the seventh column, 
                                                                         starting with the second letter (in the seventh column). 
                                                                         NB! awk numbers strings starting with 1, where many other programming and 
                                                                         scripting languages starts numbering from 0!
gawk '{print substr($7,length($7)-3,4)}' epitope2protein.HLA-D_m13.out   Print last four letters in seventh column

echo "Mary had a little lamb" |gawk '{line = $0; gsub (" ","",line);print line}'           
                                                                         Remove all spaces in all lines
gawk -v name=Mary -v animal=lamb '{print name,$1,animal}' epitope2protein.HLA-D_m13.out
                                                                         Passing variables to gawk

gawk -F "\t" '{print $1}' epitope2protein.HLA-D_m13.out                  Split only input on tabulators (rather than on any whitespace as is the default)

head epitope2protein.HLA-D_m13.out | gawk 'BEGIN{print "Here comes the data"}{print $1}END{print "No more data"}'
                                                                         statements in BEGIN{} and END{} are executed before and after 
                                                                         the data lines are read, respectively

cat epitope2protein.HLA-D_m13.out | gawk 'BEGIN{print "* Aligned protein sequences."}{s=substr($7,$3-4,9);if (length(s)==9){print s"."}}' | /home/projects/projects/vaccine/bin/logo2 -p - | gawk 'BEGIN{pr=0}{if (/\%\!PS-Adobe-3.0 EPSF-3.0/){pr=1} if(pr==1){print $0}}' > logo.ps

Sort file - sort
Example of using sort:

Getting a test file:
cp /usr/opt/www/pub/CBS/researchgroups/immunology/intro/Unix/test.out .

  sort -n test.out  				sort file numerically
  sort -n -k3 test.out				sort file numerically (big numbers last) by 3rd column
  sort -r -n -k3 test.out			sort file reverse numerically (big numbers first) by 3rd column
  sort -u pdb.mhc.spnam			Keep only one copy of each unique line
  sort pdb.mhc.spnam | uniq -c		Count the number of each unique line
  

Execute a string
putting `` around a command makes a unix execute the command corresponding to the string: echo pwd
      print the string pwd
`echo pwd`
      execute the command pwd
echo pwd|sh
      echo the string pwd to the shell - which will then execute it
This will be used in the next example.

Do something with many variables - foreach
Example 1: print each entry in list to screen

foreach entry (a b c)
      echo $entry
end

Example 2: get each swissprot entry from list and print it

foreach entry (`gawk '{print $1}' test.out`)
      echo $entry |sed 's/.*|//'| xargs getsprot
end

NB:echo ENV_HV1H2| xargs getsprot      is the same as getsprot ENV_HV1H2     

Warning: the string within () is limited to a few thousand charectors

Contatinate side by side - paste
Example:
paste pdb.mhc.nam pdb.mhc.spnam     


Get lines matching a patern - grep/egrep
Example:

  grep 1A68_HUMAN pdb.mhc.spnam	Get lines with "1A68_HUMAN"
  grep -v HUMAN pdb.mhc.spnam		Get lines that do not contain "HUMAN"
  grep _HUMAN pdb.mhc.spnam		Get lines with "_HUMAN" (Human swiss prot sequences)
  grep ^KA pdb.mhc.spnam			Get lines starting with "KA" (Human swiss prot sequences)
  grep "^KA.*MOUSE" pdb.mhc.spnam	Get lines matching "KA" - something ("." is a wildcard; "*" means repeated zero or more times) - "MOUSE"
  

What did I do
history

The history command returns the 100 - 500 last executed commands depending on the shell settings


Other usefull commands
which cat

Find out where a program (the cat program in this case) is installed. Often when you edit a program and nothing happens it is because you are editing another program than the one you are running

gunzip Unzip a zipped file (.gz files)

command line options
most unix programs take options in the form "program -option". for example head -5 will print out the first 5 lines of a file (5 is an option), or the -l option to ls (ls -l)

diff/gdiff compare tho files

chmod Change permissions (who can read, write to, or execute a file or script)
ownership chown Change ownership of a file
autocompletion Press TAB to let the unix system complete a file/program name
"arrow up" press arrow up to get old commands

<ctrl> a Go to the start of the commandline
<ctrl> e Go to the end of the commandline

Can I use it?

>1A68_HUMAN
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDRNTRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQ
MMYGCDVGSDGRFLRGYRQDAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQW
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP
SSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSL
TACKV