Scripting

make shortcut command

We can create a short cut for a commande we repeat.
A short cut for a command is an alias
alias shortcut='command' (no space surrounding the =)
hgrep='history|grep'

exercise:

create a shortcut for command which extract the bank:entryname from a blast report

make modification permanent

Each time we modify the environment this modification
is available only for the current terminal.
To turn in permanent just put it in your .bashrc

.bashrc is a file which is executed each time a terminal is created.

exercise

use vim to edit the ~/.profile to add the following lines. this way when you log again, your ~/.bashrc will be taken in account

syntax

# use the bashrc
source ${HOOME}/.bashrc

make a copy of the .bashrc file
use vim to edit the .bashrc file and add the alias.

in order to test your modifications, do the following command source ~/.bashrc

repeat an action

Some times we need to repeat the same action n times with just a different details.
for instance rename all files in a directory.
for this we use a loop:

syntax:

for var in list items
do
   do something
done

to be usefull we need :

to set variable var=value (NO spaces surrounding =)
to read variable $var

example:

remove '.fa' from all files terminating by 'fa.gde'

for f in `ls il2*.fa.gde`
do
   nam=`basename $f .fa.gde`
   mv $f $nam.gde
done

exercise:

copy the Proteique directory from the unix_training projets in central-bio in your local home
reformat all fasta file (.fa file) using squizz in gde format.

scripts

scripts are executables text files that contains:
the instruction to execute.
the flow control instructions.
a sheebang that describe the interpreter to use, eg: #! /bin/bash. the sheebang must be the first line of the script.

scripts arguments

$0 name of the script
$1, $2 ... $n positional arguments received by the script
$# number of positional arguments received
$@ list of arguments

tests

you will find 2 syntax for the test

[ expression ]
test expression

expression evaluate in true (0) or false (1)

syntax:

var="hello"
[ $var = "hello" ]
echo $?

==> 0 means true

syntax:

var=3
[ $var -eq 2 ]
echo $?

==> 1 means false

put test at work

syntax:

#! /bin/sh

# check if we got arguments
if [ $# -eq  0 ]
  then
    echo "no argument provided: exit"
    exit 1
fi

# check if file exists
if [ -f $1 ]
  then
    echo "file $1 exists"
    ret=0
  else
    echo "file $1 does not exists"
    ret=1
fi

# exit with significative return value
exit $ret