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Basic Programming in Bash PDF

The document provides information about basic programming in the Linux Bash shell. It discusses the history and components of UNIX and Linux operating systems. It then describes Bash as a command line interface and shell that allows sophisticated execution of commands through scripting. The document outlines some basic Bash commands and provides examples of creating and running simple Bash scripts using variables, conditionals, loops, and user input. It also discusses text manipulation tools like cut, grep, and pipes for transferring output between commands.

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REDJECHTA MUSTAPHA AYMEN
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© © All Rights Reserved
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64 views

Basic Programming in Bash PDF

The document provides information about basic programming in the Linux Bash shell. It discusses the history and components of UNIX and Linux operating systems. It then describes Bash as a command line interface and shell that allows sophisticated execution of commands through scripting. The document outlines some basic Bash commands and provides examples of creating and running simple Bash scripts using variables, conditionals, loops, and user input. It also discusses text manipulation tools like cut, grep, and pipes for transferring output between commands.

Uploaded by

REDJECHTA MUSTAPHA AYMEN
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Basic programming in Bash

Linux environment
• UNIX is an operating system originally developed in AT&T’s Bell labs
in the 1970s
• AT&T had to provide the source code to anyone who asked
• GNU is a UNIX-based open source project started in the 1980s
• Linux was first released in 1991 and is considered (by some) to be a
part of the GNU project
Bash
• Bash is a command language interpreter
• It is a Shell, a user interface (command-line interface)
• Sophisticated execution of commands is possible through Bash scripts
• In bash, everything is a file
• It can have Read (r), Write (w) and/or Execute (x) permissions
Simple Bash commands
• cd - change directory • less - show file content
• ls - list directory • pwd - show current directory
• cat - concatenate and print file
• head - print beginning of the file
• tail - print end of the file
• wc - word count
• rm - remove
• mkdir - make directory
• man - show manual of a command (quit by pressing 'q')
Motivation
• Basic programming is useful as it allows you to automate tasks
• MMseqs2 software suite allows creating tailored computational tools
by combining its modules and workflows in Bash scripts

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taxonomy search

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search
The script file
• The first line of a Bash script is usually:
#!/bin/bash
• This indicates this file is a Bash script
• Lines that start with ‘#’ are comments
• To print something we use ‘echo’
• A script is just a text file.
• Under your home directory, create a directory called “Bash_scripts”
• We will create Bash scripts there
Creating the Hello_Bash.sh script file
Running a Bash script
• You need to give your script execution permission:
chmod +x ~/Bash_scripts/Hello_Bash.sh
• Then you can run it from the terminal:

"~" means your home directory


try:
echo $HOME
echo ~
cd ~
Hello_Bash.sh
Create a Hello_Bash.sh script and run it
Bash variables
• A variable stores a value
• There are no variable types in Bash
• Assignment of a value is done with “=“

#!/bin/bash
NAME="Eli"
NUMBER_OF_EYES=3
echo "Hello $NAME, you have $NUMBER_OF_EYES eyes"

• Modify the Hello_Bash.sh script to have a variable and run it


Arithmetic evaluation
• In order for bash to treat the variable as numeric we need to use
brackets:

CORRECT_NUMBER_OF_EYES=$((NUMBER_OF_EYES – 1))
echo "Humans usually don't have more than
$CORRECT_NUMBER_OF_EYES eyes"

• Create a Bash script with a variable AGE and assign it your age. Print
the age you will be in one year
Conditionals
• If/else structures allow us to execute commands only in certain cases

AGE=20
if [ "$AGE" -eq 20 ]; then
echo "Wow, you are exactly 20!"
fi Description Numeric String
less than -lt <

• Comparison operators: greater than -gt >


equal -eq =
not equal -ne !=
less or equal -le
greater or equal -ge
User interaction
• This simple Bash script asks the user for their name and says hi:

#!/bin/bash
echo "Enter your name and press [ENTER]: "
read NAME
echo "Hi $NAME"

• Create a script that asks for the user’s age and serves beer only if
the user is at least 18
What does this code do?
echo "Enter a directory name and press [ENTER]: "
read DIR
if [ -d "$DIR" ]; then
ls "$DIR"
else
mkdir "$DIR"
fi
Repetitive execution of commands
• Often we would like to perform the same thing more than once:
• Say hello to all students in the class (there are 22 of you!)
• Make a copy of each file in a directory
• Refine an MMseqs2 clustering…

• Bash loops allow us to do exactly that!


For loop
#!/bin/bash
START=1
END=22
for (( i=$START; i<=$END; i++ ))
do
echo "$i. Hi, student!"
done
While loop
# continue from last slide
i=1
while [[ $i -le $END ]]
do
echo "$i. Oh hi there, student!"
((i = i + 1))
done
Exercises
1. Compute the sum of the first 40 natural numbers:
1+2+…

2. Sum the numbers the user provides you until they provide a
negative number

Can you tell how many numbers you summed?


Text files: select columns
cut command let's you select columns from a text file tab separated

Flags:
• -f: indicates columns to print (e.g.: 1,4-9,12-)
• -d: specifies column separator character (e.g.: ",")
comma separated
Redirect operator
> and >> redirects the Standard Output (stdout) to a file or elsewhere
• '>' creates and/or overwrites the file
• '>>' appends to the end of the file

Exercise: from the file 'molbio_2019.txt' print the country of


origin to a file called 'nationalities.txt'
Pipe operator
We can easily transfer the output of one command to another using
pipes

command1 | command2 | command3 ...

What do these commands do?


uniq nationalities.txt
sort nationalities.txt | uniq
More pipes
And these ones?
sort nationalities.txt | uniq | wc -l
sort nationalities.txt | uniq -c
sort nationalities.txt | uniq -c | sort -nrk1

Use the man command to find out what those flags mean
man sort
man uniq
man wc
grep
grep <pattern> <file> - extracts and prints all the lines that
match a specific pattern or string in the files
-c: counts occurrences of the pattern
-v: print only the lines that DO NOT contain the pattern
-i: case insensitive flag
Exercises:
1. Count number of students from 'India'
2. Count number of students that are not from 'Germany'
3. How many people contain the the word 'an' in their names?
grep
-E: let's you use 'regular expressions'

What does this command do?


grep -E "^\w{5}\s" molbio_2019.txt
grep - Regular Expressions (regex)
grep -E "^\w{5}\s" molbio_2019.txt

'^' : begin the line with this regex


'\w' : any letter
'{5}': exact nº of occurrences of last element
'\s' : any white space character
Exercise solutions
#!/bin/bash
echo "Hello Bash"
Exercise solutions
#!/bin/bash
AGE=99
AGE_NEXT_YEAR=$((AGE + 1))
echo "Next year you will be $AGE_NEXT_YEAR"
Exercise solutions
#!/bin/bash
echo "Enter your age and press [ENTER]: "
read USER_AGE
if [ $USER_AGE -ge 18 ]; then
echo "Here is your beer"
fi
Exercise solutions
#!/bin/bash
START=1
END=40
SUM=0
for ((i=$START; i<=$END; i++)) do
SUM=$((SUM+i))
done
echo "The result is $SUM"
Exercise solutions
#!/bin/bash
USER_NUMBER=0
NUM_NUMBERS=-1
SUM=0
while [[ $USER_NUMBER -ge 0 ]]
do
SUM=$((SUM+USER_NUMBER))
NUM_NUMBERS=$((NUM_NUMBERS+1))
echo "Insert a new number [negative number to exit]:"
read USER_NUMBER
done
echo "Final sum is $SUM and $NUM_NUMBERS numbers were summed"

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