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    Basic Programming in Bash PDF

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    REDJECHTA MUSTAPHA AYMEN
    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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    Basic Programming in Bash PDF

    Uploaded by

    REDJECHTA MUSTAPHA AYMEN
    52 views31 pages
    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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    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.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    52 views31 pages

    Basic Programming in Bash PDF

    Uploaded by

    REDJECHTA MUSTAPHA AYMEN
    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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    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

    createdb createdb

    taxonomy search

    filterdb filterdb

    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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