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Practical Assignment: Introduction To Bioinformatics Online Course: IBT

This document provides instructions for an assignment on manipulating files in Linux. It introduces basic file handling commands like creating, editing, and extracting information from files. Students are asked to complete tasks like making directories, creating files, copying and renaming files, and using commands like head, tail, and touch to work with the files.

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129 views

Practical Assignment: Introduction To Bioinformatics Online Course: IBT

This document provides instructions for an assignment on manipulating files in Linux. It introduces basic file handling commands like creating, editing, and extracting information from files. Students are asked to complete tasks like making directories, creating files, copying and renaming files, and using commands like head, tail, and touch to work with the files.

Uploaded by

Ally
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Introduction to Bioinformatics online course: IBT

Practical Assignment
Module name: Linux
Session name: Session 2: Manipulating files
Trainer: Amel Ghouila
Participant: <write your name here>
Date: <write today’s date here>

Manipulating files
Introduction

The aim of this second session practical assignment is to practice the use of the basic file
handling command lines ranging from files creation, editing and extracting information from
them.

Tools used in this session

If you do have a Linux system installed in your machine, make use of your system terminal. If
you are a windows user, we highly recommend the use of the Cywgin tool
(https://cygwin.com/index.html). You can find more information about the Cywgin
installation via this link: https://cygwin.com/install.html
Some of the commands (nano and wget) we will be using need extra packages installations
for Cygwin, if it’s not already done, no worries, it takes few minutes.

Always remember these rules while working with the Linux terminal
 Make sure you separate your command name, arguments and options using spaces
 Each option is preceded by - (examples: -l, -r, -lh)
 You can combine different options: -lh for example means a combination of -l and -h
 Linux is case-sensitive: A and a are different (it’s not the case for Cygwin and some
Mac OS terminals)
 Make use of these Wildcards while working with the command lines
Introduction to Bioinformatics online course: IBT

Please note

 Hand-in information If you are formally enrolled in the IBT course, please upload
your completed practical assignment to the Vula ‘Practical Assignments’ tab. Take
note of the final hand-in date for each practical assignment, which will be indicated
on Vula.

Some useful links

http://www.linuxcommand.org/
http://manuals.bioinformatics.ucr.edu/home/linux-basics
http://www.ee.surrey.ac.uk/Teaching/Unix/

Task 1: Create your own files and manipulate them!

Task 1: instructions
Remember the file structure you have created yesterday. Make sure you are in the right
directory each time or specify the absolute or relative paths to the files you are dealing with.
Introduction to Bioinformatics online course: IBT

1. Open a terminal in your computer


2. Create a new directory "assignment" under your Session2 directory
3. Create with nano 2 different files genes1 and genes2 under assignment (no need to
copy paste the result into your assignment form)

The content of genes1


gene1 4
gene3 66
gene7 6
The content of genes2
gene1 4
gene2 6
gene4 66

4. Copy genes1 under the directory Session1


5. Rename the copy of genes1 (that is under Session1) to test1
6. What would be the result of tail -n2 genes2?
7. What would be the result of head genes1? Explain
8. Create with touch 3 different files under assignment: genes3, genes4, genes5
9. Copy the newly created files as well as genes1 and genes2 using the wildcards into
the directory Session1
Introduction to Bioinformatics online course: IBT
Task 1: participant’s answer
<start typing your answer here>

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