Unix Exercises - Revision history

Mick at 12:07, 5 January 2026

2026-01-05T12:07:53Z

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	\|Next: [[Python Recap and Objects]]		\|Next: [[Python Recap and Objects]]
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	== Suggested resources ==		== Suggested resources ==

Mick at 12:07, 5 January 2026

2026-01-05T12:07:35Z

← Older revision		Revision as of 14:07, 5 January 2026
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	~~You did complete the [[Course preparation]], right? Otherwise, all of this will fail.~~

	== ~~Required course material for the lesson~~ ==		== Suggested resources ==
	PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix]		PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix]
	The videos are not entirely in sync with the updated PowerPoint.		The videos are not entirely in sync with the updated PowerPoint.

Mick at 12:06, 5 January 2026

2026-01-05T12:06:43Z

← Older revision		Revision as of 14:06, 5 January 2026
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	* Scripting in bash		* Scripting in bash

	== Exercises ~~to be handed in~~ ==		== Exercises ==
	Use a text editor to create a file ''mycommands.txt'' where you write all commands and observations from the exercises below.		Use a text editor to create a file ''mycommands.txt'' where you write all commands and observations from the exercises below.
	Use copy/paste to insert the commands you ran.		Use copy/paste to insert the commands you ran.
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	* Data files are available in the [https://teaching.healthtech.dtu.dk/22113/index.php/Collection_of_files collection of files].		* Data files are available in the [https://teaching.healthtech.dtu.dk/22113/index.php/Collection_of_files collection of files].

	== Exercises to do ~~after Monday~~ ==		== Exercises to do ==

	It is assumed that you have downloaded the three files: ''ex1.dat'', ''ex1.acc'' and ''orphans.sp'' before starting.		It is assumed that you have downloaded the three files: ''ex1.dat'', ''ex1.acc'' and ''orphans.sp'' before starting.
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	# From ''ex1.res'', send positive numbers to ''ex1.pos'' and negative numbers to ''ex1.neg''.		# From ''ex1.res'', send positive numbers to ''ex1.pos'' and negative numbers to ''ex1.neg''.
	# Calculate ((356+51)*123-12765)/56 directly on the command line.		# Calculate ((356+51)*123-12765)/56 directly on the command line.

	~~== Exercises to do after Thursday ==~~
	~~<ol start="26">~~
	~~<li>Repeat exercises 2 and 3, but this time use '''diff''' to check differences.</li>~~
	~~<li>In ''myfile.acc'' (a copy of ''ex1.acc''), change all occurrences of SPC to BLNK using '''sed'''. Verify changes using '''diff'''.</li>~~
	~~<li>Find the path to the '''bash''' executable.</li>~~
	~~<li>Write a bash script that solves exercises 19–24, with each exercise clearly separated and explained in both the script and the output.</li>~~
	~~<li>Write a bash script that puts all positive numbers from ''ex1.dat'' into ''ex1.pos2'' and negative numbers into ''ex1.neg2''.~~
	~~The script must clean up temporary files and include a header with the date and a short description.</li>~~
	~~<li>Write a bash script that calculates the total number of lines for all files in a directory given as a command-line argument.~~
	~~No argument means the current directory.~~
	~~Note: '''cut''' can split on symbols other than tabs.</li>~~
	~~</ol>~~

	~~== Exercises for extra practice ==~~

Mick at 14:31, 16 December 2025

2025-12-16T14:31:43Z

← Older revision		Revision as of 16:31, 16 December 2025
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	* Make sure it is clear which exercise you are solving.		* Make sure it is clear which exercise you are solving.
	* Work from your home directory unless you explicitly state otherwise.		* Work from your home directory unless you explicitly state otherwise.
	* Data files are available in the [[collection of files]].		* Data files are available in the [https://teaching.healthtech.dtu.dk/22113/index.php/Collection_of_files collection of files].

	== Exercises to do after Monday ==		== Exercises to do after Monday ==

Mick at 14:45, 19 November 2025

2025-11-19T14:45:05Z

← Older revision		Revision as of 16:45, 19 November 2025
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	Resource: [https://teaching.healthtech.dtu.dk/unix The UNIX resource used across Health Tech courses]		* Resource: [https://teaching.healthtech.dtu.dk/unix The UNIX resource used across Health Tech courses]
	Resource: [[Biological knowledge needed in the course]]		* Resource: [[Biological knowledge needed in the course]]
	Resource: [http://www.ee.surrey.ac.uk/Teaching/Unix/ UNIX Tutorial for Beginners]		* Resource: [http://www.ee.surrey.ac.uk/Teaching/Unix/ UNIX Tutorial for Beginners]
	Resource: [http://www.tutorialspoint.com/unix/ UNIX/LINUX Tutorial]		* Resource: [http://www.tutorialspoint.com/unix/ UNIX/LINUX Tutorial]

	== Subjects covered ==		== Subjects covered ==

Mick at 14:44, 19 November 2025

2025-11-19T14:44:45Z

← Older revision		Revision as of 16:44, 19 November 2025
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	The videos are not entirely in sync with the updated PowerPoint.		The videos are not entirely in sync with the updated PowerPoint.

	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation] Monday
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=88cb52db-1c77-4a98-94db-af270127d0dc Copying, Moving, Renaming files. Changing permissions] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=88cb52db-1c77-4a98-94db-af270127d0dc Copying, Moving, Renaming files. Changing permissions] Monday
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fa98c15f-5c50-4ea3-8c85-af270127aedf Using shortcuts in Unix – making it easier] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fa98c15f-5c50-4ea3-8c85-af270127aedf Using shortcuts in Unix - making it easier] Monday
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=7f775d1b-2788-45ee-b4ac-af2701279221 File inspection and ~~editors~~ in Unix] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=7f775d1b-2788-45ee-b4ac-af2701279221 File inspection and editor in Unix] Monday
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=16f1e9bd-8044-4a97-b033-af27012771e2 Manipulating files: wc, paste, cut & sort] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=16f1e9bd-8044-4a97-b033-af27012771e2 Manipulating files: wc, paste, cut & sort] Monday
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=5ecff806-b2de-42f7-ab97-af2701274f66 Manipulating files: grep and pipelines] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=5ecff806-b2de-42f7-ab97-af2701274f66 Manipulating files: grep and pipelines] Monday
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0679c534-a422-4ed6-9f52-af27012730b2 Touching upon various relevant subjects] Monday		* Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0679c534-a422-4ed6-9f52-af27012730b2 Touching upon various relevant subjects] Monday


	Resource: [https://teaching.healthtech.dtu.dk/unix The UNIX resource used across Health Tech courses]		Resource: [https://teaching.healthtech.dtu.dk/unix The UNIX resource used across Health Tech courses]

Mick: Created page with "NOTOC {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: None |Next: Python Recap and Objects |} You did complete the Course preparation, right? Otherwise, all of this will fail. == Required course material for the lesson == PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the updated PowerPoint. Video: [https:..."

2025-11-19T14:43:29Z

Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: None |Next: Python Recap and Objects |} You did complete the Course preparation, right? Otherwise, all of this will fail. == Required course material for the lesson == PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the updated PowerPoint. Video: [https:..."

New page

__NOTOC__
{| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;"
|Previous: None
|Next: [[Python Recap and Objects]]
|}

You did complete the [[Course preparation]], right? Otherwise, all of this will fail.

== Required course material for the lesson ==
PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix]
The videos are not entirely in sync with the updated PowerPoint.

Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation] Monday
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=88cb52db-1c77-4a98-94db-af270127d0dc Copying, Moving, Renaming files. Changing permissions] Monday
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fa98c15f-5c50-4ea3-8c85-af270127aedf Using shortcuts in Unix – making it easier] Monday
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=7f775d1b-2788-45ee-b4ac-af2701279221 File inspection and editors in Unix] Monday
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=16f1e9bd-8044-4a97-b033-af27012771e2 Manipulating files: wc, paste, cut & sort] Monday
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=5ecff806-b2de-42f7-ab97-af2701274f66 Manipulating files: grep and pipelines] Monday
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0679c534-a422-4ed6-9f52-af27012730b2 Touching upon various relevant subjects] Monday

Resource: [https://teaching.healthtech.dtu.dk/unix The UNIX resource used across Health Tech courses]
Resource: [[Biological knowledge needed in the course]]
Resource: [http://www.ee.surrey.ac.uk/Teaching/Unix/ UNIX Tutorial for Beginners]
Resource: [http://www.tutorialspoint.com/unix/ UNIX/LINUX Tutorial]

== Subjects covered ==
* Basic file handling in UNIX
* Understanding and navigating the file system
* Many different Unix commands
* Scripting in bash

== Exercises to be handed in ==
Use a text editor to create a file ''mycommands.txt'' where you write all commands and observations from the exercises below.
Use copy/paste to insert the commands you ran.

'''Notes:'''
* Make sure it is clear which exercise you are solving.
* Work from your home directory unless you explicitly state otherwise.
* Data files are available in the [[collection of files]].

== Exercises to do after Monday ==

It is assumed that you have downloaded the three files: ''ex1.dat'', ''ex1.acc'' and ''orphans.sp'' before starting.

# List the files in the current directory.
# Copy ''ex1.acc'' to ''myfile.acc''.
# View the contents of both files to ensure they are identical.
# Copy ''ex1.dat'' to ''myfile.acc'' (overwriting it).
# Check that the contents of ''myfile.acc'' have changed.
# Delete ''myfile.acc''.
# Create a directory called ''test'' and move the three files into it.
# Create a directory ''data'' and move the three files into ''data'' instead.
# Remove the now-empty ''test'' directory.
# Change directory to ''data'' and confirm that the three files are there. Return to your home/work directory afterwards.
# Create three new directories, each inside the previous one, like Russian dolls: ''newtest/one/two''.
# Move the ''data'' directory into the innermost ''two'' directory.
# Confirm that the three files moved along with the ''data'' directory.
# Copy the three files from ''data'' back into your home directory.
# Remove all ''newtest'' directories and ''data'' with a single command.
'''Warning:''' Make sure you are in the correct parent directory before running a recursive remove.
# Count the lines in ''ex1.acc'' and ''ex1.dat''.
# Concatenate ''ex1.acc'' and ''ex1.dat'' into ''ex1.tot''. Ensure gene IDs appear first and numerical data after.
# Merge/paste ''ex1.acc'' and ''ex1.dat'' together into ''ex1.tot'', overwriting the previous file. Verify corresponding lines appear together.
# Extract (cut) SwissProt ID and the 3rd numerical field (columns 1 and 5) from ''ex1.tot'' and save into ''ex1.res''.
# Find the three SwissProt IDs in ''ex1.res'' with the largest numbers in column 2. Display only the IDs.
# Find the lines in ''orphans.sp'' that contain a GenBank accession number using ''grep''. There are 85; verify this.
# How many human genes with SwissProt IDs exist in ''orphans.sp''? How many are hypothetical? (11)
# How many rat genes exist, and how many of those are precursors? (9)
# From ''ex1.res'', send positive numbers to ''ex1.pos'' and negative numbers to ''ex1.neg''.
# Calculate ((356+51)*123-12765)/56 directly on the command line.

== Exercises to do after Thursday ==
<ol start="26">
<li>Repeat exercises 2 and 3, but this time use '''diff''' to check differences.</li>
<li>In ''myfile.acc'' (a copy of ''ex1.acc''), change all occurrences of SPC to BLNK using '''sed'''. Verify changes using '''diff'''.</li>
<li>Find the path to the '''bash''' executable.</li>
<li>Write a bash script that solves exercises 19–24, with each exercise clearly separated and explained in both the script and the output.</li>
<li>Write a bash script that puts all positive numbers from ''ex1.dat'' into ''ex1.pos2'' and negative numbers into ''ex1.neg2''.
The script must clean up temporary files and include a header with the date and a short description.</li>
<li>Write a bash script that calculates the total number of lines for all files in a directory given as a command-line argument.
No argument means the current directory.
Note: '''cut''' can split on symbols other than tabs.</li>
</ol>

== Exercises for extra practice ==