Solo git - Revision history

WikiSysop: /* Exercises to be handed in */

2026-02-23T14:15:04Z

Exercises to be handed in

← Older revision		Revision as of 16:15, 23 February 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>		Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>
			<b>Note that any use of Jupiter Notebooks is an extremely bad idea. Git can not properly track changes in .ipynb files. Make your python programs in some editor, save them and run them from the command line, where you are going to do your git commands anyway.</b><br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.''' When the exercise talks about changing a previous exercise, you should copy the original exercise and make a new file/program where you do your changes.		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.''' When the exercise talks about changing a previous exercise, you should copy the original exercise and make a new file/program where you do your changes.
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''<br><br>		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''<br><br>

WikiSysop: /* Exercises to be handed in */

2026-02-17T12:50:55Z

Exercises to be handed in

← Older revision		Revision as of 14:50, 17 February 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>		Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.''' When the exercise talks about changing a previous exercise, you should copy the original exercise and make a new file/program where you do your changes.
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''<br><br>		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''<br><br>
	# <font color="#AA00FF">The input file ''scores.txt'' is a tab-separated file with an accession number in first column followed by 6 numbers (scores) between 0 and 1. You must find the accession numbers and scores (that means the entire line) of the 10 highest and 10 lowest "combined scores" (combined score is the metric for selection) and save the output in the file ''scoresextreme.txt''.<br>The combined score is simply the 6 numbers added together. The order of the output must be from high to low.</font><br><br>		# <font color="#AA00FF">The input file ''scores.txt'' is a tab-separated file with an accession number in first column followed by 6 numbers (scores) between 0 and 1. You must find the accession numbers and scores (that means the entire line) of the 10 highest and 10 lowest "combined scores" (combined score is the metric for selection) and save the output in the file ''scoresextreme.txt''.<br>The combined score is simply the 6 numbers added together. The order of the output must be from high to low.</font><br><br>

WikiSysop: /* Exercises to be handed in */

2026-02-17T12:49:20Z

Exercises to be handed in

← Older revision		Revision as of 14:49, 17 February 2026
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	Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>		Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''<br><br>
	# <font color="#AA00FF">The input file ''scores.txt'' is a tab-separated file with an accession number in first column followed by 6 numbers (scores) between 0 and 1. You must find the accession numbers and scores (that means the entire line) of the 10 highest and 10 lowest "combined scores" (combined score is the metric for selection) and save the output in the file ''scoresextreme.txt''.<br>The combined score is simply the 6 numbers added together. The order of the output must be from high to low.</font>		# <font color="#AA00FF">The input file ''scores.txt'' is a tab-separated file with an accession number in first column followed by 6 numbers (scores) between 0 and 1. You must find the accession numbers and scores (that means the entire line) of the 10 highest and 10 lowest "combined scores" (combined score is the metric for selection) and save the output in the file ''scoresextreme.txt''.<br>The combined score is simply the 6 numbers added together. The order of the output must be from high to low.</font><br><br>
	# Change exercise 2 in the following way: There is an input file, ''negative_list.txt'', which is a list of genes which can NOT be part of the output. They are banned from your analysis. As can be seen, the genes are identified by their swissprot id. In order to translate from swissprot id to accession number so you can relate it to the ''scores.txt'', you must use the input file ''translation.txt'', where the first item on the line is a accession number, second item is the corresponding swissprot id.		# Change exercise 2 in the following way: There is an input file, ''negative_list.txt'', which is a list of genes which can NOT be part of the output. They are banned from your analysis. As can be seen, the genes are identified by their swissprot id. In order to translate from swissprot id to accession number so you can relate it to the ''scores.txt'', you must use the input file ''translation.txt'', where the first item on the line is a accession number, second item is the corresponding swissprot id.<br><br>
	# Change exercise 2 in the following way: Make the program work no matter how many numbers there are on every line. It must be the same number of numbers, i.e. in one file it could be 10 numbers on every line, in another file it could be 7 numbers per line.		# Change exercise 2 in the following way: Make the program work no matter how many numbers there are on every line. It must be the same number of numbers, i.e. in one file it could be 10 numbers on every line, in another file it could be 7 numbers per line.
	# Change exercise 2 in the following way: Instead of using the combined score as the metric for selecting the accession numbers and scores, then use the average score as the metric. That will allow for having a different number of numbers on each line in the input file.		# Change exercise 2 in the following way: Instead of using the combined score as the metric for selecting the accession numbers and scores, then use the average score as the metric. That will allow for having a different number of numbers on each line in the input file.<br><br>
	# Change exercise 2 in the following way: When you calculate the combined score the first number should weigh 50% more than the other numbers and the last should weigh 50% less.		# Change exercise 2 in the following way: When you calculate the combined score the first number should weigh 50% more than the other numbers and the last should weigh 50% less.<br><br>
	# Change exercise 2 in the following way: When you calculate the combined score the numbers should be weighted after a linear sliding scale with the first number count for 50% more than its real value, sliding linearly down to the last number which is weighted 50% less. The weight is thus dynamically calculated according to how many numbers there are on the line and which position the number is on the line.<br>'''N''' is the number of numbers, '''P''' is the position of the number, then the weight '''W''' is calculated as: W = 1.5 - (P-1)/(N-1)<br>A more generic expression for the sliding weighting scale - '''B''' is the beginning weight, '''E''' is the ending weight: W = B - (B-E)*(P-1)/(N-1)		# Change exercise 2 in the following way: When you calculate the combined score the numbers should be weighted after a linear sliding scale with the first number count for 50% more than its real value, sliding linearly down to the last number which is weighted 50% less. The weight is thus dynamically calculated according to how many numbers there are on the line and which position the number is on the line.<br>'''N''' is the number of numbers, '''P''' is the position of the number, then the weight '''W''' is calculated as: W = 1.5 - (P-1)/(N-1)<br>A more generic expression for the sliding weighting scale - '''B''' is the beginning weight, '''E''' is the ending weight: W = B - (B-E)*(P-1)/(N-1)<br><br>
	# Change exercise 2 in the following way: Just find the 10 lines in the input file with the highest combined scores. This should be easier than the original exercise.		# Change exercise 2 in the following way: Just find the 10 lines in the input file with the highest combined scores. This should be easier than the original exercise.<br><br>
	# This is the same exercise as the previous (ex 8), however imagine that the input file is enormous - so big that you can not have it in memory. You still need to solve the problem, and this is done by having a running list of the best scores.		# This is the same exercise as the previous (ex 8), however imagine that the input file is enormous - so big that you can not have it in memory. You still need to solve the problem, and this is done by having a running list of the best scores.

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

WikiSysop: /* Exercises to be handed in */

2026-02-16T14:31:23Z

Exercises to be handed in

← Older revision		Revision as of 16:31, 16 February 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	Do the exercises in '''Python''' where applicable. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>		Do the exercises in '''Python''' where applicable. Use git to track changes. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''

WikiSysop: /* Exercises to be handed in */

2026-02-16T14:30:32Z

Exercises to be handed in

← Older revision		Revision as of 16:30, 16 February 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	Do the exercises. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>		Do the exercises in '''Python''' where applicable. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''

WikiSysop: /* Exercises to be handed in */

2026-02-16T11:02:17Z

Exercises to be handed in

← Older revision		Revision as of 13:02, 16 February 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	Do the exercises. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat''.<br>		Do the exercises. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat'' in Unix. This is going to be the way we operate for large parts of the course.<br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''

WikiSysop: /* Exercises to be handed in */

2026-02-16T11:00:24Z

Exercises to be handed in

← Older revision		Revision as of 13:00, 16 February 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
			Do the exercises. Make one program per exercise (if relevant). Commit at least once per solved exercise - more often if you feel it relevant. At the end push everything to GitHub or more frequently if that is your pleasure - backup is nice. You gather all exercises into one file and hand that in on DTU Learn, hint ''cat''.<br>
	'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''		'''In exercises 2-9 the job is to ''select'' the lines in the input file, i.e. the exercises are about which lines to select in various ways. The output is just a few of the lines in the input file.'''
	# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''		# Create a private repository for your exercises on [https://github.com GitHub] as described in the powerpoint. You can choose whatever name you like for the repository. '''All exercises now and in the future should be created/stored in this repository unless otherwise strictly stated.'''

WikiSysop: /* Required course material for the lesson */

2026-02-11T16:28:31Z

Required course material for the lesson

← Older revision		Revision as of 18:28, 11 February 2026
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	== Required course material for the lesson ==		== Required course material for the lesson ==
	Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_03-Git.ppt Git]<br>		Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_03-Git.ppt Git]<br>
			Optional - do you want to know more<br>
	Online: [https://coderefinery.github.io/git-intro/ Coderefinery's introduction to git] This is one of many git resources on the net.<br>		Online: [https://coderefinery.github.io/git-intro/ Coderefinery's introduction to git] This is one of many git resources on the net.<br>
	Online: [https://www.markdownguide.org/ Markdown guide]<br>		Online: [https://www.markdownguide.org/ Markdown guide]<br>

WikiSysop: /* Required course material for the lesson */

2026-02-11T16:27:26Z

Required course material for the lesson

← Older revision		Revision as of 18:27, 11 February 2026
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	Online: [https://coderefinery.github.io/git-intro/ Coderefinery's introduction to git] This is one of many git resources on the net.<br>		Online: [https://coderefinery.github.io/git-intro/ Coderefinery's introduction to git] This is one of many git resources on the net.<br>
	Online: [https://www.markdownguide.org/ Markdown guide]<br>		Online: [https://www.markdownguide.org/ Markdown guide]<br>
	Online: [https://about.gitlab.com/topics/ci-cd/ CI/CD - Continuous Integration and Continuous Delivery. It’s a DevOps practice used with GitHub/GitLab.		Online: [https://about.gitlab.com/topics/ci-cd/ CI/CD] - Continuous Integration and Continuous Delivery. It’s a DevOps practice used with GitHub/GitLab.
	<!-- Resource: [[Example code - File Reading]]<br> -->		<!-- Resource: [[Example code - File Reading]]<br> -->

WikiSysop: /* Required course material for the lesson */

2026-02-11T16:26:57Z

Required course material for the lesson

← Older revision		Revision as of 18:26, 11 February 2026
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	Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_03-Git.ppt Git]<br>		Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_03-Git.ppt Git]<br>
	Online: [https://coderefinery.github.io/git-intro/ Coderefinery's introduction to git] This is one of many git resources on the net.<br>		Online: [https://coderefinery.github.io/git-intro/ Coderefinery's introduction to git] This is one of many git resources on the net.<br>
	Online: [https://www.markdownguide.org/ Markdown guide]		Online: [https://www.markdownguide.org/ Markdown guide]<br>
			Online: [https://about.gitlab.com/topics/ci-cd/ CI/CD - Continuous Integration and Continuous Delivery. It’s a DevOps practice used with GitHub/GitLab.
	<!-- Resource: [[Example code - File Reading]]<br> -->		<!-- Resource: [[Example code - File Reading]]<br> -->