Changing existing code base - Revision history

WikiSysop: /* Exercises to be handed in */

2026-05-08T11:24:44Z

Exercises to be handed in

← Older revision		Revision as of 13:24, 8 May 2026
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	as FASTQ files get really big and can't all be in memory.<br>		as FASTQ files get really big and can't all be in memory.<br>
	FASTQ are often gzipped - it is nice to read them directly from the gzip file, but it makes the entire improvement harder.<br>		FASTQ are often gzipped - it is nice to read them directly from the gzip file, but it makes the entire improvement harder.<br>
	You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.		You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.<br>
			[https://teaching.healthtech.dtu.dk/material/22118/BRISCOE_0069_BD18RUACXX_L2_1_pf.fastq Example of an uncompressed FASTQ file]

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

WikiSysop: /* Exercises to be handed in */

2026-05-08T11:10:16Z

Exercises to be handed in

← Older revision		Revision as of 13:10, 8 May 2026
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	This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well. Most likely other stuff.<br>		This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well. Most likely other stuff.<br>
	Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere (f.ex. do not implement reading from stdin) or maybe generator,		Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere (f.ex. do not implement reading from stdin) or maybe generator,
	as FASTQ files get really big and can't all be in memory. ~~Also,~~ FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br>		as FASTQ files get really big and can't all be in memory.<br>
			FASTQ are often gzipped - it is nice to read them directly from the gzip file, but it makes the entire improvement harder.<br>
	You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.		You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.

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

WikiSysop: /* Exercises to be handed in */

2026-05-07T09:56:10Z

Exercises to be handed in

← Older revision		Revision as of 11:56, 7 May 2026
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	'''Make it able to read FASTQ files.'''<br>		'''Make it able to read FASTQ files.'''<br>
	This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well. Most likely other stuff.<br>		This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well. Most likely other stuff.<br>
	Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere (f.ex. do not implement reading ~~form~~ stdin) or maybe generator,		Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere (f.ex. do not implement reading from stdin) or maybe generator,
	as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br>		as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br>
	You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.		You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.

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

WikiSysop: /* Exercises to be handed in */

2026-05-07T09:55:58Z

Exercises to be handed in

← Older revision		Revision as of 11:55, 7 May 2026
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	Clone Anders Gorm's repo: ''sequencelib'' and study it.<br>		Clone Anders Gorm's repo: ''sequencelib'' and study it.<br>
	'''Make it able to read FASTQ files.'''<br>		'''Make it able to read FASTQ files.'''<br>
	This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well.<br>		This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well. Most likely other stuff.<br>
	Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere or maybe generator,		Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere (f.ex. do not implement reading form stdin) or maybe generator,
	as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br>		as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br>
	You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.		You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.

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

WikiSysop: /* Opportunity */

2026-05-04T10:57:17Z

Opportunity

← Older revision		Revision as of 12:57, 4 May 2026
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	\|}		\|}
	== Opportunity ==		== Opportunity ==
	PDF: [https://teaching.healthtech.dtu.dk/material/22118/RNA-editing_Masterproject.pdf RNA Editing] A Master project.		PDF: [https://teaching.healthtech.dtu.dk/material/22118/RNA-editing_Masterproject.pdf RNA Editing] A Master project. Contact Greg, grinos@dtu.dk

	== Required course material for the lesson ==		== Required course material for the lesson ==

WikiSysop at 09:52, 4 May 2026

2026-05-04T09:52:21Z

← Older revision		Revision as of 11:52, 4 May 2026
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	\|Next: [[Last words]]		\|Next: [[Last words]]
	\|}		\|}
			== Opportunity ==
			PDF: [https://teaching.healthtech.dtu.dk/material/22118/RNA-editing_Masterproject.pdf RNA Editing] A Master project.

	== Required course material for the lesson ==		== Required course material for the lesson ==
	GitHub: [https://github.com/agormp Professor Anders Gorm Pedersen's repositories.] Used in teaching this week.<br>		GitHub: [https://github.com/agormp Professor Anders Gorm Pedersen's repositories.] Used in teaching this week.<br>

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

2026-04-30T13:48:14Z

Required course material for the lesson

← Older revision		Revision as of 15:48, 30 April 2026
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	== Required course material for the lesson ==		== Required course material for the lesson ==
	GitHub: [https://github.com/agormp Professor Anders Gorm Pedersen's repositories.] Used in teaching this week.<br>		GitHub: [https://github.com/agormp Professor Anders Gorm Pedersen's repositories.] Used in teaching this week.<br>
	GitHub: [https://github.com/genenetwork/ Gene network.] A much larger and thus more complicated/confusing repo.<br>		GitHub: [https://github.com/genenetwork/ Gene network.] A much larger and thus more complicated/confusing repo. They are looking for help/contributers<br>
	GitHub: [https://github.com/bioinform The Bioinformatics Repository.] Different repos, various languages.<br>		GitHub: [https://github.com/bioinform The Bioinformatics Repository.] Different repos, various languages.<br>
	<!-- Resource: [[Example code - File Reading]]<br> -->		<!-- Resource: [[Example code - File Reading]]<br> -->

WikiSysop: /* Exercises to be handed in */

2026-04-30T13:42:41Z

Exercises to be handed in

← Older revision		Revision as of 15:42, 30 April 2026
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	There are going to be only one exercise. You have the project, and the exercise will be big.<br>		There are going to be only one exercise. You have the project, and the exercise will be big.<br>
	Clone Anders Gorm's repo: ''sequencelib'' and study it.<br>		Clone Anders Gorm's repo: ''sequencelib'' and study it.<br>
	Make it able to read FASTQ files.		'''Make it able to read FASTQ files.'''<br>
			This includes changing the Seqfile class, adding a new Fastqfilehandle class, and understanding the Sequence class really well.<br>
			Of course, you are using Git to handle your changes. You might make some kind of limitation somewhere or maybe generator,
			as FASTQ files get really big and can't all be in memory. Also, FASTQ are often gzipped - it is nice to read them directly from the gzip file.<br>
			You don't know FASTQ format? - look it up - this is supposed to be a "real world problem". You don't get much help.

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

WikiSysop: /* Exercises to be handed in */

2026-04-30T12:28:58Z

Exercises to be handed in

← Older revision		Revision as of 14:28, 30 April 2026
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	There are ~~no exercises for this lecture - or~~ the ~~rest of~~ the ~~course~~		There are going to be only one exercise. You have the project, and the exercise will be big.<br>
			Clone Anders Gorm's repo: ''sequencelib'' and study it.<br>
			Make it able to read FASTQ files.

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

WikiSysop at 12:22, 30 April 2026

2026-04-30T12:22:09Z

← Older revision		Revision as of 14:22, 30 April 2026
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	__NOTOC__		__NOTOC__
	{\| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;"		{\| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;"
	\|Previous: [[Runtime ~~evauation~~]]		\|Previous: [[Runtime evaluation]]
	\|Next: [[Last words]]		\|Next: [[Last words]]
	\|}		\|}