Functions - Revision history

WikiSysop: /* Exercises to be handed in */

2025-10-03T13:56:25Z

Exercises to be handed in

← Older revision		Revision as of 15:56, 3 October 2025
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	Any function you are required to make here needs a small program around it to show that it works - so you also make that as part of your hand-in.<br>		Any function you are required to make here needs a small program around it to show that it works - so you also make that as part of your hand-in.<br>
	The exercises 5 to 8 belongs together as a group and should be solved in order. They are about reading, changing and writing fasta files with many entries. You will likely find 5 especially hard.		The exercises 5 to 8 belongs together as a group and should be solved in order. They are about reading, changing and writing fasta files with many entries. You will likely find 5 especially hard.
	# The [https://en.wikipedia.org/wiki/Hamming_distance Hamming distance] is the distance between two strings of '''equal''' length. Make a function which takes two strings as arguments and calculates the distance between them. Add error handling.
	# Make a function '''fibonacci(no1, no2, count)''' which calculates the first '''count''' [https://en.wikipedia.org/wiki/Fibonacci_number fibonacci numbers] based on '''no1''' and '''no2''' and returns them in a list. The next number in a fibonacci sequence is the sum of the two previous numbers. Test it with printing the resulting list (one number per line) from fibonacci(0,1,20).		# The [https://en.wikipedia.org/wiki/Hamming_distance Hamming distance] is the distance between two strings of '''equal''' length. Make a function which takes two strings as arguments and calculates the distance between them. Add error handling.<br><br>
	# Make a function that returns the unique elements of a list as a list. Try it on the accession numbers in ''ex5.acc'', which contains 6461 unique accessions, but also make your own file with simple numbers.		# Make a function '''fibonacci(no1, no2, count)''' which calculates the first '''count''' [https://en.wikipedia.org/wiki/Fibonacci_number fibonacci numbers] based on '''no1''' and '''no2''' and returns them in a list. The next number in a fibonacci sequence is the sum of the two previous numbers. Test it with printing the resulting list (one number per line) from fibonacci(0,1,20).<br><br>
	# <font color="#AA00FF">Make a function that calculates the standard deviation of a list of numbers. Try with the file ''ex1.dat'', where you pool all the numbers in the the 3 columns into one list and get the result 1.8355. You can either do the two-pass algorithm (iteration through all the numbers twice) which is clear from the formula or the one-pass algorithm which you can derive from the formula if you are up to the challenge.</font><br> [[File:StandardDeviation.gif]]		# Make a function that returns the unique elements of a list as a list. Try it on the accession numbers in ''ex5.acc'', which contains 6461 unique accessions, but also make your own file with simple numbers.<br><br>
	# Look at the fasta file ''dna7.fsa''. It contains several fasta entries. Reading more than one entry in a file is more complex. Make a program that mostly consists of one function '''fastaread(filename)''' which takes a filename as a parameter and returns 2 lists, first list is the entry headers, second list is the entry sequences (as single strings without whitespace). Add appropriate error handling to the function. Just print the headers and sequences out pairwise as proof of concept. <br>Hint: I will point out that the reading and writing of fasta files with many entries is a regular occurrence in bioinformatics (and exam), so be sure to get it right. Many people mistakenly believe that they should use a form of stateful parsing with a flag for this - doing so confuses the issue, so abstain from that.		# <font color="#AA00FF">Make a function that calculates the standard deviation of a list of numbers. Try with the file ''ex1.dat'', where you pool all the numbers in the the 3 columns into one list and get the result 1.8355. You can either do the two-pass algorithm (iteration through all the numbers twice) which is clear from the formula or the one-pass algorithm which you can derive from the formula if you are up to the challenge.</font><br> [[File:StandardDeviation.gif]]<br><br>
	# Make a function '''fastawrite(filename, headers, sequences)''' which takes a filename, a list of headers and a corresponding list of sequences as parameters and writes a fasta file with that file name. Add appropriate error handling to the function. You can test your function using the file ''dna7.fsa'' and your previous function - reading ''dna7.fsa'' and then writing a new fasta file, should make the files identical.		# Look at the fasta file ''dna7.fsa''. It contains several fasta entries. Reading more than one entry in a file is more complex. Make a program that mostly consists of one function '''fastaread(filename)''' which takes a filename as a parameter and returns 2 lists, first list is the entry headers, second list is the entry sequences (as single strings without whitespace). Add appropriate error handling to the function. Just print the headers and sequences out pairwise as proof of concept. <br>Hint: I will point out that the reading and writing of fasta files with many entries is a regular occurrence in bioinformatics (and exam), so be sure to get it right. Many people mistakenly believe that they should use a form of stateful parsing with a flag for this - doing so confuses the issue, so abstain from that.<br><br>
	# Make a function that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write the complement strands in the new file ''revdna7.fsa''. Add 'Complement strand' to each header.		# Make a function '''fastawrite(filename, headers, sequences)''' which takes a filename, a list of headers and a corresponding list of sequences as parameters and writes a fasta file with that file name. Add appropriate error handling to the function. You can test your function using the file ''dna7.fsa'' and your previous function - reading ''dna7.fsa'' and then writing a new fasta file, should make the files identical.<br><br>
			# Make a function that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write the complement strands in the new file ''revdna7.fsa''. Add 'Complement strand' to each header.<br><br>
	# Make a function that calculates the GC-content of a DNA sequence. It takes a DNA (string) as parameter and returns the GC percentage. Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write only the sequences which has a GC-content percentage over 50% in the new file ''dna7GC.fsa''.		# Make a function that calculates the GC-content of a DNA sequence. It takes a DNA (string) as parameter and returns the GC percentage. Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write only the sequences which has a GC-content percentage over 50% in the new file ''dna7GC.fsa''.

WikiSysop: /* Exercises to be handed in */

2025-09-01T09:53:56Z

Exercises to be handed in

← Older revision		Revision as of 11:53, 1 September 2025
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	Any function you are required to make here needs a small program around it to show that it works - so you also make that as part of your hand-in.		Any function you are required to make here needs a small program around it to show that it works - so you also make that as part of your hand-in.<br>
			The exercises 5 to 8 belongs together as a group and should be solved in order. They are about reading, changing and writing fasta files with many entries. You will likely find 5 especially hard.
	# The [https://en.wikipedia.org/wiki/Hamming_distance Hamming distance] is the distance between two strings of '''equal''' length. Make a function which takes two strings as arguments and calculates the distance between them. Add error handling.		# The [https://en.wikipedia.org/wiki/Hamming_distance Hamming distance] is the distance between two strings of '''equal''' length. Make a function which takes two strings as arguments and calculates the distance between them. Add error handling.
	# Make a function '''fibonacci(no1, no2, count)''' which calculates the first '''count''' [https://en.wikipedia.org/wiki/Fibonacci_number fibonacci numbers] based on '''no1''' and '''no2''' and returns them in a list. The next number in a fibonacci sequence is the sum of the two previous numbers. Test it with printing the resulting list (one number per line) from fibonacci(0,1,20).		# Make a function '''fibonacci(no1, no2, count)''' which calculates the first '''count''' [https://en.wikipedia.org/wiki/Fibonacci_number fibonacci numbers] based on '''no1''' and '''no2''' and returns them in a list. The next number in a fibonacci sequence is the sum of the two previous numbers. Test it with printing the resulting list (one number per line) from fibonacci(0,1,20).

WikiSysop: /* Exercises to be handed in */

2025-08-29T14:09:23Z

Exercises to be handed in

← Older revision		Revision as of 16:09, 29 August 2025
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	# Make a function that returns the unique elements of a list as a list. Try it on the accession numbers in ''ex5.acc'', which contains 6461 unique accessions, but also make your own file with simple numbers.		# Make a function that returns the unique elements of a list as a list. Try it on the accession numbers in ''ex5.acc'', which contains 6461 unique accessions, but also make your own file with simple numbers.
	# <font color="#AA00FF">Make a function that calculates the standard deviation of a list of numbers. Try with the file ''ex1.dat'', where you pool all the numbers in the the 3 columns into one list and get the result 1.8355. You can either do the two-pass algorithm (iteration through all the numbers twice) which is clear from the formula or the one-pass algorithm which you can derive from the formula if you are up to the challenge.</font><br> [[File:StandardDeviation.gif]]		# <font color="#AA00FF">Make a function that calculates the standard deviation of a list of numbers. Try with the file ''ex1.dat'', where you pool all the numbers in the the 3 columns into one list and get the result 1.8355. You can either do the two-pass algorithm (iteration through all the numbers twice) which is clear from the formula or the one-pass algorithm which you can derive from the formula if you are up to the challenge.</font><br> [[File:StandardDeviation.gif]]
	# Look at the fasta file ''dna7.fsa''. It contains several fasta entries. Reading more than one entry in a file is more complex. Make a program that mostly consists of one function '''fastaread(filename)''' which takes a filename as a parameter and returns 2 lists, first list is the entry headers, second list is the entry sequences (as single strings without whitespace). Add appropriate error handling to the function. Just print the headers and sequences out pairwise as proof of concept. Hint: I will point out that the reading and writing of fasta files with many entries is a regular occurrence in bioinformatics (and exam), so be sure to get it right. Many people mistakenly believe that they should use a form of stateful parsing with a flag for this - doing so confuses the issue, so abstain from that.		# Look at the fasta file ''dna7.fsa''. It contains several fasta entries. Reading more than one entry in a file is more complex. Make a program that mostly consists of one function '''fastaread(filename)''' which takes a filename as a parameter and returns 2 lists, first list is the entry headers, second list is the entry sequences (as single strings without whitespace). Add appropriate error handling to the function. Just print the headers and sequences out pairwise as proof of concept. <br>Hint: I will point out that the reading and writing of fasta files with many entries is a regular occurrence in bioinformatics (and exam), so be sure to get it right. Many people mistakenly believe that they should use a form of stateful parsing with a flag for this - doing so confuses the issue, so abstain from that.
	# Make a function '''fastawrite(filename, headers, sequences)''' which takes a filename, a list of headers and a corresponding list of sequences as parameters and writes a fasta file with that file name. Add appropriate error handling to the function. You can test your function using the file ''dna7.fsa'' and your previous function - reading ''dna7.fsa'' and then writing a new fasta file, should make the files identical.		# Make a function '''fastawrite(filename, headers, sequences)''' which takes a filename, a list of headers and a corresponding list of sequences as parameters and writes a fasta file with that file name. Add appropriate error handling to the function. You can test your function using the file ''dna7.fsa'' and your previous function - reading ''dna7.fsa'' and then writing a new fasta file, should make the files identical.
	# Make a function that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write the complement strands in the new file ''revdna7.fsa''. Add 'Complement strand' to each header.		# Make a function that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write the complement strands in the new file ''revdna7.fsa''. Add 'Complement strand' to each header.

WikiSysop: /* Exercises to be handed in */

2025-08-29T14:09:03Z

Exercises to be handed in

← Older revision		Revision as of 16:09, 29 August 2025
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	# Make a function that returns the unique elements of a list as a list. Try it on the accession numbers in ''ex5.acc'', which contains 6461 unique accessions, but also make your own file with simple numbers.		# Make a function that returns the unique elements of a list as a list. Try it on the accession numbers in ''ex5.acc'', which contains 6461 unique accessions, but also make your own file with simple numbers.
	# <font color="#AA00FF">Make a function that calculates the standard deviation of a list of numbers. Try with the file ''ex1.dat'', where you pool all the numbers in the the 3 columns into one list and get the result 1.8355. You can either do the two-pass algorithm (iteration through all the numbers twice) which is clear from the formula or the one-pass algorithm which you can derive from the formula if you are up to the challenge.</font><br> [[File:StandardDeviation.gif]]		# <font color="#AA00FF">Make a function that calculates the standard deviation of a list of numbers. Try with the file ''ex1.dat'', where you pool all the numbers in the the 3 columns into one list and get the result 1.8355. You can either do the two-pass algorithm (iteration through all the numbers twice) which is clear from the formula or the one-pass algorithm which you can derive from the formula if you are up to the challenge.</font><br> [[File:StandardDeviation.gif]]
	# Look at the fasta file ''dna7.fsa''. It contains several fasta entries. Reading more than one entry in a file is more complex. Make a program that mostly consists of one function '''fastaread(filename)''' which takes a filename as a parameter and returns 2 lists, first list is the entry headers, second list is the entry sequences (as single strings without whitespace). Add appropriate error handling to the function. Just print the headers and sequences out pairwise as proof of concept.		# Look at the fasta file ''dna7.fsa''. It contains several fasta entries. Reading more than one entry in a file is more complex. Make a program that mostly consists of one function '''fastaread(filename)''' which takes a filename as a parameter and returns 2 lists, first list is the entry headers, second list is the entry sequences (as single strings without whitespace). Add appropriate error handling to the function. Just print the headers and sequences out pairwise as proof of concept. Hint: I will point out that the reading and writing of fasta files with many entries is a regular occurrence in bioinformatics (and exam), so be sure to get it right. Many people mistakenly believe that they should use a form of stateful parsing with a flag for this - doing so confuses the issue, so abstain from that.
	# Make a function '''fastawrite(filename, headers, sequences)''' which takes a filename, a list of headers and a corresponding list of sequences as parameters and writes a fasta file with that file name. Add appropriate error handling to the function. You can test your function using the file ''dna7.fsa'' and your previous function - reading ''dna7.fsa'' and then writing a new fasta file, should make the files identical.		# Make a function '''fastawrite(filename, headers, sequences)''' which takes a filename, a list of headers and a corresponding list of sequences as parameters and writes a fasta file with that file name. Add appropriate error handling to the function. You can test your function using the file ''dna7.fsa'' and your previous function - reading ''dna7.fsa'' and then writing a new fasta file, should make the files identical.
	# Make a function that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write the complement strands in the new file ''revdna7.fsa''. Add 'Complement strand' to each header.		# Make a function that take a DNA sequence (string) as parameter and return the complement strand (reverse complement). Make the function generic and portable, i.e. not dependent on any external factors. Together with the functions you made in exercise 5 & 6, read the fasta entries in file ''dna7.fsa'' and write the complement strands in the new file ''revdna7.fsa''. Add 'Complement strand' to each header.

WikiSysop: /* Exercises to be handed in */

2025-08-29T14:06:30Z

Exercises to be handed in

← Older revision		Revision as of 16:06, 29 August 2025
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	== Exercises to be handed in ==		== Exercises to be handed in ==
			Any function you are required to make here needs a small program around it to show that it works - so you also make that as part of your hand-in.
	# The [https://en.wikipedia.org/wiki/Hamming_distance Hamming distance] is the distance between two strings of '''equal''' length. Make a function which takes two strings as arguments and calculates the distance between them. Add error handling.		# The [https://en.wikipedia.org/wiki/Hamming_distance Hamming distance] is the distance between two strings of '''equal''' length. Make a function which takes two strings as arguments and calculates the distance between them. Add error handling.
	# Make a function '''fibonacci(no1, no2, count)''' which calculates the first '''count''' [https://en.wikipedia.org/wiki/Fibonacci_number fibonacci numbers] based on '''no1''' and '''no2''' and returns them in a list. The next number in a fibonacci sequence is the sum of the two previous numbers. Test it with printing the resulting list (one number per line) from fibonacci(0,1,20).		# Make a function '''fibonacci(no1, no2, count)''' which calculates the first '''count''' [https://en.wikipedia.org/wiki/Fibonacci_number fibonacci numbers] based on '''no1''' and '''no2''' and returns them in a list. The next number in a fibonacci sequence is the sum of the two previous numbers. Test it with printing the resulting list (one number per line) from fibonacci(0,1,20).

WikiSysop: /* Exercises for extra practice */

2025-08-29T14:04:57Z

Exercises for extra practice

← Older revision		Revision as of 16:04, 29 August 2025
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	== Exercises for extra practice ==		== Exercises for extra practice ==
	* Make a function that calculates the factorial. Add some input control to the function to make sure you get positive integers, when you ask for a number. Consider if you want to raise an exception if the function gets invalid data or you want to halt the program.		* Make a function that calculates the factorial. Add some input control to the function to make sure you get positive integers, when you ask for a number. Consider if you want to raise an exception if the function gets invalid data or you want to halt the program.
	* Make a the factorial function computation use recursion.		* Make the factorial function computation use recursion.

WikiSysop: /* Exercises for extra practice */

2025-08-29T14:04:43Z

Exercises for extra practice

← Older revision		Revision as of 16:04, 29 August 2025
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	== Exercises for extra practice ==		== Exercises for extra practice ==
	* Make a function that calculates the factorial. Add some input control to the function to make sure you get positive integers, when you ask for a number. Consider if you want to raise an exception if the function gets invalid data or you want to halt the program.		* Make a function that calculates the factorial. Add some input control to the function to make sure you get positive integers, when you ask for a number. Consider if you want to raise an exception if the function gets invalid data or you want to halt the program.
			* Make a the factorial function computation use recursion.

WikiSysop: /* Exercises for extra practice */

2025-08-29T14:03:12Z

Exercises for extra practice

← Older revision		Revision as of 16:03, 29 August 2025
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	== Exercises for extra practice ==		== Exercises for extra practice ==
			* Make a function that calculates the factorial. Add some input control to the function to make sure you get positive integers, when you ask for a number. Consider if you want to raise an exception if the function gets invalid data or you want to halt the program.

WikiSysop: /* Exercises for extra practice */

2025-08-29T14:00:54Z

Exercises for extra practice

← Older revision		Revision as of 16:00, 29 August 2025
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	== Exercises for extra practice ==		== Exercises for extra practice ==
	You will program a [https://en.wikipedia.org/wiki/Reverse_Polish_notation reverse polish notation] calculator using the functions you want. This is somewhat complicated, so I will split up the job in a number of smaller exercises, where the one exercise builds on the previous. Shortly, reverse polish notation is a mathematical notation in which operators follow their operands, i.e. adding two numbers is written by "3 4 +" instead of "3 + 4". We will utilize a [https://en.wikipedia.org/wiki/Stack_(abstract_data_type) stack], which is simply a list, where elements are added to and removed from the bottom.
	* Let's start with making the overall structure; a loop that asks for input, which is one item/command at a time. Inside the loop, there can be a number of operations depending on the input. If you enter a number, it should be simply appended to your list (the stack, which is the word I will use in the rest of the exercises here). If you enter commands '''STOP''', '''EXIT''' or '''QUIT''', the loop should end and the program stop. If you enter something that the program does not understand it should write "Illegal command", but otherwise do nothing.
	* Add the following commands: '''PEEK''', which displays the last number in the stack, and '''SHOW''' which will display the entire stack.
	* Add the standard math operations, '''+''', '''-''', '''*''' and '''/''': These remove 2 numbers from the stack (the last number in stack is the first operand and the second last number is the second operand), perform the operation and appends the result back to the stack. You notice operand order matters for - and /. At this point we have a simple but functional calculator.
	* Add single number operations '''LOG''' and '''SQRT''', which replaces the last number in the stack with the log/square root of the number.
	* Solidify your program by ensuring any operations first check if the required number of operands are on the stack before trying to perform the operation. Display "Not enough operands on the stack" and otherwise do nothing if the check fails. Hint: Maybe lists of zero, one and two operands commands could be useful.
	* Add the commands: '''DROP''' which simply removes the last number on the stack, '''=''', which removes the last number on the stack and displays it, '''SWITCH''', which switches the last two numbers on the stack, and '''DUP''' which duplicates the last number on the stack, i.e stack consists of 1, after DUP it consists of 1 1.
	* Add the commands: '''ABS''', '''NEG''' which replaces the last number on the stack which the absolute/negative value of the number.
	* At this point you can probably work out some mathematical operations to add that require one or 2 operands by yourself. I can think of the '''SIN''', '''COS''' & '''TAN''' operations, the '''INT''' taking the integer part of a number, '''EXP'''onential and '''SQUARE'''. Modulo operation with '''%'''. '''FAC'''torial. You could add constants like '''PI''' and '''E''' that simply puts an appropriate value on the stack.
	* Add stack control with '''CLEAR''' to empty the stack and extend the '''SWITCH''' to switch the numbers as two given position like "SWITCH 2 4" if given positions.

WikiSysop at 13:46, 29 August 2025

2025-08-29T13:46:02Z

← Older revision		Revision as of 15:46, 29 August 2025
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	{\| 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: [[List manipulation]]		\|Previous: [[List manipulation]]
	\|Next: [[~~Functions~~]]		\|Next: [[Simple pattern matching]]
	\|}		\|}
	== Required course material for the lesson ==		== Required course material for the lesson ==
	Powerpoint: [https://teaching.healthtech.dtu.dk/material/~~22113~~/~~22113_04~~-Functions.ppt ~~Making functions~~]<br>		Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_08-Functions.ppt Functions]<br>
	<!-- Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=f509116f-48e5-445b-bf6e-af27012ba23f Functions in Python] Monday<br>		<!-- Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=f509116f-48e5-445b-bf6e-af27012ba23f Functions in Python] Monday<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=21e9d4d0-2ba5-465c-9939-af27012b7a7e Examples and identifying data types] Monday<br> -->		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=21e9d4d0-2ba5-465c-9939-af27012b7a7e Examples and identifying data types] Monday<br> -->
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	== Subjects covered ==		== Subjects covered ==
	* Functions: a function is both a way of hiding complexity and a way of reusing code.		* Functions: a function is both a way of hiding complexity and a way of reusing code.
	* ~~Scope~~ of variables.		* Arguments, scope of variables.

	== Exercises to be handed in ==		== Exercises to be handed in ==