Stateful parsing - Revision history

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

2025-10-09T10:51:41Z

Required course material for the lesson

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	== Required course material for the lesson ==		== Required course material for the lesson ==
	Powerpoint: [https://teaching.healthtech.dtu.dk/material/~~22101~~/~~22101_08~~-StatefulParsing.ppt Stateful Parsing]<br>		Powerpoint: [https://teaching.healthtech.dtu.dk/material/22116/22116_06-StatefulParsing.ppt Stateful Parsing]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fe50507e-9009-49b1-a3a8-af27012d8cdf Stateful Parsing]<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fe50507e-9009-49b1-a3a8-af27012d8cdf Stateful Parsing]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=ce785005-14cd-424a-a406-af27012b3e1b Finding errors with Stateful Parsing]<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=ce785005-14cd-424a-a406-af27012b3e1b Finding errors with Stateful Parsing]<br>

WikiSysop: /* Exercises to be handed in */

2025-10-03T13:55:07Z

Exercises to be handed in

← Older revision		Revision as of 15:55, 3 October 2025
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	== Exercises to be handed in ==		== Exercises to be handed in ==
	The following 5 exercises deal with SwissProt. The file sprot1.dat is a SwissProt database entry. Study it carefully. Locate the SwissProt ID (SP96_DICDI), the accession number (P14328) and the amino acid sequence (MRVLLVLVAC....TTTATTTATS). There are other entries ( ''sprot2.dat'', ''sprot3.dat'', ''sprot4.dat''). Your programs should work on those, too. Also your programs must solve all the problems in ONE reading of the file. It is acceptable if you just hand in one program that solves 1 to 4. 5 is separate. These exercises are about studying and understanding the file format.		The following 5 exercises deal with SwissProt. The file sprot1.dat is a SwissProt database entry. Study it carefully. Locate the SwissProt ID (SP96_DICDI), the accession number (P14328) and the amino acid sequence (MRVLLVLVAC....TTTATTTATS). There are other entries ( ''sprot2.dat'', ''sprot3.dat'', ''sprot4.dat''). Your programs should work on those, too. Also your programs must solve all the problems in ONE reading of the file. It is acceptable if you just hand in one program that solves 1 to 4. 5 is separate. These exercises are about studying and understanding the file format.
	# Make a program that reads the ID and prints it. Try to use the "walk the line" technique.
	# Add the following functionality to the program: Read the accession number and print it. Again, walk the line.		# Make a program that reads the ID and prints it. Try to use the "walk the line" technique.<br><br>
	# <font color="AA00FF">Add the following functionality to the program: Read the amino acid sequence and print it. You really should use stateful parsing in this exercise. Maybe check the video.</font>		# Add the following functionality to the program: Read the accession number and print it. Again, walk the line.<br><br>
	# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.		# <font color="AA00FF">Add the following functionality to the program: Read the amino acid sequence and print it. You really should use stateful parsing in this exercise. Maybe check the video.</font><br><br>
	# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.		# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.<br><br>
			# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.<br><br>
	# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat'' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contains more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.		# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat'' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contains more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.

WikiSysop: /* Exercises to be handed in */

2025-08-28T19:24:36Z

Exercises to be handed in

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	# Make a program that reads the ID and prints it. Try to use the "walk the line" technique.		# Make a program that reads the ID and prints it. Try to use the "walk the line" technique.
	# Add the following functionality to the program: Read the accession number and print it. Again, walk the line.		# Add the following functionality to the program: Read the accession number and print it. Again, walk the line.
	# Add the following functionality to the program: Read the amino acid sequence and print it. You really should use stateful parsing in this exercise. Maybe check the video.		# <font color="AA00FF">Add the following functionality to the program: Read the amino acid sequence and print it. You really should use stateful parsing in this exercise. Maybe check the video.</font>
	# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.		# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.
	# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.		# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.

WikiSysop: /* Exercises to be handed in */

2025-08-28T19:21:59Z

Exercises to be handed in

← Older revision		Revision as of 21:21, 28 August 2025
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	# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.		# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.
	# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.		# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.
	# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat'' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that ~~contain~~ more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.		# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat'' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contains more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.

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

WikiSysop: /* Exercises to be handed in */

2025-08-28T19:21:41Z

Exercises to be handed in

← Older revision		Revision as of 21:21, 28 August 2025
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	# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.		# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.
	# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.		# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.
	# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contain more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.		# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat'' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contain more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.

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

WikiSysop: /* Exercises to be handed in */

2025-08-28T19:21:20Z

Exercises to be handed in

← Older revision		Revision as of 21:21, 28 August 2025
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	# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.		# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.
	# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.		# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.
	# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat' and create one fasta file ''sprotall.fsa' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contain more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.		# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat' and create one fasta file ''sprotall.fsa'' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contain more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.

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

WikiSysop: /* Exercises to be handed in */

2025-08-28T19:21:00Z

Exercises to be handed in

← Older revision		Revision as of 21:21, 28 August 2025
Line 22:		Line 22:
	# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.		# Add the following functionality to the program: Verification of amino acid number. This means extract the number from the SQ line (example: SQ SEQUENCE 629 AA;) and check that the amino acid sequence has that number of residues. It should be the program that determines if something is wrong - not the user. Imagine that before you go home, you set the computer to run through a million swisprot entries. The next day, you must be able to see what failed. In a sense you don't care about what succeeded, as that is the common case. You care about what failed, because it is here you must take action.
	# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.		# Now that you have the ID, accession number and AA sequence save it to a file ''sprot.fsa'' in FASTA format. Look in the file ''dna.fsa'' for an example of FASTA. Notice the first line starts with > and immediately after comes an unique identifier, like an accession number or a SwissProt ID. Any other data must be on the header line only, but in free format. Sequence data is on the following lines. <br>Notice that this exercise incorporates the previous 4, but uses the result in a slightly different way.
			# In reality you never have just one entry in a SwissProt file. The current SwissProt database contains more than half a million entries and it grows all the time. A bioinformatician can access the database by selecting a subset or the whole database as one file for download and extract the needed information from it. In the file ''sprotall.dat'' the 4 sprot files have been collected as a very small example of what you really meet. The exercise is to read all entries in ''sprotall.dat' and create one fasta file ''sprotall.fsa' with the ids, accessions and sequence for all entries. In short, just like the previous exercise but for a file that contain more SwissProt entries. And please, don't do anything stupid like reading the entire file into a list and start parsing that. These SwissProt excerpts can get really big and it can kill your computer memory doing that.

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

WikiSysop at 11:29, 27 August 2025

2025-08-27T11:29:08Z

← Older revision		Revision as of 13:29, 27 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: [[Exceptions and bug handling]]		\|Previous: [[Exceptions and bug handling]]
	\|Next: [[~~Functions~~]]		\|Next: [[List manipulation]]
	\|}		\|}
	== Required course material for the lesson ==		== Required course material for the lesson ==

WikiSysop at 11:28, 27 August 2025

2025-08-27T11:28:44Z

← Older revision		Revision as of 13:28, 27 August 2025
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	__NOTOC__		__NOTOC__
	{\| width=500 style="float:right; margin-left: 10px; margin-top: -56px;"		{\| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;"
	\|Previous: [[Exceptions and bug handling]]		\|Previous: [[Exceptions and bug handling]]
	\|Next: [[Functions]]		\|Next: [[Functions]]

WikiSysop at 09:35, 26 August 2025

2025-08-26T09:35:07Z

← Older revision		Revision as of 11:35, 26 August 2025
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	{\| width=500 style="float:right; margin-left: 10px; margin-top: -56px;"		{\| width=500 style="float:right; margin-left: 10px; margin-top: -56px;"
	\|Previous: [[Exceptions and bug handling]]		\|Previous: [[Exceptions and bug handling]]
	\|Next: [[~~Lists~~]]		\|Next: [[Functions]]
	\|}		\|}
	== Required course material for the lesson ==		== Required course material for the lesson ==