LZSCC.212: Advanced Programming Coursework 2

INSTRUCTIONS TO CANDIDATES

ANSWER ALL QUESTIONS

These are three assignments, I need some help

 

Task 1: Frequency Counts

You’ve been asked to produce the counts of particular sequences handed to you from a test

framework. The

framework itself has a function for you to call with the results.

In essence, if you have been given the following sequence of nucleotide letters:

CCAAATT

We should be able to generate the following counts of each pattern:

{ AA: 2, AT: 1, CC: 1, CA: 1, TT: 1 }

Note that ‘AA’ is detected as two patterns, as the first pair of ‘A’s then a second pair of overlapping

‘A’s:

CC AA ATT and CCA AA TT

Your code will be handed the input character-by-character, so it will be up to you how you decide

to buffer and detect these sequences.

LZSCC.212: Advanced Programming

For this particular task, you are required to use the testlib.frequencyTable() function to report your

frequency counts. This function expects that you supply it with an object containing keys as

specified by the patterns array in the "ready" handler, each with a count of the number of times

the program has seen that pattern.

Remember that you can access JavaScript object and array keys by square brackets.

An (extremely simple) example of how to do this might be:

let data = { “AA”: 1, “TT”: 12 };

Testlib.frequencyTable( data );

Note: To know when one sequence stop and another begins, use the "reset" hook via the

testlib.on() function!

To test your code for this task, remember to set testlib.setup( 1 )

Task 2: Short Sequence Matching

Now that you have counting and matching working, you are now tasked with reporting the precise

location of each match for each pattern.

testlib provides a testlib.foundMatch( pattern, offset ) function which should be called when a

match is found, passing it the pattern found along with the offset in characters from the start of

the current sequence.

Again, in the library you have been given, this function will simply print the details it has been

provided with.

To test your code for this task, remember to set testlib.setup( 2 )

Task 3: Complex Sequence Matching

You should have Tasks 1 and 2 working fully before attempting Task 3.

The letters A, C, G, T occurring in genetic strings identify distinct nucleotides in DNA sequences.

Unfortunately, in reality it can be quite difficult to identify the specific nucleotide when

doing DNA sequencing, so often instead of a specific organic molecule, the sequencing machine is

only able to guess at a number of options at a given position in a genetic string.

The machine indicates this by not using one of the definite chemical characters (A, C, G and T), but

with one that indicates some combination of these four, according to the table below:

 

Attachments:

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