Instructions for Assignment02

Introduction

In this assignment, you will start to put the pieces together. Note: this file is runnable in its current state, but is incomplete. You can run the file from the command line, or use the VS Code julia extension to run individual lines.

The following code is used for set up; there is no need to change it. If you do change it to figure out what it's doing, make sure you change it back or your assignment may not work correctly

using Random
Random.seed!(42)

function generate_sequence(len)
    seq = join(rand(['A','C','G','T'], len))
    println("Your sequence is: ", seq)
    return seq
end

my_seq = generate_sequence(20)

Question 1

The code above generates a random 20nt DNA sequence, and assigns it to the variable my_seq. What kind of data type is my_seq (eg Float64, Int64, String, or something else)? Assign the variable question1 to the correct type.

Hint1: rather than guess, you can just use the typeof() function.

question1 = ""

Hint2: If you're having trouble, note that your answer should not contain quotes. Eg. if you thing that seq has the type MyType, your code should read question1 = MyType and not question1 = "MyType"

Question 2

The function bellow has a "doc string", which explains what the function should do. Many julia functions have doc strings, which makes it easy to get help right from the REPL

Open a julia REPL and type ?. You will see the julia> prompt change to help?>. Now type println and hit enter. The docstring of println is printed and you're returned to a julia prompt

Evaluate the following function, including the docstring, in the REPL (that is, copy from the tripple quotes down to the "end" and paste it into the REPL, then hit enter)

"""
    question2(sequence)

Checks if `sequence` is a String.
Returns a boolean value, `true` or `false`.

Example
≡≡≡≡≡≡≡≡≡

    julia> question2("hello")
    true

    julia> question2(1001)
    false

    julia> if question2("a string")
               println("Hey, it's a string!")
           end
    Hey, it's a string!
"""
function question2()
    # put your code here
end

At the moment, this function doesn't do what it says it should. Actually, it doesn't do anything. Fix the function so that it takes one argument and returns true if the argument is a String, and returns false otherwise. You should be able to run the examples in the docstring and get the correct answer, and to run this function using my_seq as the argument (it should return true).

Hint: You haven't explicitly encountered a way to check if a type is another type. Learning to search for answers is a key programming skill! Try searching "check if type is string julia". Typically, when I see search results, I prioritize in this order:

1. stackoverflow.com
2. docs.julialang.org
3. discourse.julialang.org
4. github.com

Question 3

Let's try something a bit more complicated. The question3() function has a doc string, but is also incomplete. I've written some code to get you started, complete it so that the examples work as expected in the docstring. If you use this function on my_seq, you should get the answer 0.3

"""
    question3(sequence)

Calculates the GC ratio of a DNA sequence.
The GC ratio is the total number of G and C bases divided by the total length of the sequence.
For more info about GC content, see here:

Example
≡≡≡≡≡≡≡≡≡≡

    julia> question3("AATG")
    0.25

    julia> question3("CCCGG")
    1.0

    julia> question3("ATTA")
    0.0
"""
function question3(sequence)
    # throw an error if the string contains anything other than ACGT
    if any(c-> !in(c, ['A','C','G','T']), sequence)
        throw(ArgumentError("Sequence must only contain ACGT"))
    end

    # change line to assign `seqlength` to the length of `sequence` instead of `1`
    # If you're stuck, search for "length of string julia"
    seqlength = 1

    # count the number of G's
    gs = count(==('G'), sequence)
    # count the number of C's
    cs = count(==('C'), sequence)

    return gs + cs / seqlength # something is wrong with this line...
end

Question 4

This process should be familiar by now.

Hint: you do not need to re-write code if you already have it. That is, don't copy any code from question3, just call it!

"""
    question4(sequence)

Calculates the GC content of a DNA sequence
and prints it to the screen.

Example
≡≡≡≡≡≡≡≡≡≡

    julia> question4("AATC")
    Sequence:
    AATC
    GC Content:
    0.25

    julia> question4("CCCGG");
    Sequence:
    CCCGG
    GC Content:
    1.0
"""
function question4(sequence)
    # Your code here
end

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