Counting DNA nucleotides

Problem definition

Given: A DNA string s of length \(1000\) nucleotides

Return: Four integers (seperated by spaces) counting the respoective number of times that the symbols ‘A’ ‘C’ ‘G’ ‘T’ occur in s.

Sample Dataset:

AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC

Sample Output:

\[\begin{matrix} 20 & 12 & 17 & 21 \end{matrix}\]

Solution

We use the inbuilt julia function count(p, iter) which counts the number of elements in iter for which predicate p is true.

count

countNucs(s::String) = [
    count(==('A'), s), count(==('C'), s), count(==('G'), s), count(==('T'), s)
]

function main()
    if length(ARGS) < 2
        println("Usage: julia $(Base.PROGRAM_FILE) <fileIN> <fileOUT>")
        exit(1)
    end
    s = read(ARGS[1], String)
    data = countNucs(s)
    open(ARGS[2], "w") do file
        println(file, join(data, " "))
    end
    exit(0)
end

main()

Notes

In Rosalind, you have to ‘download the dataset’ and they give you five minuets to submit your answer. This essentially means that your solution nees to be reasonably computationally efficient to solve within that time frame. If you write bad code, sometimes this is a non-trivial requirement because their data files for testing contain a large number of data.

Github Files

The cold was ran by downloading the dataset, then running the following command:

julia countdna.jl rosalind_dna.txt output.txt