GC Count

gc_count.jl

#!/usr/bin/env julia


function gc_count(fasta::String)
    file = open(fasta, "r")
    lines = readall(file)
    gc = at = 0
    for c in lines.data
        if (c == 'G') || (c == 'C')
            gc += 1
        elseif (c == 'A') || (c == 'T')
            at += 1
        end
    end
    close(file)
    gc_frac::Float64 = gc / (gc + at)
    println("GC count: ", gc_frac)
end

function compile()
    print("Compiling... ")
    precompile(gc_count, (String,))
    println("Done!")
end

function main()
    compile()
    data = "Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa"
    @time gc_count(data)
end

main()