The Computer Language
Benchmarks Game

k-nucleotide Julia program

source code

# The Computer Language Benchmarks Game
# https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
#
# contributed by David Campbell
# based on the Go version
# modified by Jarret Revels, Alex Arslan, Yichao Yu

using Printf

import Base.isless

function count(data::AbstractString, n::Int)
    counts = Dict{AbstractString, Int}()
    top = length(data) - n + 1
    for i = 1:top
        s = data[i : i+n-1]
        if haskey(counts, s)
            counts[s] += 1
        else
            counts[s] = 1
        end
    end
    counts
end

function count_one(data::AbstractString, s::AbstractString)
    count(data, length(s))[s]
end

mutable struct KNuc
    name::AbstractString
    count::Int
end

# sort down
function isless(x::KNuc, y::KNuc)
    if x.count == y.count
        return x.name > y.name
    end
    x.count > y.count
end

function sorted_array(m::Dict{AbstractString, Int})
    kn = Vector{KNuc}(undef, length(m))
    i = 1
    for elem in m
        kn[i] = KNuc(elem...)
        i += 1
    end
    sort(kn)
end

function print_knucs(a::Array{KNuc, 1})
    sum = 0
    for kn in a
        sum += kn.count
    end
    for kn in a
        @printf("%s %.3f\n", kn.name, 100.0kn.count/sum)
    end
    println()
end

function perf_k_nucleotide()
    three = ">THREE "
    while true
        line = readline()
        if length(line) >= length(three) && line[1:length(three)] == three
            break
        end
    end
    data = collect(read(stdin, String))
    # delete the newlines and convert to upper case
    i, j = 1, 1
    while i <= length(data)
        if data[i] != '\n'
            data[j] = uppercase(data[i])
            j += 1
        end
        i += 1
    end
    str = join(data[1:j-1], "")

    arr1 = sorted_array(count(str, 1))
    arr2 = sorted_array(count(str, 2))

    print_knucs(arr1)
    print_knucs(arr2)
    for s in ["GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"]
        @printf("%d\t%s\n", count_one(str, s), s)
    end
end

perf_k_nucleotide()

    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
julia version 1.2.0
export JULIA_NUM_THREADS=4


Tue, 20 Aug 2019 16:44:26 GMT

COMMAND LINE:
/opt/src/julia-1.2.0/bin/julia -O3  -- knucleotide.julia 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT