# 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]
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
if length(line) >= length(three) && line[1:length(three)] == three
break
end
end
# 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:
julia version build 19.0.1+10-21

Wed, 25 Jan 2023 02:03:02 GMT

MAKE:
4

0.13s to complete and log all make actions

COMMAND LINE:
/opt/src/julia-1.8.5/bin/julia -O3 --cpu-target=ivybridge --math-mode=ieee  -- 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
```