# k-nucleotide Lua #2 program

## source code

```-- The Computer Language Benchmarks Game
-- https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
-- contributed by Mike Pall

local function kfrequency(seq, freq, k, frame)
local sub = string.sub
local k1 = k - 1
for i=frame,string.len(seq)-k1,k do
local c = sub(seq, i, i+k1)
freq[c] = freq[c] + 1
end
end

local function freqdefault()
return 0
end

local function count(seq, frag)
local k = string.len(frag)
local freq = setmetatable({}, { __index = freqdefault })
for frame=1,k do kfrequency(seq, freq, k, frame) end
io.write(freq[frag] or 0, "\t", frag, "\n")
end

local function frequency(seq, k)
local freq = setmetatable({}, { __index = freqdefault })
for frame=1,k do kfrequency(seq, freq, k, frame) end
local sfreq, sn = {}, 1
for c,v in pairs(freq) do sfreq[sn] = c; sn = sn + 1 end
table.sort(sfreq, function(a, b)
local fa, fb = freq[a], freq[b]
return fa == fb and a > b or fa > fb
end)
sum = string.len(seq)-k+1
for _,c in ipairs(sfreq) do
io.write(string.format("%s %0.3f\n", c, (freq[c]*100)/sum))
end
io.write("\n")
end

local sub = string.sub
for line in io.lines() do
if sub(line, 1, 1) == ">" and sub(line, 2, 6) == "THREE" then break end
end
local lines, ln = {}, 0
for line in io.lines() do
local c = sub(line, 1, 1)
if c == ">" then
break
elseif c ~= ";" then
ln = ln + 1
lines[ln] = line
end
end
return string.upper(table.concat(lines, "", 1, ln))
end

frequency(seq, 1)
frequency(seq, 2)
count(seq, "GGT")
count(seq, "GGTA")
count(seq, "GGTATT")
count(seq, "GGTATTTTAATT")
count(seq, "GGTATTTTAATTTATAGT")
```

## notes, command-line, and program output

```NOTES:
1994-2023 Lua.org, PUC-Rio

Sun, 26 May 2024 02:36:13 GMT

COMMAND LINE:
/opt/src/lua-5.4.6/install/bin/lua  knucleotide.lua-2.lua 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
```