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-- The Computer Language Benchmarks Game
-- http://benchmarksgame.alioth.debian.org/
-- 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 function readseq()
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
local seq = readseq()
frequency(seq, 1)
frequency(seq, 2)
count(seq, "GGT")
count(seq, "GGTA")
count(seq, "GGTATT")
count(seq, "GGTATTTTAATT")
count(seq, "GGTATTTTAATTTATAGT")
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