From d068f0b3c11348a50c18af1ee3b0d2e5f38c4faf Mon Sep 17 00:00:00 2001
From: Matthew Sotoudeh <matthew@masot.net>
Date: Fri, 17 May 2024 15:57:30 -0700
Subject: lua benchmarks

---
 .../tests/Lua-Benchmarks/k-nucleotide.lua          | 66 ++++++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 lua_benchmark/tests/Lua-Benchmarks/k-nucleotide.lua

(limited to 'lua_benchmark/tests/Lua-Benchmarks/k-nucleotide.lua')

diff --git a/lua_benchmark/tests/Lua-Benchmarks/k-nucleotide.lua b/lua_benchmark/tests/Lua-Benchmarks/k-nucleotide.lua
new file mode 100644
index 0000000..5deb58d
--- /dev/null
+++ b/lua_benchmark/tests/Lua-Benchmarks/k-nucleotide.lua
@@ -0,0 +1,66 @@
+-- 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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