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

---
 lua_benchmark/tests/Lua-Benchmarks/regex-dna.lua | 59 ++++++++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 lua_benchmark/tests/Lua-Benchmarks/regex-dna.lua

(limited to 'lua_benchmark/tests/Lua-Benchmarks/regex-dna.lua')

diff --git a/lua_benchmark/tests/Lua-Benchmarks/regex-dna.lua b/lua_benchmark/tests/Lua-Benchmarks/regex-dna.lua
new file mode 100644
index 0000000..2627e05
--- /dev/null
+++ b/lua_benchmark/tests/Lua-Benchmarks/regex-dna.lua
@@ -0,0 +1,59 @@
+-- The Computer Language Benchmarks Game
+-- http://benchmarksgame.alioth.debian.org/
+-- contributed by Jim Roseborough
+-- modified by Victor Tang
+-- optimized & replaced inefficient use of gsub with gmatch
+-- partitioned sequence to prevent extraneous redundant string copy
+
+seq = io.read("*a")
+ilen, seq = #seq, seq:gsub('>[^%c]*%c*', ''):gsub('%c+', '')
+clen = #seq
+
+local variants = { 'agggtaaa|tttaccct',
+                   '[cgt]gggtaaa|tttaccc[acg]',
+                   'a[act]ggtaaa|tttacc[agt]t',
+                   'ag[act]gtaaa|tttac[agt]ct',
+                   'agg[act]taaa|ttta[agt]cct',
+                   'aggg[acg]aaa|ttt[cgt]ccct',
+                   'agggt[cgt]aa|tt[acg]accct',
+                   'agggta[cgt]a|t[acg]taccct',
+                   'agggtaa[cgt]|[acg]ttaccct', }
+
+local subst = { B='(c|g|t)', D='(a|g|t)',   H='(a|c|t)', K='(g|t)',
+                M='(a|c)',   N='(a|c|g|t)', R='(a|g)',   S='(c|g)',
+                V='(a|c|g)', W='(a|t)',     Y='(c|t)' }
+
+function countmatches(variant)
+   local n = 0
+   variant:gsub('([^|]+)|?', function(pattern)
+      for _ in seq:gmatch(pattern) do n = n + 1 end
+   end)
+   return n
+end
+
+for _, p in ipairs(variants) do
+   io.write( string.format('%s %d\n', p, countmatches(p)) )
+end
+
+function partitionstring(seq)
+  local seg = math.floor( math.sqrt(#seq) )
+  local seqtable = {}
+  for nextstart = 1, #seq, seg do
+    table.insert(seqtable, seq:sub(nextstart, nextstart + seg - 1))
+  end
+  return seqtable
+end
+function chunk_gsub(t, k, v)
+  for i, p in ipairs(t) do
+    t[i] = p:find(k) and p:gsub(k, v) or t[i]
+  end
+  return t
+end
+
+seq = partitionstring(seq)
+for k, v in pairs(subst) do
+  chunk_gsub(seq, k, v)
+end
+seq = table.concat(seq)
+io.write(string.format('\n%d\n%d\n%d\n', ilen, clen, #seq))
+
-- 
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