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-- 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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