test.cr

seq = IO::Memory.new

ilen = 0
STDIN.each_line do |line|
  ilen += line.bytesize + 1
  seq << line.chomp unless line.starts_with? '>'
end

seq = seq.to_s
clen = seq.bytesize

def run(seq, clen, ilen)
  [
    /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/,
  ].each { |f| puts "#{f.source} #{seq.scan(f).size}" }

  hash = {
    "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|t)",
    "V" => "(a|c|g)",
    "W" => "(a|t)",
    "Y" => "(c|t)",
  }

  t = Time.local
  seq = seq.gsub(/B|D|H|K|M|N|R|S|V|W|Y/, hash)

  puts
  puts ilen
  puts clen
  puts seq.size
  STDERR.puts "time(#{(Time.local - t).to_f})"
end

t = (ARGV[0]? || 5).to_i
STDERR.puts "started\t#{Process.pid}"
t.times { run(seq, clen, ilen) }