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Computer Language Benchmarks Game      [[ Play ]]

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 performance measurements

Each table row shows performance measurements for this Ruby 2.0 program with a particular command-line input value N.

N	CPU secs	Elapsed secs	Memory KB	Code B	≈ CPU Load
250,000	8.76	8.82	62,976	637	0% 0% 1% 100%
2,500,000	87.93	88.05	18,076	637	0% 0% 0% 100%
25,000,000	875.86	876.62	128,016	637	0% 0% 0% 100%

Read the ↓ make, command line, and program output logs to see how this program was run.

Read k-nucleotide benchmark to see what this program should do.

 notes

ruby 2.0.0p0 (2013-02-24 revision 39474) [i686-linux]

 k-nucleotide Ruby 2.0 program source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org
#
# contributed by jose fco. gonzalez
# modified by Sokolov Yura
# Parallelism by Rick Branson

$seq = String.new

def frequency(seq, length)
  frequencies = Hash.new(0)
  ns          = seq.length + 1 - length
  
  for i in (0 ... ns)
    frequencies[seq[i, length]] += 1
  end
  
  [ns, frequencies]
end

def sort_by_freq(seq, length)
  ret       = ""
  n, table  = frequency(seq, length)

  table.sort{|a,b| b[1] <=> a[1]}.each do |v|
      ret += "%s %.3f\n" % [v[0].upcase,((v[1]*100).to_f/n)]
  end
  
  ret += "\n"
end

def find_seq(seq, s)
  n, table = frequency(seq, s.length)
  "#{table[s].to_s}\t#{s.upcase}\n"
end

line = STDIN.gets while line !~ /^>THREE/
line = STDIN.gets
while (line !~ /^>/) & line do
    $seq << line.chomp
    line = STDIN.gets
end

class Worker
  def initialize(&block)
    if RUBY_PLATFORM == "java"
      @t = Thread.new do
        Thread.current[:result] = yield
      end
    else
      @r, @w = IO.pipe
      @p = Process.fork do
        @r.close
        @w.write yield
        @w.close
      end
      
      @w.close
    end
  end
  
  def result
    if RUBY_PLATFORM == "java"
      @t.join
      @t[:result]
    else
      ret = @r.read
      @r.close
      Process.wait(@p)
      ret
    end
  end
end

FREQS   = [1, 2]
NUCLEOS = %w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt)

workers =   FREQS.map   { |i| Worker.new { sort_by_freq($seq, i) } }
workers +=  NUCLEOS.map { |s| Worker.new { find_seq($seq, s) } }
  
results = workers.map { |w| w.result }
print results.join

 make, command-line, and program output logs

Sun, 24 Feb 2013 18:49:12 GMT

COMMAND LINE:
/usr/local/src/ruby-2.0.0-p0/ruby knucleotide.yarv 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT

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