Bench marking some Complement class implementations.

benchmark.txt

       user     system      total        real
Complement_V0 with 1 Nucleotides  1.300000   0.000000   1.300000 (  1.294155)
Complement_V0 with 2 Nucleotides  1.770000   0.000000   1.770000 (  1.769186)
Complement_V0 with 4 Nucleotides  2.920000   0.000000   2.920000 (  2.941324)
Complement_V0 with 8 Nucleotides  4.500000   0.000000   4.500000 (  4.510645)
Complement_V0 with 10 Nucleotides  5.210000   0.000000   5.210000 (  5.254469)

Complement_V1 with 1 Nucleotides  6.150000   0.010000   6.160000 (  6.169194)
Complement_V1 with 2 Nucleotides  6.710000   0.010000   6.720000 (  6.764511)
Complement_V1 with 4 Nucleotides  7.590000   0.000000   7.590000 (  7.625991)
Complement_V1 with 8 Nucleotides 10.200000   0.000000  10.200000 ( 10.236003)
Complement_V1 with 10 Nucleotides 10.520000   0.030000  10.550000 ( 10.592688)

Complement_V2 with 1 Nucleotides  1.970000   0.000000   1.970000 (  1.973776)
Complement_V2 with 2 Nucleotides  2.460000   0.000000   2.460000 (  2.462186)
Complement_V2 with 4 Nucleotides  3.400000   0.000000   3.400000 (  3.406930)
Complement_V2 with 8 Nucleotides  5.110000   0.000000   5.110000 (  5.123110)
Complement_V2 with 10 Nucleotides  5.700000   0.000000   5.700000 (  5.728795)

Complement_V3 with 1 Nucleotides  5.110000   0.000000   5.110000 (  5.122803)
Complement_V3 with 2 Nucleotides  6.770000   0.000000   6.770000 (  6.782132)
Complement_V3 with 4 Nucleotides  9.470000   0.020000   9.490000 (  9.501953)
Complement_V3 with 8 Nucleotides 16.440000   0.010000  16.450000 ( 16.560662)
Complement_V3 with 10 Nucleotides 18.930000   0.010000  18.940000 ( 18.985363)

Complement_V4 with 1 Nucleotides  5.140000   0.000000   5.140000 (  5.141769)
Complement_V4 with 2 Nucleotides  6.420000   0.000000   6.420000 (  6.430745)
Complement_V4 with 4 Nucleotides  9.390000   0.000000   9.390000 (  9.393651)
Complement_V4 with 8 Nucleotides 15.120000   0.020000  15.140000 ( 15.200267)
Complement_V4 with 10 Nucleotides 17.910000   0.000000  17.910000 ( 17.975538)

Complements.rb

require 'benchmark'

class Complement_V0
  DNA_RNA_COMPLEMENTS = {
    'G' => 'C',
    'C' => 'G',
    'T' => 'A',
    'A' => 'U',
  }

  RNA_DNA_COMPLEMENTS = {
    'G' => 'C',
    'C' => 'G',
    'T' => 'A',
    'U' => 'A',
    'A' => 'T',
  }

  class << self
    def of_dna dna_string
      dna = dna_string.chars
      transcribe dna, DNA_RNA_COMPLEMENTS
    end

    def of_rna rna_string
      rna = rna_string.chars
      transcribe rna, RNA_DNA_COMPLEMENTS
    end

    private

    def transcribe nucleotides, complements
      nucleotides.map{ |nucleotide| complements[nucleotide] }.reduce(:+)
    end
  end
end
      
class Complement_V1
  DNA_NUCLEOTIDES = 'GCTA'
  RNA_COMPLEMENTS = { 'G' => 'C', 'C' => 'G', 'T' => 'A', 'A' => 'U' }

  RNA_NUCLEOTIDES = 'CGAU'
  DNA_COMPLEMENTS = { 'C' => 'G', 'G' => 'C', 'A' => 'T', 'U' => 'A' }

  class << self
    def of_dna dna
      dna.gsub(/[#{DNA_NUCLEOTIDES}]/, RNA_COMPLEMENTS)
    end

    def of_rna rna
      rna.gsub(/[#{RNA_NUCLEOTIDES}]/, DNA_COMPLEMENTS)
    end
  end
end

class Complement_V2
  RNA_COMPLEMENTS = { 'G' => 'C', 'C' => 'G', 'T' => 'A', 'A' => 'U' }
  DNA_COMPLEMENTS = { 'C' => 'G', 'G' => 'C', 'A' => 'T', 'U' => 'A' }

  class << self
    def of_dna dna
      dna.gsub(/[GCTA]/, RNA_COMPLEMENTS)
    end

    def of_rna rna
      rna.gsub(/[CGAU]/, DNA_COMPLEMENTS)
    end
  end
end

class Complement_V3
  NUCLEOTIDE_COMPLEMENTS = { 'G' => 'C', 'C' => 'G', 'T' => 'A', 'A' => 'U' }

  class << self
    def of_dna strand
      DNA.new(strand).gsub(/[GCTA]/, NUCLEOTIDE_COMPLEMENTS)
    end

    def of_rna strand
      RNA.new(stran).gsub(/[CGAU]/, NUCLEOTIDE_COMPLEMENTS.invert)
    end
  end
end

class Complement_V4
  RNA_COMPLEMENTS = { 'G' => 'C', 'C' => 'G', 'T' => 'A', 'A' => 'U' }
  DNA_COMPLEMENTS = { 'C' => 'G', 'G' => 'C', 'A' => 'T', 'U' => 'A' }

  class << self
    def of_dna strand
      DNA.new(strand).gsub(/[GCTA]/, RNA_COMPLEMENTS)
    end

    def of_rna strand
      RNA.new(strand).gsub(/[CGAU]/, DNA_COMPLEMENTS)
    end
  end
end

class DNA < String
  def initialize strand
    strand.chars.map do |n|
      throw "Illegal Nucleotide: #{n}" unless ['G', 'C', 'T', 'A'].include? n
    end
    super
  end
end

class RNA < String
  def initialize strand
    strand.chars.map do |n|
      throw "Illegal Nucleotide: #{n}" unless ['G', 'C', 'U', 'A'].include? n
    end
    super
  end
end


ITERATIONS = 1000000

def run(complement, dna, bench)
  bench.report("#{complement.name} with #{dna.length} Nucleotides") do
    ITERATIONS.times do
      complement.of_dna dna
    end
  end
end


Benchmark.bm do |bench|
  run(Complement_V0, "G", bench)
  run(Complement_V0, "GC", bench)
  run(Complement_V0, "GCCG", bench)
  run(Complement_V0, "GCCGGCCG", bench)
  run(Complement_V0, "ATTAGGGCAT", bench)
  puts ""
  run(Complement_V1, "G", bench)
  run(Complement_V1, "GC", bench)
  run(Complement_V1, "GCCG", bench)
  run(Complement_V1, "GCCGGCCG", bench)
  run(Complement_V1, "ATTAGGGCAX", bench)
  puts ""
  run(Complement_V2, "G", bench)
  run(Complement_V2, "GC", bench)
  run(Complement_V2, "GCCG", bench)
  run(Complement_V2, "GCCGGCCG", bench)
  run(Complement_V2, "ATTAGGGCAX", bench)
  puts ""
  run(Complement_V3, "G", bench)
  run(Complement_V3, "GC", bench)
  run(Complement_V3, "GCCG", bench)
  run(Complement_V3, "GCCGGCCG", bench)
  run(Complement_V3, "ATTAGGGCAT", bench)
  puts ""
  run(Complement_V4, "G", bench)
  run(Complement_V4, "GC", bench)
  run(Complement_V4, "GCCG", bench)
  run(Complement_V4, "GCCGGCCG", bench)
  run(Complement_V4, "ATTAGGGCAT", bench)
  puts ""
end