sequence_logo 1.0.3 → 1.0.4

data/lib/sequence_logo/ytilib/pmsd.rb

@@ -1,99 +1,99 @@
-#!/usr/bin/ruby
-module Ytilib
-  class PM
-    def score_sigma(trycount = 4**10, approx = false, bg = nil)
-      
-      scores = []
-      if @size <= 10 && !approx
-        (0...4**@size).each { |i| 
-          word = i.to_s(4).rjust(@size, "0").tr("0123", "ACGT")
-          scores << score(word)
-        }
-      else
-        trycount.times {
-          word = bg ? Randoom.rand_seq(@size, bg) : Randoom.rand_seq(@size)
-          scores << score(word)
-        }
-      end
-      sum1 = scores.inject(0) { |sum,s| sum += s }
-      mean = sum1 / scores.size
-      
-      sum2, sumc = 0, 0
-      scores.each { |score|
-        sum2 += (score-mean)**2
-        sumc += (score-mean)
-      }
-      variance = (sum2 - sumc**2 / scores.size) / (scores.size-1)
-      
-      sigma = Math.sqrt(variance)
-      if block_given?
-        yield(sigma, mean)
-      end
-      
-      return sigma
-    end
-    
-    def fast_score_sigma
-      n, mean, m2 = 0, 0, 0
-      
-      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
-        n = n + 1
-        delta = x - mean
-        mean = mean + delta/n
-        m2 = m2 + delta*(x-mean)
-      }
-      
-      variance = m2/(n - 1)
-      
-      if block_given?
-        yield(sigma = Math.sqrt(variance), mean)
-      end
-      
-      return sigma
-    end
-    
-    def fast_score_sigma_precise
-      n, mean = 0, 0
-      
-      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
-        n += 1
-        delta = x - mean
-        mean = mean + delta/n
-      }
-      
-      n, m2 = 0, 0
-      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
-        n = n + 1
-        delta = x - mean
-        m2 = m2 + delta*(x-mean)
-      }
-      
-      variance = m2/(n - 1)
-      
-      if block_given?
-        yield(sigma = Math.sqrt(variance), mean)
-      end
-      
-      return sigma
-    end
-    
-  private
-    def recursive_walk(matrix, score, i)
-      if i < @size
-        
-        recursive_walk(matrix, score + matrix[0][i], i+1) { |x| yield x }
-        recursive_walk(matrix, score + matrix[1][i], i+1) { |x| yield x }
-        recursive_walk(matrix, score + matrix[2][i], i+1) { |x| yield x }
-        recursive_walk(matrix, score + matrix[3][i], i+1) { |x| yield x }
-        
-      else
-        if block_given?
-          yield(score)
-        else
-          raise "no block for recursive walk"
-        end
-      end
-    end
-  
-  end
+#!/usr/bin/ruby
+module Ytilib
+  class PM
+    def score_sigma(trycount = 4**10, approx = false, bg = nil)
+      
+      scores = []
+      if @size <= 10 && !approx
+        (0...4**@size).each { |i| 
+          word = i.to_s(4).rjust(@size, "0").tr("0123", "ACGT")
+          scores << score(word)
+        }
+      else
+        trycount.times {
+          word = bg ? Randoom.rand_seq(@size, bg) : Randoom.rand_seq(@size)
+          scores << score(word)
+        }
+      end
+      sum1 = scores.inject(0) { |sum,s| sum += s }
+      mean = sum1 / scores.size
+      
+      sum2, sumc = 0, 0
+      scores.each { |score|
+        sum2 += (score-mean)**2
+        sumc += (score-mean)
+      }
+      variance = (sum2 - sumc**2 / scores.size) / (scores.size-1)
+      
+      sigma = Math.sqrt(variance)
+      if block_given?
+        yield(sigma, mean)
+      end
+      
+      return sigma
+    end
+    
+    def fast_score_sigma
+      n, mean, m2 = 0, 0, 0
+      
+      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
+        n = n + 1
+        delta = x - mean
+        mean = mean + delta/n
+        m2 = m2 + delta*(x-mean)
+      }
+      
+      variance = m2/(n - 1)
+      
+      if block_given?
+        yield(sigma = Math.sqrt(variance), mean)
+      end
+      
+      return sigma
+    end
+    
+    def fast_score_sigma_precise
+      n, mean = 0, 0
+      
+      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
+        n += 1
+        delta = x - mean
+        mean = mean + delta/n
+      }
+      
+      n, m2 = 0, 0
+      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
+        n = n + 1
+        delta = x - mean
+        m2 = m2 + delta*(x-mean)
+      }
+      
+      variance = m2/(n - 1)
+      
+      if block_given?
+        yield(sigma = Math.sqrt(variance), mean)
+      end
+      
+      return sigma
+    end
+    
+  private
+    def recursive_walk(matrix, score, i)
+      if i < @size
+        
+        recursive_walk(matrix, score + matrix[0][i], i+1) { |x| yield x }
+        recursive_walk(matrix, score + matrix[1][i], i+1) { |x| yield x }
+        recursive_walk(matrix, score + matrix[2][i], i+1) { |x| yield x }
+        recursive_walk(matrix, score + matrix[3][i], i+1) { |x| yield x }
+        
+      else
+        if block_given?
+          yield(score)
+        else
+          raise "no block for recursive walk"
+        end
+      end
+    end
+  
+  end
 end

data/lib/sequence_logo/ytilib/ppm_support.rb

@@ -1,85 +1,85 @@
-class Object
-  def deep_dup
-    Marshal.load(Marshal.dump(self))
-  end
-end
-
-def get_ppm_from_file(in_file_name)
-  case File.ext_wo_name(in_file_name)
-  when 'pat', 'pcm'
-    pm = PM.load(in_file_name)
-    pm.fixwc  if pm.words_count
-  when 'mfa', 'fasta', 'plain'
-    pm = PM.new_pcm(Ytilib.read_seqs2array(in_file_name))
-  when 'xml'
-    pm = PM.from_bismark(Bismark.new(in_file_name).elements["//PPM"])
-  when in_file_name
-    pm = PPM.from_IUPAC(in_file_name.upcase)
-  end
-  pm.get_ppm
-rescue
-  nil
-end
-
-class PPM
-  attr_accessor :name
-  
-  def get_ppm
-    self
-  end
-  
-  def get_line(v)
-    ( (v - icd4of4) / icd4of4 ).abs
-  end
-
-  def get_logo(icd_mode)
-    case icd_mode.to_s
-    when 'weblogo'
-      get_logo_weblogo
-    when 'discrete'
-      get_logo_discrete
-    end
-  end
-
-
-  def get_logo_weblogo
-    rseq = []
-    @matrix['A'].each_index { |i|
-      rseq << 2 + ['A','C','G','T'].inject(0) { |sum, l|
-        pn = @matrix[l][i]
-        sum += (pn == 0) ? 0 : pn * Math.log(pn) / Math.log(2)
-      }
-    }
-    
-    mat = {'A'=>[], 'C'=>[], 'G'=>[], 'T'=>[]}
-    @matrix['A'].each_index { |i|
-      ['A','C','G','T'].each { |l|
-        mat[l][i]= @matrix[l][i] * rseq[i] / 2 # so we can handle a '2 bit' scale here
-      }
-    }
-    
-    mat
-  end
-
-  def get_logo_discrete
-    checkerr("words count is undefined") { !words_count }
-    
-    rseq = []
-    @matrix['A'].each_index { |i|
-      rseq << (icd4of4 == 0 ? 1.0 : ( (infocod(i) - icd4of4) / icd4of4 ).abs)
-    }
-    
-    mat = {'A'=>[], 'C'=>[], 'G'=>[], 'T'=>[]}
-    @matrix['A'].each_index { |i|
-      ['A','C','G','T'].each { |l| 
-        mat[l][i] = @matrix[l][i] * rseq[i]
-      }
-    }
-    
-    mat
-  end
-  
-  def revcomp
-    deep_dup.revcomp!
-  end
-end
+class Object
+  def deep_dup
+    Marshal.load(Marshal.dump(self))
+  end
+end
+
+def get_ppm_from_file(in_file_name)
+  case File.ext_wo_name(in_file_name)
+  when 'pat', 'pcm'
+    pm = PM.load(in_file_name)
+    pm.fixwc  if pm.words_count
+  when 'mfa', 'fasta', 'plain'
+    pm = PM.new_pcm(Ytilib.read_seqs2array(in_file_name))
+  when 'xml'
+    pm = PM.from_bismark(Bismark.new(in_file_name).elements["//PPM"])
+  when in_file_name
+    pm = PPM.from_IUPAC(in_file_name.upcase)
+  end
+  pm.get_ppm
+rescue
+  nil
+end
+
+class PPM
+  attr_accessor :name
+  
+  def get_ppm
+    self
+  end
+  
+  def get_line(v)
+    ( (v - icd4of4) / icd4of4 ).abs
+  end
+
+  def get_logo(icd_mode)
+    case icd_mode.to_s
+    when 'weblogo'
+      get_logo_weblogo
+    when 'discrete'
+      get_logo_discrete
+    end
+  end
+
+
+  def get_logo_weblogo
+    rseq = []
+    @matrix['A'].each_index { |i|
+      rseq << 2 + ['A','C','G','T'].inject(0) { |sum, l|
+        pn = @matrix[l][i]
+        sum += (pn == 0) ? 0 : pn * Math.log(pn) / Math.log(2)
+      }
+    }
+    
+    mat = {'A'=>[], 'C'=>[], 'G'=>[], 'T'=>[]}
+    @matrix['A'].each_index { |i|
+      ['A','C','G','T'].each { |l|
+        mat[l][i]= @matrix[l][i] * rseq[i] / 2 # so we can handle a '2 bit' scale here
+      }
+    }
+    
+    mat
+  end
+
+  def get_logo_discrete
+    checkerr("words count is undefined") { !words_count }
+    
+    rseq = []
+    @matrix['A'].each_index { |i|
+      rseq << (icd4of4 == 0 ? 1.0 : ( (infocod(i) - icd4of4) / icd4of4 ).abs)
+    }
+    
+    mat = {'A'=>[], 'C'=>[], 'G'=>[], 'T'=>[]}
+    @matrix['A'].each_index { |i|
+      ['A','C','G','T'].each { |l| 
+        mat[l][i] = @matrix[l][i] * rseq[i]
+      }
+    }
+    
+    mat
+  end
+  
+  def revcomp
+    deep_dup.revcomp!
+  end
+end

data/lib/sequence_logo/ytilib/randoom.rb

@@ -1,131 +1,131 @@
-#!/usr/bin/ruby
-module Ytilib
-
-srand
-
-module Randoom
-  
-  private
-
-  def Randoom.new_counts
-    { 'A' => 0, 'C' => 0, 'G' => 0, 'T' => 0, 'N' => 0 }
-  end
-  
-  def Randoom.random_letter(probs)
-    random = rand()
-    return 'A' if random < probs['A']
-    return 'C' if random < probs['A'] + probs['C']
-    return 'G' if random < probs['A'] + probs['C'] + probs['G']
-    return 'T'
-  end
-
-  public
-  
-  def Randoom.calc_probs(input)
-    counts = new_counts
-    counts.default = 0
-    (0...input.length).each { |i|
-      counts[input[i,1].upcase] += 1
-    }
-    return make_probs!(counts)
-  end
-    
-  def Randoom.rand_seq(req_len, probs = DEF_PROBS, probs_m = nil)
-    randoom = ''
-    if (probs_m == nil)
-      req_len.times { randoom << random_letter(probs) }
-      return randoom  
-    end
-    random_l = random_letter(probs)
-    randoom = random_l
-    (req_len-1).times {
-      cur_probs = probs_m[random_l]
-      random_l = random_letter(cur_probs)
-      randoom << random_l
-    }
-    return randoom
-  end
-  
-  def Randoom.calc_probs_m(input)
-    probs_m = { 'A' => {}, 'C' => {}, 'G' => {}, 'T' => {} }
-    counts = { 'A' => new_counts, 'C' => new_counts, 'G' => new_counts, 'T' => new_counts, 'N' => new_counts }
-    (0...input.length-1).each { |i|
-      pair = input[i, 2].upcase
-      counts[pair[0,1]][pair[1,1]] += 1
-    }
-    probs_m['A'] = make_probs!(counts['A'])
-    probs_m['C'] = make_probs!(counts['C'])
-    probs_m['G'] = make_probs!(counts['G'])
-    probs_m['T'] = make_probs!(counts['T'])
-    return probs_m
-  end
-  
-  def Randoom.make_probs_m!(counts)
-    ['A','C','G','T','N'].each { |l2|
-      addv = counts['N'][l2] / 4.0
-      ['A','C','G','T'].each { |l1|
-        counts[l1][l2] += addv
-      }
-    }
-    
-    probs_m = { 'A' => {}, 'C' => {}, 'G' => {}, 'T' => {} }
-    probs_m['A'] = make_probs!(counts['A'])
-    probs_m['C'] = make_probs!(counts['C'])
-    probs_m['G'] = make_probs!(counts['G'])
-    probs_m['T'] = make_probs!(counts['T'])
-    return probs_m
-  end
-  
-  def Randoom.make_probs!(counts, length = nil)
-    probs = { 'A' => 0, 'C' => 0, 'G' => 0, 'T' => 0 }
-    length = counts['A'] + counts['C'] + counts['G'] + counts['T'] + counts['N'] if length == nil
-    length = length.to_f
-    ['A','C','G','T'].each { |l| counts[l] += counts['N'] / 4.0 }
-    return probs if length == 0
-    probs['A'] = counts['A'] / length
-    probs['C'] = counts['C'] / length
-    probs['G'] = counts['G'] / length
-    probs['T'] = 1 - probs['A'] - probs['C'] - probs['G']
-    return probs
-  end
-  
-  def Randoom.equalize!(probs)
-    probs['A'] = probs['T'] = (probs['A'] + probs['T']) / 2
-    probs['C'] = probs['G'] = (probs['C'] + probs['G']) / 2
-    return probs
-  end
-  
-  def Randoom.twostrand!(probs)
-    return Randoom.equalize!(probs)
-  end
-  
-  DEF_PROBS = PPM.probs2IUPAC!({ 'A' => 0.25, 'C' => 0.25, 'G' => 0.25, 'T' => 0.25, 'N' => 0.25 })
-  
-  # probabilities counted without _random.fa files for human genome
-  DMEL40_PROBS1 = {"A"=>0.287729562173578, "C"=>0.21236364146414, "G"=>0.212259972960341, "T"=>0.287646823401942}
-  DMEL40_PROBS2 = {"A"=>0.28768819278776, "C"=>0.21231180721224, "G"=>0.21231180721224, "T"=>0.28768819278776}
-  
-  DMEL40_PROBS1_M = {"A"=>{"A"=>0.350403075314602, "C"=>0.181194374386404, "G"=>0.188361404205017, "T"=>0.280041146093977}, 
-    "C"=>{"A"=>0.325366772443085, "C"=>0.222264645612127, "G"=>0.197213801868993, "T"=>0.255154780075794}, 
-    "G"=>{"A"=>0.260710563672393, "C"=>0.27150575901391, "G"=>0.222294234776053, "T"=>0.245489442537644}, 
-    "T"=>{"A"=>0.217189093089999, "C"=>0.192590127484359, "G"=>0.239869076706963, "T"=>0.350351702718679}}
-  
-  HG17_PROBS1 = {"A"=>0.295309361730334, "C"=>0.204413561169847, "G"=>0.204519414193999, "T"=>0.295757662905821}
-  HG17_PROBS2 = {"A"=>0.295533512318077, "C"=>0.204466487681923, "G"=>0.204466487681923, "T"=>0.295533512318077}
-  
-  HG17_PROBS1_M = {"A"=>{"A"=>0.331091206257755, "C"=>0.170458424092748, "G"=>0.236770972081246, "T"=>0.261679397568252}, 
-    "C"=>{"A"=>0.354813019140533, "C"=>0.254741288394943, "G"=>0.0481667110625576, "T"=>0.342278981401966}, 
-    "G"=>{"A"=>0.290057117684408, "C"=>0.208514091370804, "G"=>0.254732297362797, "T"=>0.246696493581991}, 
-    "T"=>{"A"=>0.222087715262152, "C"=>0.200697606508443, "G"=>0.245657322003887, "T"=>0.331557356225517}}
-  
-  HG18_PROBS1 = {"A"=>0.291900580635872, "C"=>0.207855064518284, "G"=>0.207968587245859, "T"=>0.292275767599985}
-  HG18_PROBS2 = {"A"=>0.292088174117929, "C"=>0.207911825882071, "G"=>0.207911825882071, "T"=>0.292088174117929}
-  
-  MM9_PROBS1 = {"A"=>0.289755259854654, "C"=>0.210085673636132, "G"=>0.210143929198141, "T"=>0.290015137311074}
-  MM9_PROBS2 = {"A"=>0.289885198582864, "C"=>0.210114801417136, "G"=>0.210114801417136, "T"=>0.289885198582864}
-  
-  MM9_PROBS1_M = {"A"=>{"A"=>0.310389104265713, "C"=>0.184962574392377, "G"=>0.251904718465914, "T"=>0.252743602875996}, "C"=>{"A"=>0.352189584318682, "C"=>0.250794045222924, "G"=>0.0494404816637487, "T"=>0.347575888794645}, "G"=>{"A"=>0.295931117515178, "C"=>0.197870954111653, "G"=>0.250756985626016, "T"=>0.255440942747154}, "T"=>{"A"=>0.219437756702452, "C"=>0.214548041970626, "G"=>0.255405334730743, "T"=>0.310608866596179}}
-
-end
-
-end
+#!/usr/bin/ruby
+module Ytilib
+
+srand
+
+module Randoom
+  
+  private
+
+  def Randoom.new_counts
+    { 'A' => 0, 'C' => 0, 'G' => 0, 'T' => 0, 'N' => 0 }
+  end
+  
+  def Randoom.random_letter(probs)
+    random = rand()
+    return 'A' if random < probs['A']
+    return 'C' if random < probs['A'] + probs['C']
+    return 'G' if random < probs['A'] + probs['C'] + probs['G']
+    return 'T'
+  end
+
+  public
+  
+  def Randoom.calc_probs(input)
+    counts = new_counts
+    counts.default = 0
+    (0...input.length).each { |i|
+      counts[input[i,1].upcase] += 1
+    }
+    return make_probs!(counts)
+  end
+    
+  def Randoom.rand_seq(req_len, probs = DEF_PROBS, probs_m = nil)
+    randoom = ''
+    if (probs_m == nil)
+      req_len.times { randoom << random_letter(probs) }
+      return randoom  
+    end
+    random_l = random_letter(probs)
+    randoom = random_l
+    (req_len-1).times {
+      cur_probs = probs_m[random_l]
+      random_l = random_letter(cur_probs)
+      randoom << random_l
+    }
+    return randoom
+  end
+  
+  def Randoom.calc_probs_m(input)
+    probs_m = { 'A' => {}, 'C' => {}, 'G' => {}, 'T' => {} }
+    counts = { 'A' => new_counts, 'C' => new_counts, 'G' => new_counts, 'T' => new_counts, 'N' => new_counts }
+    (0...input.length-1).each { |i|
+      pair = input[i, 2].upcase
+      counts[pair[0,1]][pair[1,1]] += 1
+    }
+    probs_m['A'] = make_probs!(counts['A'])
+    probs_m['C'] = make_probs!(counts['C'])
+    probs_m['G'] = make_probs!(counts['G'])
+    probs_m['T'] = make_probs!(counts['T'])
+    return probs_m
+  end
+  
+  def Randoom.make_probs_m!(counts)
+    ['A','C','G','T','N'].each { |l2|
+      addv = counts['N'][l2] / 4.0
+      ['A','C','G','T'].each { |l1|
+        counts[l1][l2] += addv
+      }
+    }
+    
+    probs_m = { 'A' => {}, 'C' => {}, 'G' => {}, 'T' => {} }
+    probs_m['A'] = make_probs!(counts['A'])
+    probs_m['C'] = make_probs!(counts['C'])
+    probs_m['G'] = make_probs!(counts['G'])
+    probs_m['T'] = make_probs!(counts['T'])
+    return probs_m
+  end
+  
+  def Randoom.make_probs!(counts, length = nil)
+    probs = { 'A' => 0, 'C' => 0, 'G' => 0, 'T' => 0 }
+    length = counts['A'] + counts['C'] + counts['G'] + counts['T'] + counts['N'] if length == nil
+    length = length.to_f
+    ['A','C','G','T'].each { |l| counts[l] += counts['N'] / 4.0 }
+    return probs if length == 0
+    probs['A'] = counts['A'] / length
+    probs['C'] = counts['C'] / length
+    probs['G'] = counts['G'] / length
+    probs['T'] = 1 - probs['A'] - probs['C'] - probs['G']
+    return probs
+  end
+  
+  def Randoom.equalize!(probs)
+    probs['A'] = probs['T'] = (probs['A'] + probs['T']) / 2
+    probs['C'] = probs['G'] = (probs['C'] + probs['G']) / 2
+    return probs
+  end
+  
+  def Randoom.twostrand!(probs)
+    return Randoom.equalize!(probs)
+  end
+  
+  DEF_PROBS = PPM.probs2IUPAC!({ 'A' => 0.25, 'C' => 0.25, 'G' => 0.25, 'T' => 0.25, 'N' => 0.25 })
+  
+  # probabilities counted without _random.fa files for human genome
+  DMEL40_PROBS1 = {"A"=>0.287729562173578, "C"=>0.21236364146414, "G"=>0.212259972960341, "T"=>0.287646823401942}
+  DMEL40_PROBS2 = {"A"=>0.28768819278776, "C"=>0.21231180721224, "G"=>0.21231180721224, "T"=>0.28768819278776}
+  
+  DMEL40_PROBS1_M = {"A"=>{"A"=>0.350403075314602, "C"=>0.181194374386404, "G"=>0.188361404205017, "T"=>0.280041146093977}, 
+    "C"=>{"A"=>0.325366772443085, "C"=>0.222264645612127, "G"=>0.197213801868993, "T"=>0.255154780075794}, 
+    "G"=>{"A"=>0.260710563672393, "C"=>0.27150575901391, "G"=>0.222294234776053, "T"=>0.245489442537644}, 
+    "T"=>{"A"=>0.217189093089999, "C"=>0.192590127484359, "G"=>0.239869076706963, "T"=>0.350351702718679}}
+  
+  HG17_PROBS1 = {"A"=>0.295309361730334, "C"=>0.204413561169847, "G"=>0.204519414193999, "T"=>0.295757662905821}
+  HG17_PROBS2 = {"A"=>0.295533512318077, "C"=>0.204466487681923, "G"=>0.204466487681923, "T"=>0.295533512318077}
+  
+  HG17_PROBS1_M = {"A"=>{"A"=>0.331091206257755, "C"=>0.170458424092748, "G"=>0.236770972081246, "T"=>0.261679397568252}, 
+    "C"=>{"A"=>0.354813019140533, "C"=>0.254741288394943, "G"=>0.0481667110625576, "T"=>0.342278981401966}, 
+    "G"=>{"A"=>0.290057117684408, "C"=>0.208514091370804, "G"=>0.254732297362797, "T"=>0.246696493581991}, 
+    "T"=>{"A"=>0.222087715262152, "C"=>0.200697606508443, "G"=>0.245657322003887, "T"=>0.331557356225517}}
+  
+  HG18_PROBS1 = {"A"=>0.291900580635872, "C"=>0.207855064518284, "G"=>0.207968587245859, "T"=>0.292275767599985}
+  HG18_PROBS2 = {"A"=>0.292088174117929, "C"=>0.207911825882071, "G"=>0.207911825882071, "T"=>0.292088174117929}
+  
+  MM9_PROBS1 = {"A"=>0.289755259854654, "C"=>0.210085673636132, "G"=>0.210143929198141, "T"=>0.290015137311074}
+  MM9_PROBS2 = {"A"=>0.289885198582864, "C"=>0.210114801417136, "G"=>0.210114801417136, "T"=>0.289885198582864}
+  
+  MM9_PROBS1_M = {"A"=>{"A"=>0.310389104265713, "C"=>0.184962574392377, "G"=>0.251904718465914, "T"=>0.252743602875996}, "C"=>{"A"=>0.352189584318682, "C"=>0.250794045222924, "G"=>0.0494404816637487, "T"=>0.347575888794645}, "G"=>{"A"=>0.295931117515178, "C"=>0.197870954111653, "G"=>0.250756985626016, "T"=>0.255440942747154}, "T"=>{"A"=>0.219437756702452, "C"=>0.214548041970626, "G"=>0.255405334730743, "T"=>0.310608866596179}}
+
+end
+
+end