sequence_logo 1.0.3 → 1.0.4

data/lib/sequence_logo/ytilib/pm.rb

@@ -1,562 +1,562 @@
-module Ytilib
-  class PM
-
-    attr_reader :matrix, :size
-    attr_accessor :words_count
-    
-    alias length size
-    
-    def score_mean(bckgr = Randoom::DEF_PROBS)
-      (0...@size).inject(0.0) { |mean, i| mean += ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i] * bckgr[l] } }
-    end
-    
-    def score_variance(bckgr = Randoom::DEF_PROBS)
-      (0...@size).inject(0.0) { |m2, i| 
-        deltai = ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i]**2 * bckgr[l] } - ['A','C','G','T'].inject(0.0) { |sum,l| sum += matrix[l][i] * bckgr[l] }**2
-        m2 += deltai
-      }
-    end
-    
-    def p_value(threshold, mean = nil, variance = nil)
-      mean = mean ? mean : score_mean
-      variance = variance ? variance : score_variance
-      n_ = (threshold - mean) / Math.sqrt(variance)
-      p_value = (1 - Math.erf2(n_/Math.sqrt(2))) / 2.0
-    end
-    
-    def best_word
-      return (0...size).inject("") { |word, i|
-        max = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
-        maxlets = ['A', 'C', 'G', 'T'].select { |l| @matrix[l][i] == max }
-        word << (maxlets.size == 1 ? maxlets.first : "N")
-      }
-    end
-    
-    def strict_consensus
-      return IUPAC.new((0...size).inject("") { |word, i|
-        max = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
-        maxlets = ['A', 'C', 'G', 'T'].inject("") { |lets, l| lets += @matrix[l][i] == max ? l : ""}
-        word += IUPAC::CODE[maxlets]
-      })
-    end
-    
-    def consensus_string(beautiful = false)
-      checkerr("words count is undefined") { !@words_count }
-      i2o4, thc, tlc = icd2of4, icdThc, icdTlc
-      icd = infocod
-      
-      return String.new((0...size).inject("") { |word, i|
-
-        scores = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.uniq.sort.reverse
-        
-        if icd[i] > i2o4
-          scores = [scores.first]
-        elsif icd[i] > thc
-          scores = scores[0..1]
-        elsif icd[i] > tlc
-          scores = scores[0..2]
-        end
-        
-        lets = ['A', 'C', 'G', 'T'].inject("") { |lets, l| lets += scores.include?(@matrix[l][i]) ? l : ""}
-        
-        reslet = IUPAC::CODE[lets]
-        reslet = reslet.downcase if beautiful && lets.size > 2
-        
-        word += reslet
-      })
-    end
-    
-    def consensus
-      checkerr("words count is undefined") { !@words_count }
-      i2o4, thc, tlc = icd2of4, icdThc, icdTlc
-      icd = infocod
-      
-      return IUPAC.new((0...size).inject("") { |word, i|
-
-        scores = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.uniq.sort.reverse
-        
-        if icd[i] > i2o4
-          scores = [scores.first]
-        elsif icd[i] > thc
-          scores = scores[0..1]
-        elsif icd[i] > tlc
-          scores = scores[0..2]
-        end
-        
-        lets = ['A', 'C', 'G', 'T'].inject("") { |lets, l| lets += scores.include?(@matrix[l][i]) ? l : ""}
-        
-        word += IUPAC::CODE[lets]
-      })
-    end
-    
-    def find_hit(s, score_g, use2strands = true)
-      (0..(s.size - @size)).each { |i|
-        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
-        score_p, score_rc = score(seq), score(seq_rc)
-        r = use2strands ? [score_p,score_rc].max : score_p
-        return i if r >= score_g
-      }
-      return nil
-    end
-    
-    def find_hits(s, score_g, use2strands = true)
-      (0..(s.size - @size)).select { |i|
-        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
-        score_p, score_rc = score(seq), score(seq_rc)
-        r = use2strands ? [score_p,score_rc].max : score_p
-        r >= score_g ? i : nil
-      }.compact
-    end
-    
-    def collect_hits(s, score_g, use2strands = true)
-      result = []
-      (0..(s.size - @size)).each { |i|
-        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
-        score_p, score_rc = score(seq.upcase), score(seq_rc.upcase)
-        result << [score_p, seq, false, i] if score_p >= score_g
-        result << [score_rc, seq_rc, true, i] if score_rc >= score_g
-      }
-      result
-    end
-    
-    def best_hit(s, use2strands = true)
-      
-      checkerr("too short sequence") { s.size < @size }
-      return (0..(s.size - @size)).inject(-Float::MAX) { |r, i|
-        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
-        score_p, score_rc = score(seq), score(seq_rc)
-        r = use2strands ? [r,score_p,score_rc].max : [r,score_p].max
-      }
-    end
-    
-    def eql?(pm)
-      return ['A','C','G','T'].inject(true) { |equal, letter|
-        equal = equal && @matrix[letter].eql?(pm.matrix[letter])
-      }
-    end
-    
-    def flexeql?(pm)
-      checkerr("for what?") { true }
-      return ['A','C','G','T'].inject(true) { |equal, letter|
-        # report "letter=#{letter}"
-        equal = equal && (0...@size).inject(true) { |deepequal, position| 
-          # report "position=#{position}, delta=#{@matrix[letter][position] - pm.matrix[letter][position]}"
-          deepequal = deepequal && (@matrix[letter][position] - pm.matrix[letter][position]).abs < 10**-11 
-        }
-      }
-    end
-    
-    def initialize(size, matrix = nil, words_count = nil)
-      checkerr("matrix['A'].size != size, #{matrix['A'].size} != #{size}") { matrix != nil && size != matrix['A'].size }
-      @size = size
-      @matrix = matrix == nil ? PM.new_matrix(size) : matrix
-      if !words_count || words_count <= 0
-        words_count = col_sum(0)
-        @words_count = words_count.round >= 2 ? words_count.round : nil
-      else
-        @words_count = words_count
-      end
-    end
-    
-    def col_sum(index = 0, letset = ['A','C','G','T'])
-      return letset.inject(0) { |sum, l| sum += @matrix[l][index] }
-    end
-    
-    def PM.col_sum(matrix, index = 0)
-      return matrix['A'][index] + matrix['C'][index] + matrix['G'][index] + matrix['T'][index]
-    end
-      
-    def to_pwm!(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1)
-      @words_count = words_count if words_count && words_count > 0
-      
-      @matrix.each_key do |letter|
-        (0...@size).each { |pos|
-          
-          #p "pcm"
-          #p @matrix[letter][pos]
-          #p @matrix[letter][pos] + (probs[letter] * pseudocount)
-          #p ( (@words_count + pseudocount) * probs[letter])
-          #exit
-          
-          @matrix[letter][pos] = Math::log( (@matrix[letter][pos] + (probs[letter] * pseudocount)) / ( (@words_count + pseudocount) * probs[letter]) )
-          
-        }
-      end
-      
-      return self
-    end
-    
-    def get_pwm(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1)
-      return self.dup.to_pwm!(words_count, probs, pseudocount)
-    end
-    alias to_pwm get_pwm
-    
-    def get_ppm(words_count = nil)
-      words_count = @words_count unless words_count
-      checkerr("undefined words count") { !words_count || words_count <= 0 }
-      ppm = @matrix['N'] ?  PM.new_matrix_iupac(@size) : PM.new_matrix(@size)
-      @matrix.each_key { |letter|
-        (0...@size).each { |i|
-          ppm[letter][i] = @matrix[letter][i].to_f / words_count
-        }
-      }
-      return PPM.new(@size, ppm, words_count)
-    end
-    alias to_ppm get_ppm
-    
-    def score(word)
-      checkerr("word size != pwm.size") { @size != word.size }
-      checkerr("word #{word} has strange characters") { 
-        @matrix.keys.include?('N') ? word.tr('ACGTRYKMSWBDHVN', '').size > 0 : word.tr('ACGT', '').size > 0
-      }
-      return (0...@size).inject(0) { |sum, i| 
-        sum += @matrix[word[i,1]][i]
-      }
-    end
-    
-    def best_score
-      return (0...size).inject(0) { |sum, i|
-        sum += ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
-      }
-    end
-    
-    def worst_score
-      return (0...size).inject(0) { |sum, i|
-        sum += ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.min
-      }
-    end
-    
-    def dup
-      new_matrix = {}
-      @matrix.each_key { |letter| new_matrix[letter] = @matrix[letter].dup }
-      return PM.new(@size, new_matrix, @words_count)
-    end
-    
-    def PM.new_pcm(words, iupacomp = false)
-      size = words[0].size
-      counts = PM.new_matrix(size)
-      counts.each_value { |arr| arr.fill(0) }
-      words.each { |word|
-        0.upto(size-1) { |i|
-          letter = word[i,1].upcase
-          checkerr("unknown letter #{letter}") { !['A', 'C', 'G', 'T', 'N'].include?(letter) }
-          if letter != 'N'
-            counts[letter][i] += 1
-          else
-            ['A', 'C', 'G', 'T'].each { |l| counts[l][i] += 0.25 }
-          end
-        }
-      }
-      newpcm = PM.new(size, counts, words.size)
-      newpcm.iupacomp! if iupacomp
-      return newpcm
-    end
-    
-    def PM.new_pwm(words)
-      pcm = PM.new_pcm(words)
-      pcm.to_pwm!
-      return pcm
-    end
-    
-    def PM.load(filename)
-      # supporting pat & pwm formats (letter-column and letter-row format)
-      input = IO.read(filename)
-      tm = []
-      input.each_line { |line| 
-        l_a = line.split
-        begin
-          l_a = l_a.collect { |a_i| Float(a_i) }
-        rescue
-          next
-        end
-        tm << l_a
-      }
-      tm = tm.transpose if tm.size == 4
-      matrix = PM.new_matrix(tm.size)
-      tm.each_index { |i| ['A', 'C', 'G', 'T'].each_with_index { |l, j| matrix[l][i] = tm[i][j] }  }
-      
-      ppm_mode = (0...tm.size).inject(true) { |ppm_ya, i| ppm_ya &= col_sum(matrix, i).round == 1 }
-      
-      return ppm_mode ? PPM.new(tm.size, matrix) : PM.new(tm.size, matrix)
-    end
-    
-    def save(filename)
-      File.open(filename, "w") { |out_f|
-        case File.ext_wo_name(filename)
-        when "pwm"
-          ['A', 'C', 'G', 'T'].each { |letter|
-            @matrix[letter].each { |e|
-              out_f << "#{e} "
-            }
-            out_f << $/
-          }
-        when "pat"
-          out_f.puts File.name_wo_ext(filename)
-          (0...@size).each { |i|
-            ['A', 'C', 'G', 'T'].each { |letter|
-              out_f << "#{@matrix[letter][i]} "
-            }
-            out_f << $/
-          }
-        when "xml"
-          checkerr("small-BiSMark is not supported at this moment")
-        else
-          checkerr("unknown motif file format specified")
-        end
-      }
-    end
-    
-    def positiv!
-      min = @matrix.values.collect { |v| v.min }.min.abs
-      @matrix.each_value { |v| (0...v.size).each { |i| v[i] += min } }
-      return self
-    end
-    
-    def revcomp!
-      @matrix['A'], @matrix['T'] = @matrix['T'], @matrix['A']
-      @matrix['C'], @matrix['G'] = @matrix['G'], @matrix['C']
-      @matrix.each_value { |v| v.reverse! }
-      self
-    end
-    
-    def to_bismark(b)
-      pwm = @matrix['A'][0].is_a?(Float)
-      attributes = {"length" => @size}
-      attributes["words-count"] = @words_count if @words_count && @words_count > 0
-      pe = b.add_element( pwm ? "PWM" : "PCM", attributes )
-      (0...@matrix['A'].size).each { |i|
-        pm_c = pe.add_element("pm-column", {"position" => i+1})
-        ['A', 'C', 'G', 'T'].each { |l|
-          pm_c.add_element(l.downcase).add_text(@matrix[l][i].to_s)
-        }
-      }
-    end
-    
-    def PM.from_bismark(b, iupacomp = false)
-      
-      checkerr("empty small-BiSMark file?") { !b }
-      float_m = (b.name == "PPM" || b.name == "PWM" || b.name == "WPCM")
-      words_count = b.attributes["words-count"] ? b.attributes["words-count"].to_f : nil
-      
-      matrix = {"A" => [], "C" => [], "G" => [], "T" => []}
-      b.elements.each("pm-column") { |pmc|
-        position = pmc.attributes["position"].to_i
-        ['A', 'C', 'G', 'T'].each { |l| matrix[l][position-1] = float_m ? pmc.elements[l.downcase].get_text.to_s.to_f : pmc.elements[l.downcase].get_text.to_s.to_i }
-      }
-      if b.name == "PPM"
-        newppm = PPM.new(matrix['A'].size, matrix, words_count)
-        newppm.iupacomp! if iupacomp
-        return newppm
-      end
-      if b.name == "PCM"
-        @words_count = col_sum(matrix)
-        newpcm = PM.new(matrix['A'].size, matrix, words_count)
-        newpcm.iupacomp! if iupacomp
-        return newpcm
-      end
-      if b.name == "PWM" && iupacomp
-        raise "cannot force IUPAC compatible PWM"
-      end
-      return PM.new(matrix['A'].size, matrix, words_count)
-    end
-    
-    IUPAC_LS = (IUPAC::CODE.keys - ['A','C','G','T']).collect { |iul| [IUPAC::CODE[iul], iul.split(//)] }
-    def iupacomp!
-      @words_count = (0...@size).collect { |i| col_sum(i) }.max unless @words_count # for unbalanced matrices (Genomatix has some)
-      # @words_count = @words_count.round < 2.0 ? nil : @words_count.round
-      
-      IUPAC_LS.each { |iul_ls|
-        @matrix[iul_ls[0]] = (0...@size).collect { |i| col_sum(i, iul_ls[1]) / iul_ls[1].size }
-      }
-      
-      return self
-    end
-    
-    def m3sd(bckgr = Randoom::DEF_PROBS)
-    
-      mean = (0...@size).inject(0.0) { |mean, i| mean += ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i] * bckgr[l] } }
-      dev = (0...@size).inject(0.0) { |m2, i| 
-        deltai = ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i]**2 * bckgr[l] } - ['A','C','G','T'].inject(0.0) { |sum,l| sum += matrix[l][i] * bckgr[l] }**2
-        m2 += deltai
-      }
-      sigma = Math.sqrt(dev)
-      
-      mean+3*sigma
-    end
-    
-    def fixwc
-      return unless @words_count
-      @words_count = (0...@size).collect { |i| col_sum(i) }.max
-    end
-    
-    protected
-    def PM.new_matrix(size)
-      return {
-        'A' => Array.new(size),
-        'C' => Array.new(size),
-        'G' => Array.new(size),
-        'T' => Array.new(size) }
-    end
-    
-    def PM.new_matrix_iupac(size)
-      return {
-        'A' => Array.new(size),
-        'C' => Array.new(size),
-        'G' => Array.new(size),
-        'T' => Array.new(size),
-        'R' => Array.new(size),
-        'Y' => Array.new(size),
-        'K' => Array.new(size),
-        'M' => Array.new(size),
-        'S' => Array.new(size),
-        'W' => Array.new(size),
-        'B' => Array.new(size),
-        'D' => Array.new(size),
-        'H' => Array.new(size),
-        'V' => Array.new(size),
-        'N' => Array.new(size)
-        }
-    end
-    
-  end
-
-  class PPM < PM
-    
-    #DEPRECATED, use iupacomp! instead
-    #def make_N_comp!
-    #  @matrix['N'] = (0...size).collect { 0.25 }
-    #  return self
-    #end
-    
-    def initialize(size, matrix = nil, words_count = nil)
-      checkerr("matrix['A'].size != size") { matrix != nil && size != matrix['A'].size }
-      @size = size
-      @matrix = matrix == nil ? PM.new_matrix(size) : matrix
-      @words_count = words_count
-    end
-    
-    def iupacomp!
-      @words_count = 4.0 unless @words_count
-      
-      IUPAC_LS.each { |iul_ls|
-        @matrix[iul_ls[0]] = (0...@size).collect { |i| col_sum(i, iul_ls[1]) / iul_ls[1].size }
-      }
-      
-      return self
-    end
-    
-    def score(word)
-      checkerr("word size != ppm.size") { @size != word.size }
-      checkerr("word #{word} has strange characters") { 
-        @matrix.keys.include?('N') ? word.tr('ACGTRYKMSWBDHVN', '').size > 0 : word.tr('ACGT', '').size > 0
-      }
-      return (0...@size).inject(1) { |mul, i| 
-        mul *= @matrix[word[i,1]][i]
-      }
-    end
-    
-    def best_score
-      return (0...size).inject(1) { |mul, i|
-        mul *= ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
-      }    
-    end
-    
-    def worst_score
-      return (0...size).inject(0) { |mul, i|
-        mul *= ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.min
-      }
-    end
-    
-    def to_bismark(b)
-      attributes = {"length" => @size}
-      attributes["words-count"] = @words_count if @words_count
-      pe = b.add_element("PPM", attributes)
-      (0...@matrix['A'].size).each { |i|
-        pm_c = pe.add_element("pm-column", {"position" => i+1})
-        ['A', 'C', 'G', 'T'].each { |l|
-          pm_c.add_element(l.downcase).add_text(@matrix[l][i].to_s)
-        }
-      }
-    end
-    
-    def PPM.probs2IUPAC!(probs)
-      IUPAC_LS.each { |iul_ls|
-        probs[iul_ls[0]] = iul_ls[1].inject(0) { |sum, l| sum += probs[l] } / iul_ls[1].size
-      }
-      return probs
-    end
-    
-    def get_pwm(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1.0)
-      
-      probs = PPM.probs2IUPAC!(probs.dup)
-      
-      words_count = @words_count if !words_count || words_count == 0
-      checkerr("undefined words count") { !words_count }
-      
-      pwm = @matrix['N'] ? PM.new_matrix_iupac(@size) : PM.new_matrix(@size)
-      
-      @matrix.each_key do |letter|
-        (0...@size).each { |pos|
-          
-          pwm[letter][pos] = Math::log( (@matrix[letter][pos] * words_count + (probs[letter] * pseudocount) ) / ( (words_count + pseudocount) * probs[letter]) )
-          
-        }
-      end
-      return PM.new(@size, pwm, words_count)
-      #pcm = get_pcm(words_count)
-      #pcm.iupacomp! if @matrix['N']
-      #return pcm.to_pwm!(words_count, probs, pseudocount)
-    end
-    alias to_pwm get_pwm
-    
-    def get_pwm0pc(probs = Randoom::DEF_PROBS)
-      new_matrix = {}
-      @matrix.each_key { |letter| new_matrix[letter] = @matrix[letter].dup }
-      newpm = PM.new(@size, new_matrix, nil)
-      
-      new_matrix.each_key do |letter|
-        (0...@size).each { |pos|
-          new_matrix[letter][pos] = Math::log(@matrix[letter][pos] / probs[letter])
-        }
-      end
-      
-      return newpm
-    end
-    
-    def to_pwm!
-      raise "cannot force PPM class to PWM, use to_pwm instead"
-    end
-    
-    def get_pcm(words_count = nil)
-      words_count = @words_count unless words_count
-      checkerr("undefined words count") { !words_count }
-      counts = PM.new_matrix(@size)
-      (0...size).each { |i|
-        ['A', 'C', 'G', 'T'].each { |l|
-          counts[l][i] = @matrix[l][i] * words_count
-        }
-      }
-      newpcm = PM.new(size, counts, words_count).iupacomp!
-      return newpcm
-    end
-    alias to_pcm get_pcm
-    
-    def PPM.from_IUPAC(iupac)
-      matrix = {"A" => [], "C" => [], "G" => [], "T" => []}
-      
-      (0...iupac.size).each { |i|
-        matrix.each_key { |k| matrix[k] << 0.0 }
-        letters = IUPAC::REVCODE[iupac[i]]
-        (0...letters.size).each { |j|
-          matrix[letters[j]][-1] = 1.0/letters.size
-        }
-      }
-      
-      newppm = PPM.new(iupac.size, matrix, 4.0)
-      newppm.iupacomp!
-      
-      newppm
-    end
-    
-  end
-end
+module Ytilib
+  class PM
+
+    attr_reader :matrix, :size
+    attr_accessor :words_count
+    
+    alias length size
+    
+    def score_mean(bckgr = Randoom::DEF_PROBS)
+      (0...@size).inject(0.0) { |mean, i| mean += ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i] * bckgr[l] } }
+    end
+    
+    def score_variance(bckgr = Randoom::DEF_PROBS)
+      (0...@size).inject(0.0) { |m2, i| 
+        deltai = ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i]**2 * bckgr[l] } - ['A','C','G','T'].inject(0.0) { |sum,l| sum += matrix[l][i] * bckgr[l] }**2
+        m2 += deltai
+      }
+    end
+    
+    def p_value(threshold, mean = nil, variance = nil)
+      mean = mean ? mean : score_mean
+      variance = variance ? variance : score_variance
+      n_ = (threshold - mean) / Math.sqrt(variance)
+      p_value = (1 - Math.erf2(n_/Math.sqrt(2))) / 2.0
+    end
+    
+    def best_word
+      return (0...size).inject("") { |word, i|
+        max = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
+        maxlets = ['A', 'C', 'G', 'T'].select { |l| @matrix[l][i] == max }
+        word << (maxlets.size == 1 ? maxlets.first : "N")
+      }
+    end
+    
+    def strict_consensus
+      return IUPAC.new((0...size).inject("") { |word, i|
+        max = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
+        maxlets = ['A', 'C', 'G', 'T'].inject("") { |lets, l| lets += @matrix[l][i] == max ? l : ""}
+        word += IUPAC::CODE[maxlets]
+      })
+    end
+    
+    def consensus_string(beautiful = false)
+      checkerr("words count is undefined") { !@words_count }
+      i2o4, thc, tlc = icd2of4, icdThc, icdTlc
+      icd = infocod
+      
+      return String.new((0...size).inject("") { |word, i|
+
+        scores = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.uniq.sort.reverse
+        
+        if icd[i] > i2o4
+          scores = [scores.first]
+        elsif icd[i] > thc
+          scores = scores[0..1]
+        elsif icd[i] > tlc
+          scores = scores[0..2]
+        end
+        
+        lets = ['A', 'C', 'G', 'T'].inject("") { |lets, l| lets += scores.include?(@matrix[l][i]) ? l : ""}
+        
+        reslet = IUPAC::CODE[lets]
+        reslet = reslet.downcase if beautiful && lets.size > 2
+        
+        word += reslet
+      })
+    end
+    
+    def consensus
+      checkerr("words count is undefined") { !@words_count }
+      i2o4, thc, tlc = icd2of4, icdThc, icdTlc
+      icd = infocod
+      
+      return IUPAC.new((0...size).inject("") { |word, i|
+
+        scores = ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.uniq.sort.reverse
+        
+        if icd[i] > i2o4
+          scores = [scores.first]
+        elsif icd[i] > thc
+          scores = scores[0..1]
+        elsif icd[i] > tlc
+          scores = scores[0..2]
+        end
+        
+        lets = ['A', 'C', 'G', 'T'].inject("") { |lets, l| lets += scores.include?(@matrix[l][i]) ? l : ""}
+        
+        word += IUPAC::CODE[lets]
+      })
+    end
+    
+    def find_hit(s, score_g, use2strands = true)
+      (0..(s.size - @size)).each { |i|
+        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
+        score_p, score_rc = score(seq), score(seq_rc)
+        r = use2strands ? [score_p,score_rc].max : score_p
+        return i if r >= score_g
+      }
+      return nil
+    end
+    
+    def find_hits(s, score_g, use2strands = true)
+      (0..(s.size - @size)).select { |i|
+        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
+        score_p, score_rc = score(seq), score(seq_rc)
+        r = use2strands ? [score_p,score_rc].max : score_p
+        r >= score_g ? i : nil
+      }.compact
+    end
+    
+    def collect_hits(s, score_g, use2strands = true)
+      result = []
+      (0..(s.size - @size)).each { |i|
+        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
+        score_p, score_rc = score(seq.upcase), score(seq_rc.upcase)
+        result << [score_p, seq, false, i] if score_p >= score_g
+        result << [score_rc, seq_rc, true, i] if score_rc >= score_g
+      }
+      result
+    end
+    
+    def best_hit(s, use2strands = true)
+      
+      checkerr("too short sequence") { s.size < @size }
+      return (0..(s.size - @size)).inject(-Float::MAX) { |r, i|
+        seq, seq_rc = s[i, @size], s[i, @size].revcomp!
+        score_p, score_rc = score(seq), score(seq_rc)
+        r = use2strands ? [r,score_p,score_rc].max : [r,score_p].max
+      }
+    end
+    
+    def eql?(pm)
+      return ['A','C','G','T'].inject(true) { |equal, letter|
+        equal = equal && @matrix[letter].eql?(pm.matrix[letter])
+      }
+    end
+    
+    def flexeql?(pm)
+      checkerr("for what?") { true }
+      return ['A','C','G','T'].inject(true) { |equal, letter|
+        # report "letter=#{letter}"
+        equal = equal && (0...@size).inject(true) { |deepequal, position| 
+          # report "position=#{position}, delta=#{@matrix[letter][position] - pm.matrix[letter][position]}"
+          deepequal = deepequal && (@matrix[letter][position] - pm.matrix[letter][position]).abs < 10**-11 
+        }
+      }
+    end
+    
+    def initialize(size, matrix = nil, words_count = nil)
+      checkerr("matrix['A'].size != size, #{matrix['A'].size} != #{size}") { matrix != nil && size != matrix['A'].size }
+      @size = size
+      @matrix = matrix == nil ? PM.new_matrix(size) : matrix
+      if !words_count || words_count <= 0
+        words_count = col_sum(0)
+        @words_count = words_count.round >= 2 ? words_count.round : nil
+      else
+        @words_count = words_count
+      end
+    end
+    
+    def col_sum(index = 0, letset = ['A','C','G','T'])
+      return letset.inject(0) { |sum, l| sum += @matrix[l][index] }
+    end
+    
+    def PM.col_sum(matrix, index = 0)
+      return matrix['A'][index] + matrix['C'][index] + matrix['G'][index] + matrix['T'][index]
+    end
+      
+    def to_pwm!(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1)
+      @words_count = words_count if words_count && words_count > 0
+      
+      @matrix.each_key do |letter|
+        (0...@size).each { |pos|
+          
+          #p "pcm"
+          #p @matrix[letter][pos]
+          #p @matrix[letter][pos] + (probs[letter] * pseudocount)
+          #p ( (@words_count + pseudocount) * probs[letter])
+          #exit
+          
+          @matrix[letter][pos] = Math::log( (@matrix[letter][pos] + (probs[letter] * pseudocount)) / ( (@words_count + pseudocount) * probs[letter]) )
+          
+        }
+      end
+      
+      return self
+    end
+    
+    def get_pwm(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1)
+      return self.dup.to_pwm!(words_count, probs, pseudocount)
+    end
+    alias to_pwm get_pwm
+    
+    def get_ppm(words_count = nil)
+      words_count = @words_count unless words_count
+      checkerr("undefined words count") { !words_count || words_count <= 0 }
+      ppm = @matrix['N'] ?  PM.new_matrix_iupac(@size) : PM.new_matrix(@size)
+      @matrix.each_key { |letter|
+        (0...@size).each { |i|
+          ppm[letter][i] = @matrix[letter][i].to_f / words_count
+        }
+      }
+      return PPM.new(@size, ppm, words_count)
+    end
+    alias to_ppm get_ppm
+    
+    def score(word)
+      checkerr("word size != pwm.size") { @size != word.size }
+      checkerr("word #{word} has strange characters") { 
+        @matrix.keys.include?('N') ? word.tr('ACGTRYKMSWBDHVN', '').size > 0 : word.tr('ACGT', '').size > 0
+      }
+      return (0...@size).inject(0) { |sum, i| 
+        sum += @matrix[word[i,1]][i]
+      }
+    end
+    
+    def best_score
+      return (0...size).inject(0) { |sum, i|
+        sum += ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
+      }
+    end
+    
+    def worst_score
+      return (0...size).inject(0) { |sum, i|
+        sum += ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.min
+      }
+    end
+    
+    def dup
+      new_matrix = {}
+      @matrix.each_key { |letter| new_matrix[letter] = @matrix[letter].dup }
+      return PM.new(@size, new_matrix, @words_count)
+    end
+    
+    def PM.new_pcm(words, iupacomp = false)
+      size = words[0].size
+      counts = PM.new_matrix(size)
+      counts.each_value { |arr| arr.fill(0) }
+      words.each { |word|
+        0.upto(size-1) { |i|
+          letter = word[i,1].upcase
+          checkerr("unknown letter #{letter}") { !['A', 'C', 'G', 'T', 'N'].include?(letter) }
+          if letter != 'N'
+            counts[letter][i] += 1
+          else
+            ['A', 'C', 'G', 'T'].each { |l| counts[l][i] += 0.25 }
+          end
+        }
+      }
+      newpcm = PM.new(size, counts, words.size)
+      newpcm.iupacomp! if iupacomp
+      return newpcm
+    end
+    
+    def PM.new_pwm(words)
+      pcm = PM.new_pcm(words)
+      pcm.to_pwm!
+      return pcm
+    end
+    
+    def PM.load(filename)
+      # supporting pat & pwm formats (letter-column and letter-row format)
+      input = IO.read(filename)
+      tm = []
+      input.each_line { |line| 
+        l_a = line.split
+        begin
+          l_a = l_a.collect { |a_i| Float(a_i) }
+        rescue
+          next
+        end
+        tm << l_a
+      }
+      tm = tm.transpose if tm.size == 4
+      matrix = PM.new_matrix(tm.size)
+      tm.each_index { |i| ['A', 'C', 'G', 'T'].each_with_index { |l, j| matrix[l][i] = tm[i][j] }  }
+      
+      ppm_mode = (0...tm.size).inject(true) { |ppm_ya, i| ppm_ya &= col_sum(matrix, i).round == 1 }
+      
+      return ppm_mode ? PPM.new(tm.size, matrix) : PM.new(tm.size, matrix)
+    end
+    
+    def save(filename)
+      File.open(filename, "w") { |out_f|
+        case File.ext_wo_name(filename)
+        when "pwm"
+          ['A', 'C', 'G', 'T'].each { |letter|
+            @matrix[letter].each { |e|
+              out_f << "#{e} "
+            }
+            out_f << $/
+          }
+        when "pat"
+          out_f.puts File.name_wo_ext(filename)
+          (0...@size).each { |i|
+            ['A', 'C', 'G', 'T'].each { |letter|
+              out_f << "#{@matrix[letter][i]} "
+            }
+            out_f << $/
+          }
+        when "xml"
+          checkerr("small-BiSMark is not supported at this moment")
+        else
+          checkerr("unknown motif file format specified")
+        end
+      }
+    end
+    
+    def positiv!
+      min = @matrix.values.collect { |v| v.min }.min.abs
+      @matrix.each_value { |v| (0...v.size).each { |i| v[i] += min } }
+      return self
+    end
+    
+    def revcomp!
+      @matrix['A'], @matrix['T'] = @matrix['T'], @matrix['A']
+      @matrix['C'], @matrix['G'] = @matrix['G'], @matrix['C']
+      @matrix.each_value { |v| v.reverse! }
+      self
+    end
+    
+    def to_bismark(b)
+      pwm = @matrix['A'][0].is_a?(Float)
+      attributes = {"length" => @size}
+      attributes["words-count"] = @words_count if @words_count && @words_count > 0
+      pe = b.add_element( pwm ? "PWM" : "PCM", attributes )
+      (0...@matrix['A'].size).each { |i|
+        pm_c = pe.add_element("pm-column", {"position" => i+1})
+        ['A', 'C', 'G', 'T'].each { |l|
+          pm_c.add_element(l.downcase).add_text(@matrix[l][i].to_s)
+        }
+      }
+    end
+    
+    def PM.from_bismark(b, iupacomp = false)
+      
+      checkerr("empty small-BiSMark file?") { !b }
+      float_m = (b.name == "PPM" || b.name == "PWM" || b.name == "WPCM")
+      words_count = b.attributes["words-count"] ? b.attributes["words-count"].to_f : nil
+      
+      matrix = {"A" => [], "C" => [], "G" => [], "T" => []}
+      b.elements.each("pm-column") { |pmc|
+        position = pmc.attributes["position"].to_i
+        ['A', 'C', 'G', 'T'].each { |l| matrix[l][position-1] = float_m ? pmc.elements[l.downcase].get_text.to_s.to_f : pmc.elements[l.downcase].get_text.to_s.to_i }
+      }
+      if b.name == "PPM"
+        newppm = PPM.new(matrix['A'].size, matrix, words_count)
+        newppm.iupacomp! if iupacomp
+        return newppm
+      end
+      if b.name == "PCM"
+        @words_count = col_sum(matrix)
+        newpcm = PM.new(matrix['A'].size, matrix, words_count)
+        newpcm.iupacomp! if iupacomp
+        return newpcm
+      end
+      if b.name == "PWM" && iupacomp
+        raise "cannot force IUPAC compatible PWM"
+      end
+      return PM.new(matrix['A'].size, matrix, words_count)
+    end
+    
+    IUPAC_LS = (IUPAC::CODE.keys - ['A','C','G','T']).collect { |iul| [IUPAC::CODE[iul], iul.split(//)] }
+    def iupacomp!
+      @words_count = (0...@size).collect { |i| col_sum(i) }.max unless @words_count # for unbalanced matrices (Genomatix has some)
+      # @words_count = @words_count.round < 2.0 ? nil : @words_count.round
+      
+      IUPAC_LS.each { |iul_ls|
+        @matrix[iul_ls[0]] = (0...@size).collect { |i| col_sum(i, iul_ls[1]) / iul_ls[1].size }
+      }
+      
+      return self
+    end
+    
+    def m3sd(bckgr = Randoom::DEF_PROBS)
+    
+      mean = (0...@size).inject(0.0) { |mean, i| mean += ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i] * bckgr[l] } }
+      dev = (0...@size).inject(0.0) { |m2, i| 
+        deltai = ['A','C','G','T'].inject(0.0) { |sum,l| sum += @matrix[l][i]**2 * bckgr[l] } - ['A','C','G','T'].inject(0.0) { |sum,l| sum += matrix[l][i] * bckgr[l] }**2
+        m2 += deltai
+      }
+      sigma = Math.sqrt(dev)
+      
+      mean+3*sigma
+    end
+    
+    def fixwc
+      return unless @words_count
+      @words_count = (0...@size).collect { |i| col_sum(i) }.max
+    end
+    
+    protected
+    def PM.new_matrix(size)
+      return {
+        'A' => Array.new(size),
+        'C' => Array.new(size),
+        'G' => Array.new(size),
+        'T' => Array.new(size) }
+    end
+    
+    def PM.new_matrix_iupac(size)
+      return {
+        'A' => Array.new(size),
+        'C' => Array.new(size),
+        'G' => Array.new(size),
+        'T' => Array.new(size),
+        'R' => Array.new(size),
+        'Y' => Array.new(size),
+        'K' => Array.new(size),
+        'M' => Array.new(size),
+        'S' => Array.new(size),
+        'W' => Array.new(size),
+        'B' => Array.new(size),
+        'D' => Array.new(size),
+        'H' => Array.new(size),
+        'V' => Array.new(size),
+        'N' => Array.new(size)
+        }
+    end
+    
+  end
+
+  class PPM < PM
+    
+    #DEPRECATED, use iupacomp! instead
+    #def make_N_comp!
+    #  @matrix['N'] = (0...size).collect { 0.25 }
+    #  return self
+    #end
+    
+    def initialize(size, matrix = nil, words_count = nil)
+      checkerr("matrix['A'].size != size") { matrix != nil && size != matrix['A'].size }
+      @size = size
+      @matrix = matrix == nil ? PM.new_matrix(size) : matrix
+      @words_count = words_count
+    end
+    
+    def iupacomp!
+      @words_count = 4.0 unless @words_count
+      
+      IUPAC_LS.each { |iul_ls|
+        @matrix[iul_ls[0]] = (0...@size).collect { |i| col_sum(i, iul_ls[1]) / iul_ls[1].size }
+      }
+      
+      return self
+    end
+    
+    def score(word)
+      checkerr("word size != ppm.size") { @size != word.size }
+      checkerr("word #{word} has strange characters") { 
+        @matrix.keys.include?('N') ? word.tr('ACGTRYKMSWBDHVN', '').size > 0 : word.tr('ACGT', '').size > 0
+      }
+      return (0...@size).inject(1) { |mul, i| 
+        mul *= @matrix[word[i,1]][i]
+      }
+    end
+    
+    def best_score
+      return (0...size).inject(1) { |mul, i|
+        mul *= ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
+      }    
+    end
+    
+    def worst_score
+      return (0...size).inject(0) { |mul, i|
+        mul *= ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.min
+      }
+    end
+    
+    def to_bismark(b)
+      attributes = {"length" => @size}
+      attributes["words-count"] = @words_count if @words_count
+      pe = b.add_element("PPM", attributes)
+      (0...@matrix['A'].size).each { |i|
+        pm_c = pe.add_element("pm-column", {"position" => i+1})
+        ['A', 'C', 'G', 'T'].each { |l|
+          pm_c.add_element(l.downcase).add_text(@matrix[l][i].to_s)
+        }
+      }
+    end
+    
+    def PPM.probs2IUPAC!(probs)
+      IUPAC_LS.each { |iul_ls|
+        probs[iul_ls[0]] = iul_ls[1].inject(0) { |sum, l| sum += probs[l] } / iul_ls[1].size
+      }
+      return probs
+    end
+    
+    def get_pwm(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1.0)
+      
+      probs = PPM.probs2IUPAC!(probs.dup)
+      
+      words_count = @words_count if !words_count || words_count == 0
+      checkerr("undefined words count") { !words_count }
+      
+      pwm = @matrix['N'] ? PM.new_matrix_iupac(@size) : PM.new_matrix(@size)
+      
+      @matrix.each_key do |letter|
+        (0...@size).each { |pos|
+          
+          pwm[letter][pos] = Math::log( (@matrix[letter][pos] * words_count + (probs[letter] * pseudocount) ) / ( (words_count + pseudocount) * probs[letter]) )
+          
+        }
+      end
+      return PM.new(@size, pwm, words_count)
+      #pcm = get_pcm(words_count)
+      #pcm.iupacomp! if @matrix['N']
+      #return pcm.to_pwm!(words_count, probs, pseudocount)
+    end
+    alias to_pwm get_pwm
+    
+    def get_pwm0pc(probs = Randoom::DEF_PROBS)
+      new_matrix = {}
+      @matrix.each_key { |letter| new_matrix[letter] = @matrix[letter].dup }
+      newpm = PM.new(@size, new_matrix, nil)
+      
+      new_matrix.each_key do |letter|
+        (0...@size).each { |pos|
+          new_matrix[letter][pos] = Math::log(@matrix[letter][pos] / probs[letter])
+        }
+      end
+      
+      return newpm
+    end
+    
+    def to_pwm!
+      raise "cannot force PPM class to PWM, use to_pwm instead"
+    end
+    
+    def get_pcm(words_count = nil)
+      words_count = @words_count unless words_count
+      checkerr("undefined words count") { !words_count }
+      counts = PM.new_matrix(@size)
+      (0...size).each { |i|
+        ['A', 'C', 'G', 'T'].each { |l|
+          counts[l][i] = @matrix[l][i] * words_count
+        }
+      }
+      newpcm = PM.new(size, counts, words_count).iupacomp!
+      return newpcm
+    end
+    alias to_pcm get_pcm
+    
+    def PPM.from_IUPAC(iupac)
+      matrix = {"A" => [], "C" => [], "G" => [], "T" => []}
+      
+      (0...iupac.size).each { |i|
+        matrix.each_key { |k| matrix[k] << 0.0 }
+        letters = IUPAC::REVCODE[iupac[i]]
+        (0...letters.size).each { |j|
+          matrix[letters[j]][-1] = 1.0/letters.size
+        }
+      }
+      
+      newppm = PPM.new(iupac.size, matrix, 4.0)
+      newppm.iupacomp!
+      
+      newppm
+    end
+    
+  end
+end