Class: Ytilib::PM

Inherits:
Object show all
Defined in:
lib/sequence_logo/ytilib/pm.rb,
lib/sequence_logo/ytilib/pmsd.rb,
lib/sequence_logo/ytilib/infocod.rb

Direct Known Subclasses

PPM

Constant Summary collapse

IUPAC_LS = 
(IUPAC::CODE.keys - ['A','C','G','T']).collect { |iul| [IUPAC::CODE[iul], iul.split(//)] }

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(size, matrix = nil, words_count = nil) ⇒ PM

Returns a new instance of PM.



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# File 'lib/sequence_logo/ytilib/pm.rb', line 161

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

Instance Attribute Details

#matrix ⇒ Object (readonly)

Returns the value of attribute matrix.



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# File 'lib/sequence_logo/ytilib/pm.rb', line 4

def matrix
  @matrix
end

#size ⇒ Object (readonly) Also known as: length

Returns the value of attribute size.



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# File 'lib/sequence_logo/ytilib/pm.rb', line 4

def size
  @size
end

#words_count ⇒ Object

Returns the value of attribute words_count.



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# File 'lib/sequence_logo/ytilib/pm.rb', line 5

def words_count
  @words_count
end

Class Method Details

.col_sum(matrix, index = 0) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 177

def PM.col_sum(matrix, index = 0)
  return matrix['A'][index] + matrix['C'][index] + matrix['G'][index] + matrix['T'][index]
end

.from_bismark(b, iupacomp = false) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 347

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

.load(filename) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 273

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

.new_pcm(words, iupacomp = false) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 247

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

.new_pwm(words) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 267

def PM.new_pwm(words)
  pcm = PM.new_pcm(words)
  pcm.to_pwm!
  return pcm
end

Instance Method Details

#best_hit(s, use2strands = true) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 134

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

#best_score ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 229

def best_score
  return (0...size).inject(0) { |sum, i|
    sum += ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.max
  }
end

#best_word ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 39

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

#col_sum(index = 0, letset = ['A','C','G','T']) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 173

def col_sum(index = 0, letset = ['A','C','G','T'])
  return letset.inject(0) { |sum, l| sum += @matrix[l][index] }
end

#collect_hits(s, score_g, use2strands = true) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 123

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

#consensus ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 81

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

#consensus_string(beautiful = false) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 55

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

#dup ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 241

def dup
  new_matrix = {}
  @matrix.each_key { |letter| new_matrix[letter] = @matrix[letter].dup }
  return PM.new(@size, new_matrix, @words_count)
end

#each_position(&block) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 13

def each_position(&block)
  return enum_for(:each_position)  unless block_given?
  @matrix['A'].each_index do |i|
    position =  ['A', 'C', 'G', 'T'].map{|letter| @matrix[letter][i] }
    yield position
  end
end

#each_position_index(&block) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 9

def each_position_index(&block)
  @matrix['A'].each_index(&block)
end

#eql?(pm) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequence_logo/ytilib/pm.rb', line 144

def eql?(pm)
  return ['A','C','G','T'].inject(true) { |equal, letter|
    equal = equal && @matrix[letter].eql?(pm.matrix[letter])
  }
end

#fast_score_sigma ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pmsd.rb', line 36

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

#fast_score_sigma_precise ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pmsd.rb', line 55

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

#find_hit(s, score_g, use2strands = true) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 104

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

#find_hits(s, score_g, use2strands = true) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 114

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

#fixwc ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 399

def fixwc
  return unless @words_count
  @words_count = (0...@size).collect { |i| col_sum(i) }.max
end

#flexeql?(pm) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequence_logo/ytilib/pm.rb', line 150

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

#get_ppm(words_count = nil) ⇒ Object Also known as: to_ppm 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 206

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

#get_pwm(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1) ⇒ Object Also known as: to_pwm 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 201

def get_pwm(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1)
  return self.dup.to_pwm!(words_count, probs, pseudocount)
end

#icd2of4(floor = false) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/infocod.rb', line 50

def icd2of4(floor = false)
  i2o4 = @words_count / 2.0
  i2o4 = i2o4.floor if floor
  ([i2o4, i2o4, 0, 0].inject(0.0) { |sum, k_i| sum += k_i.log_fact  } - @words_count.log_fact ) / @words_count
  # 0 is equal to @words_count % 2, because 0! = 1!
end

#icd3of4(floor = false) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/infocod.rb', line 57

def icd3of4(floor = false)
  i3o4 = @words_count / 3.0
  i3o4 = i3o4.floor if floor
  addon = floor ? @words_count % 3 : 0
  ([i3o4, i3o4, i3o4, addon].inject(0.0) { |sum, k_i| sum += k_i.log_fact  } - @words_count.log_fact ) / @words_count
end

#icd4of4(floor = false) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/infocod.rb', line 73

def icd4of4(floor = false)
  i4o4 = @words_count / 4.0
  i4o4 = i4o4.floor if floor
  ([i4o4, i4o4, i4o4, i4o4].inject(0.0) { |sum, k_i| sum += k_i.log_fact  } - @words_count.log_fact ) / @words_count
end

#icdThc ⇒ Object 



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# File 'lib/sequence_logo/ytilib/infocod.rb', line 64

def icdThc
  icd3of4
end

#icdTlc ⇒ Object 



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# File 'lib/sequence_logo/ytilib/infocod.rb', line 68

def icdTlc
  io = @words_count / 6.0
  ([2*io, 2*io, io, io].inject(0.0) { |sum, k_i| sum += k_i.log_fact  } - @words_count.log_fact ) / @words_count
end

#infocod(position = nil) ⇒ Object Also known as: icd 



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# File 'lib/sequence_logo/ytilib/infocod.rb', line 44

def infocod(position = nil)
  return infocod_private(position) if position
  (0...@size).collect { |i| infocod_private(i) }
end

#iupacomp! ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 376

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

#m3sd(bckgr = Randoom::DEF_PROBS) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 387

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

#p_value(threshold, mean = nil, variance = nil) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 32

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

#positiv! ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 321

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

#revcomp! ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 327

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

#save(filename) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 295

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

#score(word) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 219

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

#score_mean(bckgr = Randoom::DEF_PROBS) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 21

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

#score_sigma(trycount = 4**10, approx = false, bg = nil) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pmsd.rb', line 4

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

#score_variance(bckgr = Randoom::DEF_PROBS) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 25

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

#strict_consensus ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 47

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

#to_bismark(b) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 334

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 )
  each_position_index do |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
end

#to_pwm!(words_count = nil, probs = Randoom::DEF_PROBS, pseudocount = 1) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 181

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

#worst_score ⇒ Object 



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# File 'lib/sequence_logo/ytilib/pm.rb', line 235

def worst_score
  return (0...size).inject(0) { |sum, i|
    sum += ['A', 'C', 'G', 'T'].collect { |l| @matrix[l][i] }.min
  }
end