Class: IUPAC

Inherits:
String show all
Defined in:
lib/sequence_logo/ytilib/iupac.rb

Constant Summary collapse

CODE = 
{"A" => "A", "C" => "C", "G" => "G", "T" => "T", 
"AG" => "R", "CT" => "Y", "GT" => "K", "AC" => "M", 
"CG" => "S", "AT" => "W", "CGT" => "B", "AGT" => "D", "ACT" => "H", "ACG" => "V", "ACGT" => "N"}
REVCODE = 
CODE.invert

Instance Method Summary collapse

Methods inherited from String

#prev, #prev!, #revcomp, #revcomp!, #to_id

Constructor Details

#initialize(words) ⇒ IUPAC

Returns a new instance of IUPAC.



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 11

def initialize(words)
  if words.is_a?(Array)
    iupac = (0...words[0].size).collect { |i|
      (0...words.size).collect { |j| words[j][i,1] }.uniq.sort.inject("") { |cola, letter| cola += letter }
    }.inject("") { |iup, cola|
      checkerr("bad letter set #{cola}") { !CODE.has_key?(cola) }
      iup += CODE[cola]
    }
    super(iupac)
  elsif words.is_a?(IUPAC)
    super(words)
  elsif words.is_a?(String)
    checkerr("word #{words} has strange characters") { words.tr('ACGTURYKMSWBDHVN', '').size > 0 }
    super(words)
  end
end

Instance Method Details

#==(iupac) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 28

def ==(iupac)
  return false if self.size != iupac.size
  (0...self.size).inject(true) { |result, i| result &= IUPACOM[self[i,1]][iupac[i,1]] }
end

#compl ⇒ Object Also known as: comp, complement 



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

def compl
  return self.tr("ACGTRYKMSWBDHVN", "TGCAYRMKSWVHDBN")
end

#compl! ⇒ Object Also known as: comp!, complement! 



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 54

def compl!
  self.tr!("ACGTRYKMSWBDHVN", "TGCAYRMKSWVHDBN")
  return self
end

#dup ⇒ Object 



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 7

def dup
  IUPAC.new(self)
end

#include?(iupac) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequence_logo/ytilib/iupac.rb', line 42

def include?(iupac)
  return false if self.size < iupac.size || !iupac.is_a?(IUPAC)
  (0..self.size-iupac.size).each { |i|
    return i if IUPAC.new(self[i,iupac.size]) == iupac
  }
  return false
end

#merge(iupac) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 33

def merge(iupac)
  return nil if self.size != iupac.size
  res = (0...self.size).inject("") { |res, i|
    merges = REVCODE[self[i,1]].split(//).concat(REVCODE[iupac[i,1]].split(//)).uniq.sort.inject("") { |s, c| s += c}
    res << CODE[merges]
  }
  return IUPAC.new(res)
end

#reverse ⇒ Object 



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 60

def reverse
  return IUPAC.new(reverse_string)
end

#reverse_string ⇒ Object 



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# File 'lib/sequence_logo/ytilib/iupac.rb', line 59

alias reverse_string reverse