Method: Bio::RestrictionEnzyme::DoubleStranded#create_action_at

Defined in:
lib/bio/util/restriction_enzyme/double_stranded.rb

#create_action_at(offset) ⇒ Object

Takes a RestrictionEnzyme object and a numerical offset to the sequence and returns an EnzymeAction

restriction_enzyme

RestrictionEnzyme

offset

Numerical offset of where the enzyme action occurs on the seqeunce



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# File 'lib/bio/util/restriction_enzyme/double_stranded.rb', line 160

def create_action_at( offset )
  # x is the size of the fully aligned sequence with maximum padding needed
  # to make a match on the primary and complement strand.
  #
  # For example -
  # Note how EcoRII needs extra padding on the beginning and ending of the
  # sequence 'ccagg' to make the match since the cut must occur between 
  # two nucleotides and can not occur on the very end of the sequence.
  #   
  #   EcoRII:
  #     :blunt: "0"
  #     :c2: "5"
  #     :c4: "0"
  #     :c1: "-1"
  #     :pattern: CCWGG
  #     :len: "5"
  #     :name: EcoRII
  #     :c3: "0"
  #     :ncuts: "2"
  #   
  #        -1 1 2 3 4 5
  #   5' - n^c c w g g n - 3'
  #   3' - n g g w c c^n - 5'
  #   
  #   (w == [at])
  
  x = aligned_strands.primary.size
  
  enzyme_action = EnzymeAction.new( offset,
                                    offset + x-1,
                                    offset,
                                    offset + x-1)

  @cut_locations.each do |cut_location_pair|
    # cut_pair is a DoubleStranded::CutLocationPair
    p, c = cut_location_pair.primary, cut_location_pair.complement
    if c >= p
      enzyme_action.add_cut_range(offset+p, nil, nil, offset+c)
    else
      enzyme_action.add_cut_range(nil, offset+p, offset+c, nil)
    end
  end

  enzyme_action
end