Method: Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands.align_with_cuts

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

.align_with_cuts(a, b, a_cuts, b_cuts) ⇒ Object

Pad and align two String objects with cut symbols.

Example:

AlignedStrands.with_cuts('nngattacannnnn', 'nnnnnctaatgtnn', [0, 10, 12], [0, 2, 12]) # => 
  <struct Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
    primary="n n n n^n g a t t a c a n n^n n^n",
    complement="n^n n^n n c t a a t g t n^n n n n">

Notes:

  • To make room for the cut symbols each nucleotide is spaced out.

  • This is meant to be able to handle multiple cuts and completely unrelated cutsites on the two strands, therefore no biological algorithm assumptions (shortcuts) are made.

The sequences stripped of left and right ‘n’ padding must be of equal length.

Arguments

  • a: Primary sequence

  • b: Complementary sequence

  • a_cuts: Primary strand cut locations in 0-based index notation

  • b_cuts: Complementary strand cut locations in 0-based index notation

Returns

Result object with equal padding on both strings and spacing between bases



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# File 'lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb', line 87

def self.align_with_cuts(a,b,a_cuts,b_cuts)
  a = a.to_s
  b = b.to_s
  validate_input( strip_padding(a), strip_padding(b) )

  a_left, a_right = left_padding(a), right_padding(a)
  b_left, b_right = left_padding(b), right_padding(b)

  left_diff = a_left.length - b_left.length
  right_diff = a_right.length - b_right.length

  (right_diff > 0) ? (b_right += 'n' * right_diff) : (a_right += 'n' * right_diff.abs)

  a_adjust = b_adjust = 0

  if left_diff > 0
    b_left += 'n' * left_diff
    b_adjust = left_diff
  else
    a_left += 'n' * left_diff.abs
    a_adjust = left_diff.abs
  end

  a = a_left + strip_padding(a) + a_right
  b = b_left + strip_padding(b) + b_right

  a_cuts.sort.reverse.each { |c| a.insert(c+1+a_adjust, cut_symbol) }
  b_cuts.sort.reverse.each { |c| b.insert(c+1+b_adjust, cut_symbol) }

  Result.new( add_spacing(a), add_spacing(b) )
end