class Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands

Align two SingleStrand objects and return a Result object with primary and complement accessors.

Constants

Result

The object returned for alignments

Public Class Methods

align(a, b) click to toggle source

Pad and align two String objects without cut symbols.

This will look for the sub-sequence without left and right 'n' padding and re-apply 'n' padding to both strings on both sides equal to the maximum previous padding on that side.

The sub-sequences stripped of left and right 'n' padding must be of equal length.

Example:

AlignedStrands.align('nngattacannnnn', 'nnnnnctaatgtnn') # => 
 <struct Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
   primary="nnnnngattacannnnn",
   complement="nnnnnctaatgtnnnnn">

Arguments

  • a: Primary strand

  • b: Complementary strand

Returns

Result object with equal padding on both strings

# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 51
def self.align(a, b)
  a = a.to_s
  b = b.to_s
  validate_input( strip_padding(a), strip_padding(b) )
  left = [left_padding(a), left_padding(b)].sort.last
  right = [right_padding(a), right_padding(b)].sort.last

  p = left + strip_padding(a) + right
  c = left + strip_padding(b) + right
  Result.new(p,c)
end
align_with_cuts(a,b,a_cuts,b_cuts) click to toggle source

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

# 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
new() click to toggle source

Creates a new object.


Returns

Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands object

Calls superclass method
# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 26
def initialize; super; end

Protected Class Methods

validate_input(a,b) click to toggle source
# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 123
def self.validate_input(a,b)
  unless a.size == b.size
    err = "Result sequences are not the same size.  Does not align sequences with differing lengths after strip_padding.\n"
    err += "#{a.size}, #{a.inspect}\n"
    err += "#{b.size}, #{b.inspect}"
    raise ArgumentError, err
  end
end