Class: Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands

Inherits:
Object
  • Object
show all
Extended by:
CutSymbol, StringFormatting
Defined in:
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb

Overview

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

Defined Under Namespace

Classes: Result

Class Method Summary collapse

Instance Method Summary collapse

Methods included from CutSymbol

cut_symbol, escaped_cut_symbol, re_cut_symbol, re_cut_symbol_adjacent, set_cut_symbol

Methods included from StringFormatting

add_spacing, left_padding, right_padding, strip_cuts_and_padding, strip_padding

Constructor Details

#initialize ⇒ AlignedStrands

Creates a new object.

Returns

Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands object



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# File 'lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb', line 26

def initialize; super; end

Class Method Details

.align(a, b) ⇒ Object

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



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# 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) ⇒ 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