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
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 44 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
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 80 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
Creates a new object.
- Returns
-
Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
object
# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 19 def initialize; super; end
Protected Class Methods
# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 116 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