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

Constants

Result = Struct.new(:primary, :complement) 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

[Source]

    # File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 47
47:   def self.align(a, b)
48:     a = a.to_s
49:     b = b.to_s
50:     validate_input( strip_padding(a), strip_padding(b) )
51:     left = [left_padding(a), left_padding(b)].sort.last
52:     right = [right_padding(a), right_padding(b)].sort.last
53: 
54:     p = left + strip_padding(a) + right
55:     c = left + strip_padding(b) + right
56:     Result.new(p,c)
57:   end

align_with_cuts(a,b,a_cuts,b_cuts)

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

[Source]

     # File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 83
 83:   def self.align_with_cuts(a,b,a_cuts,b_cuts)
 84:     a = a.to_s
 85:     b = b.to_s
 86:     validate_input( strip_padding(a), strip_padding(b) )
 87: 
 88:     a_left, a_right = left_padding(a), right_padding(a)
 89:     b_left, b_right = left_padding(b), right_padding(b)
 90: 
 91:     left_diff = a_left.length - b_left.length
 92:     right_diff = a_right.length - b_right.length
 93: 
 94:     (right_diff > 0) ? (b_right += 'n' * right_diff) : (a_right += 'n' * right_diff.abs)
 95: 
 96:     a_adjust = b_adjust = 0
 97: 
 98:     if left_diff > 0
 99:       b_left += 'n' * left_diff
100:       b_adjust = left_diff
101:     else
102:       a_left += 'n' * left_diff.abs
103:       a_adjust = left_diff.abs
104:     end
105: 
106:     a = a_left + strip_padding(a) + a_right
107:     b = b_left + strip_padding(b) + b_right
108: 
109:     a_cuts.sort.reverse.each { |c| a.insert(c+1+a_adjust, cut_symbol) }
110:     b_cuts.sort.reverse.each { |c| b.insert(c+1+b_adjust, cut_symbol) }
111: 
112:     Result.new( add_spacing(a), add_spacing(b) )
113:   end

Protected Class methods

validate_input(a,b)

[Source]

     # File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 119
119:   def self.validate_input(a,b)
120:     unless a.size == b.size
121:       err = "Result sequences are not the same size.  Does not align sequences with differing lengths after strip_padding.\n"
122:       err += "#{a.size}, #{a.inspect}\n"
123:       err += "#{b.size}, #{b.inspect}"
124:       raise ArgumentError, err
125:     end
126:   end

Methods

Constants

Public Class methods

Protected Class methods