Class | Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands |
In: |
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
|
Parent: | Object |
Align two SingleStrand objects and return a Result object with primary and complement accessors.
Result | = | Struct.new(:primary, :complement) | The object returned for alignments |
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
Returns: | Result object with equal padding on both strings |
# 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
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:
The sequences stripped of left and right ‘n’ padding must be of equal length.
Arguments
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 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
# 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