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 51 51: def self.align(a, b) 52: a = a.to_s 53: b = b.to_s 54: validate_input( strip_padding(a), strip_padding(b) ) 55: left = [left_padding(a), left_padding(b)].sort.last 56: right = [right_padding(a), right_padding(b)].sort.last 57: 58: p = left + strip_padding(a) + right 59: c = left + strip_padding(b) + right 60: Result.new(p,c) 61: 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 87 87: def self.align_with_cuts(a,b,a_cuts,b_cuts) 88: a = a.to_s 89: b = b.to_s 90: validate_input( strip_padding(a), strip_padding(b) ) 91: 92: a_left, a_right = left_padding(a), right_padding(a) 93: b_left, b_right = left_padding(b), right_padding(b) 94: 95: left_diff = a_left.length - b_left.length 96: right_diff = a_right.length - b_right.length 97: 98: (right_diff > 0) ? (b_right += 'n' * right_diff) : (a_right += 'n' * right_diff.abs) 99: 100: a_adjust = b_adjust = 0 101: 102: if left_diff > 0 103: b_left += 'n' * left_diff 104: b_adjust = left_diff 105: else 106: a_left += 'n' * left_diff.abs 107: a_adjust = left_diff.abs 108: end 109: 110: a = a_left + strip_padding(a) + a_right 111: b = b_left + strip_padding(b) + b_right 112: 113: a_cuts.sort.reverse.each { |c| a.insert(c+1+a_adjust, cut_symbol) } 114: b_cuts.sort.reverse.each { |c| b.insert(c+1+b_adjust, cut_symbol) } 115: 116: Result.new( add_spacing(a), add_spacing(b) ) 117: end
Creates a new object.
Returns: | Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands object |
# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 26 26: def initialize; super; end
# File lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb, line 123 123: def self.validate_input(a,b) 124: unless a.size == b.size 125: err = "Result sequences are not the same size. Does not align sequences with differing lengths after strip_padding.\n" 126: err += "#{a.size}, #{a.inspect}\n" 127: err += "#{b.size}, #{b.inspect}" 128: raise ArgumentError, err 129: end 130: end