Class: Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Inherits:
-
Object
- Object
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- 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
-
.align(a, b) ⇒ Object
Pad and align two String objects without cut symbols.
-
.align_with_cuts(a, b, a_cuts, b_cuts) ⇒ Object
Pad and align two String objects with cut symbols.
Instance Method Summary collapse
-
#initialize ⇒ AlignedStrands
constructor
Creates a new object.
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 19 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 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 |
.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 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 |