Class: Bio::RestrictionEnzyme::SingleStrand

Inherits:
Sequence::NA show all
Includes:
CutSymbol, StringFormatting
Defined in:
lib/bio/util/restriction_enzyme/single_strand.rb,
lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb

Overview

A single strand of restriction enzyme sequence pattern with a 5’ to 3’ orientation.

DoubleStranded puts the SingleStrand and SingleStrandComplement together to create the sequence pattern with cuts on both strands.

Direct Known Subclasses

SingleStrandComplement

Defined Under Namespace

Classes: CutLocationsInEnzymeNotation

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from StringFormatting

#add_spacing, #left_padding, #right_padding, #strip_cuts_and_padding, #strip_padding

Methods included from CutSymbol

#cut_symbol, #escaped_cut_symbol, #re_cut_symbol, #re_cut_symbol_adjacent, #set_cut_symbol

Methods inherited from Sequence::NA

#at_content, #at_skew, #codon_usage, #cut_with_enzyme, #dna, #dna!, #forward_complement, #forward_complement!, #gc_content, #gc_percent, #gc_skew, #illegal_bases, #molecular_weight, #names, #pikachu, randomize, #reverse_complement, #reverse_complement!, #rna, #rna!, #splicing, #to_midi, #to_re, #translate

Methods included from Sequence::Common

#+, #<<, #composition, #concat, #normalize!, #randomize, #seq, #splice, #subseq, #to_fasta, #to_s, #total, #window_search

Methods inherited from String

#fill, #fold, #skip, #step, #to_aaseq, #to_naseq

Constructor Details

#initialize(sequence, *c) ⇒ SingleStrand

Constructor for a Bio::RestrictionEnzyme::StingleStrand object.

A single strand of restriction enzyme sequence pattern with a 5’ to 3’ orientation.

Arguments

  • sequence: (required) The enzyme sequence.

  • c: (optional) Cut locations in enzyme notation.

    See Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation

Constraints

  • sequence cannot contain immediately adjacent cut symbols (ex. atg^^c).

  • c is in enzyme index notation and therefore cannot contain a 0.

  • If c is omitted, sequence must contain a cut symbol.

  • You cannot provide both a sequence with cut symbols and provide cut locations - ambiguous.

sequence must be a kind of:

  • String

  • Bio::Sequence::NA

  • Bio::RestrictionEnzyme::SingleStrand

c must be a kind of:

  • Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation

  • Integer, one or more

  • Array

Returns

nothing



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 69

def initialize( sequence, *c )
  c.flatten! # if an array was supplied as an argument
# NOTE t| 2009-09-19 commented out for library efficiency
  # validate_args(sequence, c)
  sequence = sequence.downcase
  
  if sequence =~ re_cut_symbol
    @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( strip_padding(sequence) )
  else
    @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( c )
  end

  @stripped = Bio::Sequence::NA.new( strip_cuts_and_padding( sequence ) )
  super( pattern )
  @cut_locations = @cut_locations_in_enzyme_notation.to_array_index
  return
end

Instance Attribute Details

#cut_locations ⇒ Object (readonly)

The cut locations transformed from enzyme index notation to 0-based array index notation. Contains an Array.



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 37

def cut_locations
  @cut_locations
end

#cut_locations_in_enzyme_notation ⇒ Object (readonly)

The cut locations in enzyme notation. Contains a CutLocationsInEnzymeNotation object set when the SingleStrand object is initialized.



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 33

def cut_locations_in_enzyme_notation
  @cut_locations_in_enzyme_notation
end

#stripped ⇒ Object (readonly)

Sequence pattern with no cut symbols and no ‘n’ padding.

  • SingleStrand.new('garraxt', [-2, 1, 7]).stripped # => "garraxt"



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 109

def stripped
  @stripped
end

Instance Method Details

#orientation ⇒ Object

Orientation of the strand, 5’ to 3’



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 40

def orientation; [5,3]; end

#palindromic? ⇒ Boolean

Returns true if this enzyme is palindromic with its reverse complement. Does not report if the cut_locations are palindromic or not.

Examples:

  • This would be palindromic: 

    5' - ATGCAT - 3'
     TACGTA

  • This would not be palindromic: 

    5' - ATGCGTA - 3'
     TACGCAT

Arguments

  • none

Returns

true or false

Returns:

  • (Boolean) 


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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 103

def palindromic?
  @stripped.reverse_complement == @stripped
end

#pattern ⇒ Object

The sequence with ‘n’ padding on the left and right for cuts larger than the sequence.

  • SingleStrand.new('garraxt', [-2, 1, 7]).pattern # => "nngarraxtn"

Arguments

  • none

Returns

The sequence with ‘n’ padding on the left and right for cuts larger than the sequence.



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 131

def pattern
  return stripped if @cut_locations_in_enzyme_notation.min == nil
  left = (@cut_locations_in_enzyme_notation.min < 0 ? 'n' * @cut_locations_in_enzyme_notation.min.abs : '')

  # Add one more 'n' if a cut is at the last position 
  right = ( (@cut_locations_in_enzyme_notation.max >= @stripped.length) ? ('n' * (@cut_locations_in_enzyme_notation.max - @stripped.length + 1)) : '')
  [left, stripped, right].join('')
end

#with_cut_symbols ⇒ Object

The sequence with ‘n’ padding and cut symbols.

  • SingleStrand.new('garraxt', [-2, 1, 7]).with_cut_symbols # => "n^ng^arraxt^n"

Arguments

  • none

Returns

The sequence with ‘n’ padding and cut symbols.



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 118

def with_cut_symbols
  s = pattern
  @cut_locations_in_enzyme_notation.to_array_index.sort.reverse.each { |c| s.insert(c+1, cut_symbol) }
  s
end

#with_spaces ⇒ Object

The sequence with ‘n’ pads, cut symbols, and spacing for alignment.

  • SingleStrand.new('garraxt', [-2, 1, 7]).with_spaces # => "n^n g^a r r a x t^n"

Arguments

  • none

Returns

The sequence with ‘n’ pads, cut symbols, and spacing for alignment.



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# File 'lib/bio/util/restriction_enzyme/single_strand.rb', line 147

def with_spaces
  add_spacing( with_cut_symbols )
end