Class Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
In: lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
Parent: Array

Stores the cut location in thier enzyme index notation

May be initialized with a series of cuts or an enzyme pattern marked with cut symbols.

Enzyme index notation:1..n, value before 1 is -1
example:[-3][-2][-1][1][2][3][4][5]

Negative values are used to indicate when a cut may occur at a specified distance before the sequence begins. This would be padded with ‘n’ nucleotides to represent wildcards.

Notes:

  • 0 is invalid as it does not refer to any index
  • nil is not allowed here as it has no meaning
  • nil values are kept track of in DoubleStranded::CutLocations as they need a reference point on the correlating strand. In DoubleStranded::CutLocations nil represents no cut or a partial digestion.

Methods

new   to_array_index   validate_cut_locations  

Included Modules

CutSymbol

Attributes

max  [R]  Last cut, in enzyme-index notation
min  [R]  First cut, in enzyme-index notation

Public Class methods

new(*a)

Constructor for CutLocationsInEnzymeNotation

Arguments

  • a: Locations of cuts represented as a string with cuts or an array of values

Examples:

  • n^ng^arraxt^n
  • 2
  • -1, 5
  • [-1, 5]
Returns:nothing

[Source]

    # File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 59
59:   def initialize(*a)
60:     a.flatten! # in case an array was passed as an argument
61: 
62:     if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol
63:       # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n'
64:       s = a[0]
65:       a = []
66:       i = -( s.tr(cut_symbol, '') =~ %r{[^n]} )  # First character that's not 'n'
67:       s.each_byte { |c| (a << i; next) if c.chr == cut_symbol; i += 1 }
68:       a.collect! { |n| n <= 0 ? n-1 : n } # 0 is not a valid enzyme index, decrement from 0 and all negative
69:     else
70:       a.collect! { |n| n.to_i } # Cut locations are always integers
71:     end
72: 
73:     validate_cut_locations( a )
74:     super(a)
75:     self.sort!
76:     @min = self.first
77:     @max = self.last
78:     self.freeze
79:   end

Public Instance methods

to_array_index()

Transform the cut locations from enzyme index notation to 0-based index notation. 

  input -> output
  [  1, 2, 3 ] -> [ 0, 1, 2 ]
  [  1, 3, 5 ] -> [ 0, 2, 4 ]
  [ -1, 1, 2 ] -> [ 0, 1, 2 ]
  [ -2, 1, 3 ] -> [ 0, 2, 4 ]

Arguments

  • none
Returns:Array of cuts in 0-based index notation

[Source]

     # File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 94
 94:   def to_array_index
 95:     return [] if @min == nil
 96:     if @min < 0
 97:       calc = lambda do |n| 
 98:         n -= 1 unless n < 0
 99:         n + @min.abs
100:       end
101:     else
102:       calc = lambda { |n| n - 1 }
103:     end
104:     self.collect(&calc)
105:   end

Protected Instance methods

validate_cut_locations( input_cut_locations )

[Source]

     # File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 111
111:   def validate_cut_locations( input_cut_locations )
112:     unless input_cut_locations == input_cut_locations.uniq
113:       err = "The cut locations supplied contain duplicate values.  Redundant / undefined meaning.\n"
114:       err += "cuts: #{input_cut_locations.inspect}\n"
115:       err += "unique: #{input_cut_locations.uniq.inspect}"
116:       raise ArgumentError, err
117:     end
118: 
119:     if input_cut_locations.include?(nil)
120:       err = "The cut locations supplied contained a nil.  nil has no index for enzyme notation, alternative meaning is 'no cut'.\n"
121:       err += "cuts: #{input_cut_locations.inspect}"
122:       raise ArgumentError, err
123:     end
124: 
125:     if input_cut_locations.include?(0)
126:       err = "The cut locations supplied contained a '0'.  '0' has no index for enzyme notation, alternative meaning is 'no cut'.\n"
127:       err += "cuts: #{input_cut_locations.inspect}"
128:       raise ArgumentError, err
129:     end
130: 
131:   end

[Validate]