class Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
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][-1][2][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::CutLocationsnil
represents no cut or a partial digestion.
Attributes
Last cut, in enzyme-index notation
First cut, in enzyme-index notation
Public Class Methods
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
# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 58 def initialize(*a) a.flatten! # in case an array was passed as an argument if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n' s = a[0] a = [] i = -( s.tr(cut_symbol, '') =~ %r{[^n]} ) # First character that's not 'n' s.each_byte { |c| (a << i; next) if c.chr == cut_symbol; i += 1 } a.collect! { |n| n <= 0 ? n-1 : n } # 0 is not a valid enzyme index, decrement from 0 and all negative else a.collect! { |n| n.to_i } # Cut locations are always integers end validate_cut_locations( a ) super(a) self.sort! @min = self.first @max = self.last self.freeze end
Public Instance Methods
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
# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 93 def to_array_index return [] if @min == nil if @min < 0 calc = lambda do |n| n -= 1 unless n < 0 n + @min.abs end else calc = lambda { |n| n - 1 } end self.collect(&calc) end
Protected Instance Methods
# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 110 def validate_cut_locations( input_cut_locations ) unless input_cut_locations == input_cut_locations.uniq err = "The cut locations supplied contain duplicate values. Redundant / undefined meaning.\n" err += "cuts: #{input_cut_locations.inspect}\n" err += "unique: #{input_cut_locations.uniq.inspect}" raise ArgumentError, err end if input_cut_locations.include?(nil) err = "The cut locations supplied contained a nil. nil has no index for enzyme notation, alternative meaning is 'no cut'.\n" err += "cuts: #{input_cut_locations.inspect}" raise ArgumentError, err end if input_cut_locations.include?(0) err = "The cut locations supplied contained a '0'. '0' has no index for enzyme notation, alternative meaning is 'no cut'.\n" err += "cuts: #{input_cut_locations.inspect}" raise ArgumentError, err end end