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:
max | [R] | Last cut, in enzyme-index notation |
min | [R] | First cut, in enzyme-index notation |
Constructor for CutLocationsInEnzymeNotation
Arguments
Examples:
Returns: | nothing |
# 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
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
Returns: | Array of cuts in 0-based index notation |
# 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
# 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