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 58 58: def initialize(*a) 59: a.flatten! # in case an array was passed as an argument 60: 61: if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol 62: # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n' 63: s = a[0] 64: a = [] 65: i = -( s.tr(cut_symbol, '') =~ %r{[^n]} ) # First character that's not 'n' 66: s.each_byte { |c| (a << i; next) if c.chr == cut_symbol; i += 1 } 67: a.collect! { |n| n <= 0 ? n-1 : n } # 0 is not a valid enzyme index, decrement from 0 and all negative 68: else 69: a.collect! { |n| n.to_i } # Cut locations are always integers 70: end 71: 72: validate_cut_locations( a ) 73: super(a) 74: self.sort! 75: @min = self.first 76: @max = self.last 77: self.freeze 78: 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 93 93: def to_array_index 94: return [] if @min == nil 95: if @min < 0 96: calc = lambda do |n| 97: n -= 1 unless n < 0 98: n + @min.abs 99: end 100: else 101: calc = lambda { |n| n - 1 } 102: end 103: self.collect(&calc) 104: end
# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 110 110: def validate_cut_locations( input_cut_locations ) 111: unless input_cut_locations == input_cut_locations.uniq 112: err = "The cut locations supplied contain duplicate values. Redundant / undefined meaning.\n" 113: err += "cuts: #{input_cut_locations.inspect}\n" 114: err += "unique: #{input_cut_locations.uniq.inspect}" 115: raise ArgumentError, err 116: end 117: 118: if input_cut_locations.include?(nil) 119: err = "The cut locations supplied contained a nil. nil has no index for enzyme notation, alternative meaning is 'no cut'.\n" 120: err += "cuts: #{input_cut_locations.inspect}" 121: raise ArgumentError, err 122: end 123: 124: if input_cut_locations.include?(0) 125: err = "The cut locations supplied contained a '0'. '0' has no index for enzyme notation, alternative meaning is 'no cut'.\n" 126: err += "cuts: #{input_cut_locations.inspect}" 127: raise ArgumentError, err 128: end 129: 130: end