Class | Bio::RestrictionEnzyme::SingleStrand |
In: |
lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
lib/bio/util/restriction_enzyme/single_strand.rb |
Parent: | Object |
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.
cut_locations | [R] | The cut locations transformed from enzyme index notation to 0-based array index notation. Contains an Array. |
cut_locations_in_enzyme_notation | [R] | The cut locations in enzyme notation. Contains a CutLocationsInEnzymeNotation object set when the SingleStrand object is initialized. |
stripped | [R] |
Sequence pattern with no cut symbols and no
‘n’ padding.
|
Constructor for a Bio::RestrictionEnzyme::StingleStrand object.
A single strand of restriction enzyme sequence pattern with a 5’ to 3’ orientation.
Arguments
Constraints
sequence must be a kind of:
c must be a kind of:
Returns: | nothing |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 69 69: def initialize( sequence, *c ) 70: c.flatten! # if an array was supplied as an argument 71: validate_args(sequence, c) 72: sequence.downcase! 73: 74: if sequence =~ re_cut_symbol 75: @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( strip_padding(sequence) ) 76: else 77: @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( c ) 78: end 79: 80: @stripped = Bio::Sequence::NA.new( strip_cuts_and_padding( sequence ) ) 81: super( pattern ) 82: @cut_locations = @cut_locations_in_enzyme_notation.to_array_index 83: return 84: end
Orientation of the strand, 5’ to 3‘
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 40 40: def orientation; [5,3]; end
Returns true if this enzyme is palindromic with its reverse complement. Does not report if the cut_locations are palindromic or not.
Examples:
5' - ATGCAT - 3' TACGTA
5' - ATGCGTA - 3' TACGCAT
Arguments
Returns: | true or false |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 102 102: def palindromic? 103: @stripped.reverse_complement == @stripped 104: end
The sequence with ‘n’ padding on the left and right for cuts larger than the sequence.
Arguments
Returns: | The sequence with ‘n’ padding on the left and right for cuts larger than the sequence. |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 130 130: def pattern 131: return stripped if @cut_locations_in_enzyme_notation.min == nil 132: left = (@cut_locations_in_enzyme_notation.min < 0 ? 'n' * @cut_locations_in_enzyme_notation.min.abs : '') 133: 134: # Add one more 'n' if a cut is at the last position 135: right = ( (@cut_locations_in_enzyme_notation.max >= @stripped.length) ? ('n' * (@cut_locations_in_enzyme_notation.max - @stripped.length + 1)) : '') 136: [left, stripped, right].join('') 137: end
The sequence with ‘n’ padding and cut symbols.
Arguments
Returns: | The sequence with ‘n’ padding and cut symbols. |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 117 117: def with_cut_symbols 118: s = pattern 119: @cut_locations_in_enzyme_notation.to_array_index.sort.reverse.each { |c| s.insert(c+1, cut_symbol) } 120: s 121: end
The sequence with ‘n’ pads, cut symbols, and spacing for alignment.
Arguments
Returns: | The sequence with ‘n’ pads, cut symbols, and spacing for alignment. |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 146 146: def with_spaces 147: add_spacing( with_cut_symbols ) 148: end
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 154 154: def validate_args( input_pattern, input_cut_locations ) 155: unless input_pattern.kind_of?(String) 156: err = "input_pattern is not a String, Bio::Sequence::NA, or Bio::RestrictionEnzyme::SingleStrand object\n" 157: err += "pattern: #{input_pattern}\n" 158: err += "class: #{input_pattern.class}" 159: raise ArgumentError, err 160: end 161: 162: if ( input_pattern =~ re_cut_symbol ) and !input_cut_locations.empty? 163: err = "Cut symbol found in sequence, but cut locations were also supplied. Ambiguous.\n" 164: err += "pattern: #{input_pattern}\n" 165: err += "symbol: #{cut_symbol}\n" 166: err += "locations: #{input_cut_locations.inspect}" 167: raise ArgumentError, err 168: end 169: 170: input_pattern.each_byte do |c| 171: c = c.chr.downcase 172: unless Bio::NucleicAcid::NAMES.has_key?(c) or c == 'x' or c == 'X' or c == cut_symbol 173: err = "Invalid character in pattern.\n" 174: err += "Not a nucleotide or representation of possible nucleotides. See Bio::NucleicAcid::NAMES for more information.\n" 175: err += "char: #{c}\n" 176: err += "input_pattern: #{input_pattern}" 177: raise ArgumentError, err 178: end 179: end 180: end