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.
The cut locations transformed from enzyme index notation to 0-based array index notation. Contains an Array.
The cut locations in enzyme notation. Contains a CutLocationsInEnzymeNotation object set when the SingleStrand object is initialized.
Sequence pattern with no cut symbols and no 'n' padding.
SingleStrand.new('garraxt', [-2, 1, 7]).stripped # => "garraxt"
Constructor for a Bio::RestrictionEnzyme::StingleStrand object.
A single strand of restriction enzyme sequence pattern with a 5' to 3' orientation.
Arguments
sequence: (required) The enzyme sequence.
c: (optional) Cut locations in enzyme notation. See Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
Constraints
sequence cannot contain immediately adjacent cut symbols (ex. atg^^c).
c is in enzyme index notation and therefore cannot contain a 0.
If c is omitted, sequence must contain a cut symbol.
You cannot provide both a sequence with cut symbols and provide cut locations - ambiguous.
sequence must be a kind of:
c must be a kind of:
Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
Integer, one or more
Array
Returns |
nothing |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 69 def initialize( sequence, *c ) c.flatten! # if an array was supplied as an argument # NOTE t| 2009-09-19 commented out for library efficiency # validate_args(sequence, c) sequence = sequence.downcase if sequence =~ re_cut_symbol @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( strip_padding(sequence) ) else @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( c ) end @stripped = Bio::Sequence::NA.new( strip_cuts_and_padding( sequence ) ) super( pattern ) @cut_locations = @cut_locations_in_enzyme_notation.to_array_index return end
Orientation of the strand, 5' to 3'
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 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:
This would be palindromic:
5' - ATGCAT - 3' TACGTA
This would not be palindromic:
5' - ATGCGTA - 3' TACGCAT
Arguments
none
Returns |
true or false |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 103 def palindromic? @stripped.reverse_complement == @stripped end
The sequence with 'n' padding on the left and right for cuts larger than the sequence.
SingleStrand.new('garraxt', [-2, 1, 7]).pattern # => "nngarraxtn"
Arguments
none
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 131 def pattern return stripped if @cut_locations_in_enzyme_notation.min == nil left = (@cut_locations_in_enzyme_notation.min < 0 ? 'n' * @cut_locations_in_enzyme_notation.min.abs : '') # Add one more 'n' if a cut is at the last position right = ( (@cut_locations_in_enzyme_notation.max >= @stripped.length) ? ('n' * (@cut_locations_in_enzyme_notation.max - @stripped.length + 1)) : '') [left, stripped, right].join('') end
The sequence with 'n' padding and cut symbols.
SingleStrand.new('garraxt', [-2, 1, 7]).with_cut_symbols # => "n^ng^arraxt^n"
Arguments
none
Returns |
The sequence with 'n' padding and cut symbols. |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 118 def with_cut_symbols s = pattern @cut_locations_in_enzyme_notation.to_array_index.sort.reverse.each { |c| s.insert(c+1, cut_symbol) } s end
The sequence with 'n' pads, cut symbols, and spacing for alignment.
SingleStrand.new('garraxt', [-2, 1, 7]).with_spaces # => "n^n g^a r r a x t^n"
Arguments
none
Returns |
The sequence with 'n' pads, cut symbols, and spacing for alignment. |
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 147 def with_spaces add_spacing( with_cut_symbols ) end
# File lib/bio/util/restriction_enzyme/single_strand.rb, line 155 def validate_args( input_pattern, input_cut_locations ) unless input_pattern.kind_of?(String) err = "input_pattern is not a String, Bio::Sequence::NA, or Bio::RestrictionEnzyme::SingleStrand object\n" err += "pattern: #{input_pattern}\n" err += "class: #{input_pattern.class}" raise ArgumentError, err end if ( input_pattern =~ re_cut_symbol ) and !input_cut_locations.empty? err = "Cut symbol found in sequence, but cut locations were also supplied. Ambiguous.\n" err += "pattern: #{input_pattern}\n" err += "symbol: #{cut_symbol}\n" err += "locations: #{input_cut_locations.inspect}" raise ArgumentError, err end input_pattern.each_byte do |c| c = c.chr.downcase unless Bio::NucleicAcid::NAMES.has_key?(c) or c == 'x' or c == 'X' or c == cut_symbol err = "Invalid character in pattern.\n" err += "Not a nucleotide or representation of possible nucleotides. See Bio::NucleicAcid::NAMES for more information.\n" err += "char: #{c}\n" err += "input_pattern: #{input_pattern}" raise ArgumentError, err end end end
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