### Home Classes Methods

### In Files

- lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
- lib/bio/util/restriction_enzyme/double_stranded.rb

### Parent

Object

### Namespace

- CLASS Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- CLASS Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- CLASS Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- CLASS Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- CLASS Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- CLASS Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction

### Methods

- ::new
- #aligned_strands
- #aligned_strands_with_cuts
- #blunt?
- #create_action_at
- #create_cut_locations
- #create_primary_and_complement
- #initialize_with_pattern_and_cut_locations
- #initialize_with_pattern_and_cut_symbols
- #initialize_with_rebase
- #sticky?

### Included Modules

- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::StringFormatting

### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

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No matching classes.

# Bio::RestrictionEnzyme::DoubleStranded

A pair of SingleStrand and SingleStrandComplement objects with methods to add utility to their relation.

# Notes

- This is created by Bio::RestrictionEnzyme.new for convenience.

- The two strands accessible are `primary` and `complement`.

- SingleStrand methods may be used on DoubleStranded and they will be passed to `primary`.

FIXME needs better docs

### Attributes

complement[R]

The complement strand

cut_locations[R]

Cut locations in 0-based index format, DoubleStranded::CutLocations object

cut_locations_in_enzyme_notation[R]

Cut locations in enzyme index notation, DoubleStranded::CutLocationsInEnzymeNotation object

primary[R]

The primary strand

### Public Class Methods

new(erp, *raw_cut_pairs) click to toggle source

`erp`

  One of three possible parameters: The name of an enzyme, a REBASE::EnzymeEntry object, or a nucleotide pattern with a cut mark.

`raw_cut_pairs`

  The cut locations in enzyme index notation.

Enzyme index notation | 1..n, value before 1 is -1

Examples of the allowable cut locations for `raw_cut_pairs` follows. 'p' and 'c' refer to a cut location on the 'p'rimary and 'c'omplement strands.

    1, [3,2], [20,22], 57
    p, [p,c], [p, c],  p

Which is the same as:

    1, (3..2), (20..22), 57
    p, (p..c), (p..c),   p

Examples of partial cuts:

    1, [nil,2], [20,nil], 57
    p, [p,  c], [p, c],   p

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 70
    def initialize(erp, *raw_cut_pairs)
      # 'erp' : 'E'nzyme / 'R'ebase / 'P'attern
      k = erp.class

      if k == Bio::REBASE::EnzymeEntry
        # Passed a Bio::REBASE::EnzymeEntry object

        unless raw_cut_pairs.empty?
          err = "A Bio::REBASE::EnzymeEntry object was passed, however the cut locations contained values.  Ambiguous or redundant.\n"
          err += "inspect = #{raw_cut_pairs.inspect}"
          raise ArgumentError, err
        end
        initialize_with_rebase( erp )

      elsif erp.kind_of? String
        # Passed something that could be an enzyme pattern or an anzyme name

        # Decide if this String is an enzyme name or a pattern
        if Bio::RestrictionEnzyme.enzyme_name?( erp )
          # FIXME we added this to rebase...
          # Check if it's a known name
          known_enzyme = false
          known_enzyme = true if Bio::RestrictionEnzyme.rebase[ erp ]

          # Try harder to find the enzyme
          unless known_enzyme
            re = %^#{erp}$"
            Bio::RestrictionEnzyme.rebase.each { |name, v| (known_enzyme = true; erp = name; break) if name =~ re }
          end

          if known_enzyme
            initialize_with_rebase( Bio::RestrictionEnzyme.rebase[erp] )
          else
            raise IndexError, "No entry found for enzyme named '#{erp}'"
          end

        else
          # Not an enzyme name, so a pattern is assumed
          if erp =~ re_cut_symbol
            initialize_with_pattern_and_cut_symbols( erp )
          else
            initialize_with_pattern_and_cut_locations( erp, raw_cut_pairs )
          end
        end

      elsif k == NilClass
        err = "Passed a nil value.  Perhaps you tried to pass a Bio::REBASE::EnzymeEntry that does not exist?\n"
        err += "inspect = #{erp.inspect}"
        raise ArgumentError, err
      else
        err = "I don't know what to do with class #{k} for erp.\n"
        err += "inspect = #{erp.inspect}"
        raise ArgumentError, err
      end

    end

### Public Instance Methods

aligned_strands() click to toggle source

See AlignedStrands.align

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 128
    def aligned_strands
      AlignedStrands.align(@primary.pattern, @complement.pattern)
    end

aligned_strands_with_cuts() click to toggle source

See AlignedStrands.align_with_cuts

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 133
    def aligned_strands_with_cuts
      AlignedStrands.align_with_cuts(@primary.pattern, @complement.pattern, @primary.cut_locations, @complement.cut_locations)
    end

blunt?() click to toggle source

Returns `true` if the cut pattern creates blunt fragments. (opposite of sticky)

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 139
    def blunt?
      as = aligned_strands_with_cuts
      ary = [as.primary, as.complement]
      ary.collect! { |seq| seq.split( cut_symbol ) }
      # convert the cut sections to their lengths
      ary.each { |i| i.collect! { |c| c.length } }
      ary[0] == ary[1]
    end

create_action_at( offset ) click to toggle source

Takes a RestrictionEnzyme object and a numerical offset to the sequence and returns an EnzymeAction

`restriction_enzyme` | RestrictionEnzyme
`offset` | Numerical offset of where the enzyme action occurs on the seqeunce

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 159
    def create_action_at( offset )
      # x is the size of the fully aligned sequence with maximum padding needed
      # to make a match on the primary and complement strand.
      #
      # For example -
      # Note how EcoRII needs extra padding on the beginning and ending of the
      # sequence 'ccagg' to make the match since the cut must occur between
      # two nucleotides and can not occur on the very end of the sequence.
      #
      #   EcoRII:
      #     :blunt: "0"
      #     :c2: "5"
      #     :c4: "0"
      #     :c1: "-1"
      #     :pattern: CCWGG
      #     :len: "5"
      #     :name: EcoRII
      #     :c3: "0"
      #     :ncuts: "2"
      #
      #        -1 1 2 3 4 5
      #   5' - n^c c w g g n - 3'
      #   3' - n g g w c c^n - 5'
      #
      #   (w == [at])

      x = aligned_strands.primary.size

      enzyme_action = EnzymeAction.new( offset,
                                        offset + x-1,
                                        offset,
                                        offset + x-1)

      @cut_locations.each do |cut_location_pair|
        # cut_pair is a DoubleStranded::CutLocationPair
        p, c = cut_location_pair.primary, cut_location_pair.complement
        if c >= p
          enzyme_action.add_cut_range(offset+p, nil, nil, offset+c)
        else
          enzyme_action.add_cut_range(nil, offset+p, offset+c, nil)
        end
      end

      enzyme_action
    end

sticky?() click to toggle source

Returns `true` if the cut pattern creates sticky fragments. (opposite of blunt)

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 150
    def sticky?
      !blunt?
    end

### Protected Instance Methods

create_cut_locations(raw_cl) click to toggle source

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 301
    def create_cut_locations(raw_cl)
      @cut_locations_in_enzyme_notation = CutLocationsInEnzymeNotation.new( *raw_cl.collect {|cl| CutLocationPairInEnzymeNotation.new(cl)} )
      @cut_locations = @cut_locations_in_enzyme_notation.to_array_index
    end

create_primary_and_complement(primary_seq, p_cuts, c_cuts) click to toggle source

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 296
    def create_primary_and_complement(primary_seq, p_cuts, c_cuts)
      @primary = SingleStrand.new( primary_seq, p_cuts )
      @complement = SingleStrandComplement.new( primary_seq.forward_complement, c_cuts )
    end

initialize_with_pattern_and_cut_locations( s, raw_cl ) click to toggle source

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 291
    def initialize_with_pattern_and_cut_locations( s, raw_cl )
      create_cut_locations(raw_cl)
      create_primary_and_complement( Bio::Sequence::NA.new(s), @cut_locations_in_enzyme_notation.primary, @cut_locations_in_enzyme_notation.complement )
    end

initialize_with_pattern_and_cut_symbols( s ) click to toggle source

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 279
    def initialize_with_pattern_and_cut_symbols( s )
      p_cl = SingleStrand::CutLocationsInEnzymeNotation.new( strip_padding(s) )
      s = Bio::Sequence::NA.new( strip_cuts_and_padding(s) )

      # * Reflect cuts that are in enzyme notation
      # * 0 is not a valid enzyme index, decrement 0 and all negative
      c_cl = p_cl.collect {|n| (n >= s.length or n < 1) ? ((s.length - n) - 1) : (s.length - n)}

      create_cut_locations( p_cl.zip(c_cl) )
      create_primary_and_complement( s, p_cl, c_cl )
    end

initialize_with_rebase( e ) click to toggle source

    # File lib/bio/util/restriction_enzyme/double_stranded.rb, line 306
    def initialize_with_rebase( e )
      p_cl = [e.primary_strand_cut1, e.primary_strand_cut2]
      c_cl = [e.complementary_strand_cut1, e.complementary_strand_cut2]

      # If there's no cut in REBASE it's represented as a 0.
      # 0 is an invalid index, it just means no cut.
      p_cl.delete(0)
      c_cl.delete(0)
      raise IndexError unless p_cl.size == c_cl.size
      initialize_with_pattern_and_cut_locations( e.pattern, p_cl.zip(c_cl) )
    end

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