Class: Bio::RestrictionEnzyme::DoubleStranded

Inherits:
Object
  • Object
show all
Extended by:
CutSymbol, StringFormatting
Includes:
CutSymbol, StringFormatting
Defined in:
lib/bio/util/restriction_enzyme/double_stranded.rb,
lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.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

Overview

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

Defined Under Namespace

Classes: AlignedStrands, CutLocationPair, CutLocationPairInEnzymeNotation, CutLocations, CutLocationsInEnzymeNotation, EnzymeAction

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from CutSymbol

cut_symbol, escaped_cut_symbol, re_cut_symbol, re_cut_symbol_adjacent, set_cut_symbol

Methods included from StringFormatting

add_spacing, left_padding, right_padding, strip_cuts_and_padding, strip_padding

Constructor Details

#initialize(erp, *raw_cut_pairs) ⇒ DoubleStranded

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



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# 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 = %r"^#{erp}$"i
        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

Instance Attribute Details

#complement ⇒ Object (readonly)

The complement strand



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# File 'lib/bio/util/restriction_enzyme/double_stranded.rb', line 42

def complement
  @complement
end

#cut_locations ⇒ Object (readonly)

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



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# File 'lib/bio/util/restriction_enzyme/double_stranded.rb', line 45

def cut_locations
  @cut_locations
end

#cut_locations_in_enzyme_notation ⇒ Object (readonly)

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



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# File 'lib/bio/util/restriction_enzyme/double_stranded.rb', line 48

def cut_locations_in_enzyme_notation
  @cut_locations_in_enzyme_notation
end

#primary ⇒ Object (readonly)

The primary strand



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# File 'lib/bio/util/restriction_enzyme/double_stranded.rb', line 39

def primary
  @primary
end

Instance Method Details

#aligned_strands ⇒ Object

See AlignedStrands.align



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# 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 ⇒ Object

See AlignedStrands.align_with_cuts



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# 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? ⇒ Boolean

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

Returns:

  • (Boolean) 


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# 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) ⇒ Object

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



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# 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? ⇒ Boolean

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

Returns:

  • (Boolean) 


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# File 'lib/bio/util/restriction_enzyme/double_stranded.rb', line 150

def sticky?
  !blunt?
end