Class: Bio::RestrictionEnzyme::Analysis

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/util/restriction_enzyme/analysis.rb,
lib/bio/util/restriction_enzyme/analysis_basic.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.cut(sequence, *args) ⇒ Object

See cut instance method



23
24
25
 
# File 'lib/bio/util/restriction_enzyme/analysis.rb', line 23

def self.cut( sequence, *args )
  self.new.cut( sequence, *args )
end

.cut_without_permutations(sequence, *args) ⇒ Object

See cut_without_permutations instance method



21
22
23
 
# File 'lib/bio/util/restriction_enzyme/analysis_basic.rb', line 21

def self.cut_without_permutations( sequence, *args )
  self.new.cut_without_permutations( sequence, *args )
end

Instance Method Details

#cut(sequence, *args) ⇒ Object

See main documentation for Bio::RestrictionEnzyme

cut takes into account permutations of cut variations based on competitiveness of enzymes for an enzyme cutsite or enzyme bindsite on a sequence.

Example:

FIXME add output

Bio::RestrictionEnzyme::Analysis.cut('gaattc', 'EcoRI')

_same as:_

Bio::RestrictionEnzyme::Analysis.cut('gaattc', 'g^aattc')

Arguments

  • sequence: String kind of object that will be used as a nucleic acid sequence.

  • args: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.

Returns

Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) or a Symbol containing an error code



48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
 
# File 'lib/bio/util/restriction_enzyme/analysis.rb', line 48

def cut( sequence, *args )
  view_ranges = false
  
  args.select { |i| i.class == Hash }.each do |hsh|
    hsh.each do |key, value|
      if key == :view_ranges
        unless ( value.kind_of?(TrueClass) or value.kind_of?(FalseClass) )
          raise ArgumentError, "view_ranges must be set to true or false, currently #{value.inspect}."
        end
        view_ranges = value
      end
    end
  end
  
  res = cut_and_return_by_permutations( sequence, *args )
  return res if res.class == Symbol
  # Format the fragments for the user
  fragments_for_display( res, view_ranges )
end

#cut_without_permutations(sequence, *args) ⇒ Object

See main documentation for Bio::RestrictionEnzyme

Bio::RestrictionEnzyme.cut is preferred over this!

USE AT YOUR OWN RISK

This is a simpler version of method cut. cut takes into account permutations of cut variations based on competitiveness of enzymes for an enzyme cutsite or enzyme bindsite on a sequence. This does not take into account those possibilities and is therefore faster, but less likely to be accurate.

This code is mainly included as an academic example without having to wade through the extra layer of complexity added by the permutations.

Example:

FIXME add output

Bio::RestrictionEnzyme::Analysis.cut_without_permutations('gaattc', 'EcoRI')

_same as:_

Bio::RestrictionEnzyme::Analysis.cut_without_permutations('gaattc', 'g^aattc')

Arguments

  • sequence: String kind of object that will be used as a nucleic acid sequence.

  • args: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.

Returns

Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)



55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
 
# File 'lib/bio/util/restriction_enzyme/analysis_basic.rb', line 55

def cut_without_permutations( sequence, *args )
  return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
  sequence = Bio::Sequence::NA.new( sequence )

  # create_enzyme_actions returns two seperate array elements, they're not
  # needed separated here so we put them into one array
  enzyme_actions = create_enzyme_actions( sequence, *args ).flatten
  return fragments_for_display( {} ) if enzyme_actions.empty?
  
  # Primary and complement strands are both measured from '0' to 'sequence.size-1' here
  sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 )
  
  # Add the cuts to the sequence_range from each enzyme_action
  enzyme_actions.each do |enzyme_action|
    enzyme_action.cut_ranges.each do |cut_range|
      sequence_range.add_cut_range(cut_range)
    end
  end

  # Fill in the source sequence for sequence_range so it knows what bases
  # to use
  sequence_range.fragments.primary = sequence
  sequence_range.fragments.complement = sequence.forward_complement
  
  # Format the fragments for the user
  fragments_for_display( {0 => sequence_range} )
end