See cut instance method
# File lib/bio/util/restriction_enzyme/analysis.rb, line 23 def self.cut( sequence, *args ) self.new.cut( sequence, *args ) end
See cut_without_permutations instance method
# 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
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 |
# 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
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) |
# 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
Creates an array of EnzymeActions based on the DNA sequence and supplied enzymes.
Arguments
sequence: The string of DNA to match the enzyme recognition sites against
args |
The enzymes to use. |
Returns |
Array with the first element being an array of EnzymeAction objects that sometimes_cut, and are subject to competition. The second is an array of EnzymeAction objects that always_cut and are not subject to competition. |
# File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 120 def create_enzyme_actions( sequence, *args ) all_enzyme_actions = [] args.each do |enzyme| enzyme = Bio::RestrictionEnzyme.new(enzyme) unless enzyme.class == Bio::RestrictionEnzyme::DoubleStranded # make sure pattern is the proper size # for more info see the internal documentation of # Bio::RestrictionEnzyme::DoubleStranded.create_action_at pattern = Bio::Sequence::NA.new( Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands.align( enzyme.primary, enzyme.complement ).primary ).to_re find_match_locations( sequence, pattern ).each do |offset| all_enzyme_actions << enzyme.create_action_at( offset ) end end # FIXME VerticalCutRange should really be called VerticalAndHorizontalCutRange # * all_enzyme_actions is now full of EnzymeActions at specific locations across # the sequence. # * all_enzyme_actions will now be examined to see if any EnzymeActions may # conflict with one another, and if they do they'll be made note of in # indicies_of_sometimes_cut. They will then be remove FIXME # * a conflict occurs if another enzyme's bind site is compromised do due # to another enzyme's cut. Enzyme's bind sites may overlap and not be # competitive, however neither bind site may be part of the other # enzyme's cut or else they do become competitive. # # Take current EnzymeAction's entire bind site and compare it to all other # EzymeAction's cut ranges. Only look for vertical cuts as boundaries # since trailing horizontal cuts would have no influence on the bind site. # # If example Enzyme A makes this cut pattern (cut range 2..5): # # 0 1 2|3 4 5 6 7 # +-----+ # 0 1 2 3 4 5|6 7 # # Then the bind site (and EnzymeAction range) for Enzyme B would need it's # right side to be at index 2 or less, or it's left side to be 6 or greater. competition_indexes = Set.new all_enzyme_actions[0..-2].each_with_index do |current_enzyme_action, i| next if competition_indexes.include? i next if current_enzyme_action.cut_ranges.empty? # no cuts, some enzymes are like this (ex. CjuI) all_enzyme_actions[i+1..-1].each_with_index do |comparison_enzyme_action, j| j += (i + 1) next if competition_indexes.include? j next if comparison_enzyme_action.cut_ranges.empty? # no cuts if (current_enzyme_action.right <= comparison_enzyme_action.cut_ranges.min_vertical) or (current_enzyme_action.left > comparison_enzyme_action.cut_ranges.max_vertical) # no conflict else competition_indexes += [i, j] # merge both indexes into the flat set end end end sometimes_cut = all_enzyme_actions.values_at( *competition_indexes ) always_cut = all_enzyme_actions always_cut.delete_if {|x| sometimes_cut.include? x } [sometimes_cut, always_cut] end
See cut instance method
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.
May also supply a Hash with the key “:max_permutations” to specificy how many permutations are allowed - a value of 0 indicates no permutations are allowed.
Returns |
Hash Keys are a permutation ID, values are SequenceRange objects that have cuts applied. |
also may return the Symbol ':sequence_empty', ':no_cuts_found', or ':too_many_permutations'
# File lib/bio/util/restriction_enzyme/analysis.rb, line 81 def cut_and_return_by_permutations( sequence, *args ) my_hash = {} maximum_permutations = nil hashes_in_args = args.select { |i| i.class == Hash } args.delete_if { |i| i.class == Hash } hashes_in_args.each do |hsh| hsh.each do |key, value| case key when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations' maximum_permutations = value.to_i unless value == nil when :view_ranges else raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' and ':view_ranges' currently. Hash passed: #{hsh.inspect}" end end end if !sequence.kind_of?(String) or sequence.empty? logger.warn "The supplied sequence is empty." if defined?(logger) return :sequence_empty end sequence = Bio::Sequence::NA.new( sequence ) enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args ) if enzyme_actions.empty? and initial_cuts.empty? logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger) return :no_cuts_found end # * When enzyme_actions.size is equal to '1' that means there are no permutations. # * If enzyme_actions.size is equal to '2' there is one # permutation ("[0, 1]") # * If enzyme_actions.size is equal to '3' there are two # permutations ("[0, 1, 2]") # * and so on.. if maximum_permutations and enzyme_actions.size > 1 if (enzyme_actions.size - 1) > maximum_permutations.to_i logger.warn "More permutations than maximum, skipping. Found: #{enzyme_actions.size-1} Max: #{maximum_permutations.to_i}" if defined?(logger) return :too_many_permutations end end if enzyme_actions.size > 1 permutations = permute(enzyme_actions.size) permutations.each do |permutation| previous_cut_ranges = [] # 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 contained # in initial_cuts. These are the cuts that have no competition so are # not subject to permutations. initial_cuts.each do |enzyme_action| enzyme_action.cut_ranges.each do |cut_range| sequence_range.add_cut_range(cut_range) end end permutation.each do |id| enzyme_action = enzyme_actions[id] # conflict is false if the current enzyme action may cut in it's range. # conflict is true if it cannot due to a previous enzyme action making # a cut where this enzyme action needs a whole recognition site. conflict = false # If current size of enzyme_action overlaps with previous cut_range, don't cut # note that the enzyme action may fall in the middle of a previous enzyme action # so all cut locations must be checked that would fall underneath. previous_cut_ranges.each do |cut_range| next unless cut_range.class == Bio::RestrictionEnzyme::Range::VerticalCutRange # we aren't concerned with horizontal cuts previous_cut_left = cut_range.range.first previous_cut_right = cut_range.range.last # Keep in mind: # * The cut location is to the immediate right of the base located at the index. # ex: at^gc -- the cut location is at index 1 # * The enzyme action location is located at the base of the index. # ex: atgc -- 0 => 'a', 1 => 't', 2 => 'g', 3 => 'c' # method create_enzyme_actions has similar commentary if interested if (enzyme_action.right <= previous_cut_left) or (enzyme_action.left > previous_cut_right) or (enzyme_action.left > previous_cut_left and enzyme_action.right <= previous_cut_right) # in between cuts # no conflict else conflict = true end end next if conflict == true enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) } previous_cut_ranges += enzyme_action.cut_ranges end # permutation.each # 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 my_hash[permutation] = sequence_range end # permutations.each else # if enzyme_actions.size == 1 # no permutations, just do it sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 ) initial_cuts.each { |enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) } } sequence_range.fragments.primary = sequence sequence_range.fragments.complement = sequence.forward_complement my_hash[0] = sequence_range end my_hash end
Returns an Array of the match indicies of a RegExp to a string.
Example:
find_match_locations('abccdefeg', /[ce]/) # => [2,3,5,7]
Arguments
string: The string to scan
re: A RegExp to use
Returns |
Array with indicies of match locations |
# File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 203 def find_match_locations( string, re ) md = string.match( re ) locations = [] counter = 0 while md # save the match index relative to the original string locations << (counter += md.begin(0)) # find the next match md = string[ (counter += 1)..-1 ].match( re ) end locations end
Take the fragments from SequenceRange objects generated from add_cut_range and return unique results as a Bio::RestrictionEnzyme::Analysis::Fragment object.
Arguments
hsh: Hash Keys are a permutation ID, if any. Values are SequenceRange objects that have cuts applied.
Returns |
Bio::RestrictionEnzyme::Analysis::Fragments object populated with Bio::RestrictionEnzyme::Analysis::Fragment objects. |
# File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 94 def fragments_for_display( hsh, view_ranges=false ) ary = Fragments.new return ary unless hsh hsh.each do |permutation_id, sequence_range| sequence_range.fragments.for_display.each do |fragment| if view_ranges ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement, fragment.p_left, fragment.p_right, fragment.c_left, fragment.c_right) else ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement) end end end ary.uniq! unless view_ranges ary end
Returns permutation orders for a given number of elements.
Examples:
permute(0) # => [[0]] permute(1) # => [[0]] permute(2) # => [[1, 0], [0, 1]] permute(3) # => [[2, 1, 0], [2, 0, 1], [1, 2, 0], [0, 2, 1], [1, 0, 2], [0, 1, 2]] permute(4) # => [[3, 2, 1, 0], [3, 2, 0, 1], [3, 1, 2, 0], [3, 0, 2, 1], [3, 1, 0, 2], [3, 0, 1, 2], [2, 3, 1, 0], [2, 3, 0, 1], [1, 3, 2, 0], [0, 3, 2, 1], [1, 3, 0, 2], [0, 3, 1, 2], [2, 1, 3, 0], [2, 0, 3, 1], [1, 2, 3, 0], [0, 2, 3, 1], [1, 0, 3, 2], [0, 1, 3, 2], [2, 1, 0, 3], [2, 0, 1, 3], [1, 2, 0, 3], [0, 2, 1, 3], [1, 0, 2, 3], [0, 1, 2, 3]]
Arguments
count: Number of different elements to be permuted
permutations: ignore - for the recursive algorithm
Returns |
Array of Array objects with different possible permutation orders. See examples. |
# File lib/bio/util/restriction_enzyme/analysis.rb, line 235 def permute(count, permutations = [[0]]) return permutations if count <= 1 new_arrays = [] new_array = [] (permutations[0].size + 1).times do |n| new_array.clear permutations.each { |a| new_array << a.dup } new_array.each { |e| e.insert(n, permutations[0].size) } new_arrays += new_array end permute(count-1, new_arrays) end
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