Class | Bio::RestrictionEnzyme::Analysis |
In: |
lib/bio/util/restriction_enzyme/analysis.rb
lib/bio/util/restriction_enzyme/analysis_basic.rb |
Parent: | Object |
See cut_without_permutations instance method
# File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 21 21: def self.cut_without_permutations( sequence, *args ) 22: self.new.cut_without_permutations( sequence, *args ) 23: 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
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 48: def cut( sequence, *args ) 49: view_ranges = false 50: 51: args.select { |i| i.class == Hash }.each do |hsh| 52: hsh.each do |key, value| 53: if key == :view_ranges 54: unless ( value.kind_of?(TrueClass) or value.kind_of?(FalseClass) ) 55: raise ArgumentError, "view_ranges must be set to true or false, currently #{value.inspect}." 56: end 57: view_ranges = value 58: end 59: end 60: end 61: 62: res = cut_and_return_by_permutations( sequence, *args ) 63: return res if res.class == Symbol 64: # Format the fragments for the user 65: fragments_for_display( res, view_ranges ) 66: 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
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 55: def cut_without_permutations( sequence, *args ) 56: return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty? 57: sequence = Bio::Sequence::NA.new( sequence ) 58: 59: # create_enzyme_actions returns two seperate array elements, they're not 60: # needed separated here so we put them into one array 61: enzyme_actions = create_enzyme_actions( sequence, *args ).flatten 62: return fragments_for_display( {} ) if enzyme_actions.empty? 63: 64: # Primary and complement strands are both measured from '0' to 'sequence.size-1' here 65: sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 ) 66: 67: # Add the cuts to the sequence_range from each enzyme_action 68: enzyme_actions.each do |enzyme_action| 69: enzyme_action.cut_ranges.each do |cut_range| 70: sequence_range.add_cut_range(cut_range) 71: end 72: end 73: 74: # Fill in the source sequence for sequence_range so it knows what bases 75: # to use 76: sequence_range.fragments.primary = sequence 77: sequence_range.fragments.complement = sequence.forward_complement 78: 79: # Format the fragments for the user 80: fragments_for_display( {0 => sequence_range} ) 81: end
Creates an array of EnzymeActions based on the DNA sequence and supplied enzymes.
Arguments
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 120 120: def create_enzyme_actions( sequence, *args ) 121: all_enzyme_actions = [] 122: 123: args.each do |enzyme| 124: enzyme = Bio::RestrictionEnzyme.new(enzyme) unless enzyme.class == Bio::RestrictionEnzyme::DoubleStranded 125: 126: # make sure pattern is the proper size 127: # for more info see the internal documentation of 128: # Bio::RestrictionEnzyme::DoubleStranded.create_action_at 129: pattern = Bio::Sequence::NA.new( 130: Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands.align( 131: enzyme.primary, enzyme.complement 132: ).primary 133: ).to_re 134: 135: find_match_locations( sequence, pattern ).each do |offset| 136: all_enzyme_actions << enzyme.create_action_at( offset ) 137: end 138: end 139: 140: # FIXME VerticalCutRange should really be called VerticalAndHorizontalCutRange 141: 142: # * all_enzyme_actions is now full of EnzymeActions at specific locations across 143: # the sequence. 144: # * all_enzyme_actions will now be examined to see if any EnzymeActions may 145: # conflict with one another, and if they do they'll be made note of in 146: # indicies_of_sometimes_cut. They will then be remove FIXME 147: # * a conflict occurs if another enzyme's bind site is compromised do due 148: # to another enzyme's cut. Enzyme's bind sites may overlap and not be 149: # competitive, however neither bind site may be part of the other 150: # enzyme's cut or else they do become competitive. 151: # 152: # Take current EnzymeAction's entire bind site and compare it to all other 153: # EzymeAction's cut ranges. Only look for vertical cuts as boundaries 154: # since trailing horizontal cuts would have no influence on the bind site. 155: # 156: # If example Enzyme A makes this cut pattern (cut range 2..5): 157: # 158: # 0 1 2|3 4 5 6 7 159: # +-----+ 160: # 0 1 2 3 4 5|6 7 161: # 162: # Then the bind site (and EnzymeAction range) for Enzyme B would need it's 163: # right side to be at index 2 or less, or it's left side to be 6 or greater. 164: 165: competition_indexes = Set.new 166: 167: all_enzyme_actions[0..-2].each_with_index do |current_enzyme_action, i| 168: next if competition_indexes.include? i 169: next if current_enzyme_action.cut_ranges.empty? # no cuts, some enzymes are like this (ex. CjuI) 170: 171: all_enzyme_actions[i+1..-1].each_with_index do |comparison_enzyme_action, j| 172: j += (i + 1) 173: next if competition_indexes.include? j 174: next if comparison_enzyme_action.cut_ranges.empty? # no cuts 175: 176: if (current_enzyme_action.right <= comparison_enzyme_action.cut_ranges.min_vertical) or 177: (current_enzyme_action.left > comparison_enzyme_action.cut_ranges.max_vertical) 178: # no conflict 179: else 180: competition_indexes += [i, j] # merge both indexes into the flat set 181: end 182: end 183: end 184: 185: sometimes_cut = all_enzyme_actions.values_at( *competition_indexes ) 186: always_cut = all_enzyme_actions 187: always_cut.delete_if {|x| sometimes_cut.include? x } 188: 189: [sometimes_cut, always_cut] 190: end
See cut instance method
Arguments
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 81: def cut_and_return_by_permutations( sequence, *args ) 82: my_hash = {} 83: maximum_permutations = nil 84: 85: hashes_in_args = args.select { |i| i.class == Hash } 86: args.delete_if { |i| i.class == Hash } 87: hashes_in_args.each do |hsh| 88: hsh.each do |key, value| 89: case key 90: when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations' 91: maximum_permutations = value.to_i unless value == nil 92: when :view_ranges 93: else 94: raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' and ':view_ranges' currently. Hash passed: #{hsh.inspect}" 95: end 96: end 97: end 98: 99: if !sequence.kind_of?(String) or sequence.empty? 100: logger.warn "The supplied sequence is empty." if defined?(logger) 101: return :sequence_empty 102: end 103: sequence = Bio::Sequence::NA.new( sequence ) 104: 105: enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args ) 106: 107: if enzyme_actions.empty? and initial_cuts.empty? 108: logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger) 109: return :no_cuts_found 110: end 111: 112: # * When enzyme_actions.size is equal to '1' that means there are no permutations. 113: # * If enzyme_actions.size is equal to '2' there is one 114: # permutation ("[0, 1]") 115: # * If enzyme_actions.size is equal to '3' there are two 116: # permutations ("[0, 1, 2]") 117: # * and so on.. 118: if maximum_permutations and enzyme_actions.size > 1 119: if (enzyme_actions.size - 1) > maximum_permutations.to_i 120: logger.warn "More permutations than maximum, skipping. Found: #{enzyme_actions.size-1} Max: #{maximum_permutations.to_i}" if defined?(logger) 121: return :too_many_permutations 122: end 123: end 124: 125: if enzyme_actions.size > 1 126: permutations = permute(enzyme_actions.size) 127: 128: permutations.each do |permutation| 129: previous_cut_ranges = [] 130: # Primary and complement strands are both measured from '0' to 'sequence.size-1' here 131: sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 ) 132: 133: # Add the cuts to the sequence_range from each enzyme_action contained 134: # in initial_cuts. These are the cuts that have no competition so are 135: # not subject to permutations. 136: initial_cuts.each do |enzyme_action| 137: enzyme_action.cut_ranges.each do |cut_range| 138: sequence_range.add_cut_range(cut_range) 139: end 140: end 141: 142: permutation.each do |id| 143: enzyme_action = enzyme_actions[id] 144: 145: # conflict is false if the current enzyme action may cut in it's range. 146: # conflict is true if it cannot due to a previous enzyme action making 147: # a cut where this enzyme action needs a whole recognition site. 148: conflict = false 149: 150: # If current size of enzyme_action overlaps with previous cut_range, don't cut 151: # note that the enzyme action may fall in the middle of a previous enzyme action 152: # so all cut locations must be checked that would fall underneath. 153: previous_cut_ranges.each do |cut_range| 154: next unless cut_range.class == Bio::RestrictionEnzyme::Range::VerticalCutRange # we aren't concerned with horizontal cuts 155: previous_cut_left = cut_range.range.first 156: previous_cut_right = cut_range.range.last 157: 158: # Keep in mind: 159: # * The cut location is to the immediate right of the base located at the index. 160: # ex: at^gc -- the cut location is at index 1 161: # * The enzyme action location is located at the base of the index. 162: # ex: atgc -- 0 => 'a', 1 => 't', 2 => 'g', 3 => 'c' 163: # method create_enzyme_actions has similar commentary if interested 164: if (enzyme_action.right <= previous_cut_left) or 165: (enzyme_action.left > previous_cut_right) or 166: (enzyme_action.left > previous_cut_left and enzyme_action.right <= previous_cut_right) # in between cuts 167: # no conflict 168: else 169: conflict = true 170: end 171: end 172: 173: next if conflict == true 174: enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) } 175: previous_cut_ranges += enzyme_action.cut_ranges 176: end # permutation.each 177: 178: # Fill in the source sequence for sequence_range so it knows what bases 179: # to use 180: sequence_range.fragments.primary = sequence 181: sequence_range.fragments.complement = sequence.forward_complement 182: my_hash[permutation] = sequence_range 183: end # permutations.each 184: 185: else # if enzyme_actions.size == 1 186: # no permutations, just do it 187: sequence_range = Bio::RestrictionEnzyme::Range::SequenceRange.new( 0, 0, sequence.size-1, sequence.size-1 ) 188: initial_cuts.each { |enzyme_action| enzyme_action.cut_ranges.each { |cut_range| sequence_range.add_cut_range(cut_range) } } 189: sequence_range.fragments.primary = sequence 190: sequence_range.fragments.complement = sequence.forward_complement 191: my_hash[0] = sequence_range 192: end 193: 194: my_hash 195: 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
Returns: | Array with indicies of match locations |
# File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 203 203: def find_match_locations( string, re ) 204: md = string.match( re ) 205: locations = [] 206: counter = 0 207: while md 208: # save the match index relative to the original string 209: locations << (counter += md.begin(0)) 210: # find the next match 211: md = string[ (counter += 1)..-1 ].match( re ) 212: end 213: locations 214: end
Take the fragments from SequenceRange objects generated from add_cut_range and return unique results as a Bio::RestrictionEnzyme::Analysis::Fragment object.
Arguments
Returns: | Bio::RestrictionEnzyme::Analysis::Fragments object populated with Bio::RestrictionEnzyme::Analysis::Fragment objects. |
# File lib/bio/util/restriction_enzyme/analysis_basic.rb, line 94 94: def fragments_for_display( hsh, view_ranges=false ) 95: ary = Fragments.new 96: return ary unless hsh 97: 98: hsh.each do |permutation_id, sequence_range| 99: sequence_range.fragments.for_display.each do |fragment| 100: if view_ranges 101: ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement, fragment.p_left, fragment.p_right, fragment.c_left, fragment.c_right) 102: else 103: ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement) 104: end 105: end 106: end 107: 108: ary.uniq! unless view_ranges 109: 110: ary 111: 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
Returns: | Array of Array objects with different possible permutation orders. See examples. |
# File lib/bio/util/restriction_enzyme/analysis.rb, line 235 235: def permute(count, permutations = [[0]]) 236: return permutations if count <= 1 237: new_arrays = [] 238: new_array = [] 239: 240: (permutations[0].size + 1).times do |n| 241: new_array.clear 242: permutations.each { |a| new_array << a.dup } 243: new_array.each { |e| e.insert(n, permutations[0].size) } 244: new_arrays += new_array 245: end 246: 247: permute(count-1, new_arrays) 248: end