Class | Bio::RestrictionEnzyme::Analysis
In: | lib/bio/util/restriction_enzyme/analysis_basic.rb lib/bio/util/restriction_enzyme/analysis.rb
Parent: | Object

### Methods

create_enzyme_actions cut cut cut_and_return_by_permutations cut_without_permutations cut_without_permutations find_match_locations fragments_for_display permute

### Public Class methods

cut( sequence, *args )

See cut instance method

[Source]

        # File lib/bio/util/restriction_enzyme/analysis.rb, line 23
    23:   def self.cut( sequence, *args )
    24:     self.new.cut( sequence, *args )
    25:   end

cut_without_permutations( sequence, *args )

See cut_without_permutations instance method

[Source]

        # 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

### Public Instance methods

cut( sequence, *args )

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

[Source]

        # 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

cut_without_permutations( sequence, *args )

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)

[Source]

        # 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

### Protected Instance methods

create_enzyme_actions( sequence, *args )

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.

[Source]

         # 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

cut_and_return_by_permutations( sequence, *args )

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‘

[Source]

         # 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

find_match_locations( string, re )

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

[Source]

         # 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

fragments_for_display( hsh, view_ranges=false )

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.

[Source]

         # 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

permute(count, permutations = [[0]])

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.

[Source]

         # 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

[Validate]