Class Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
In: lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
Parent: Object

cc = CalculatedCuts.new(@size) cc.add_cuts_from_cut_ranges(@cut_ranges) cc.remove_incomplete_cuts

   1 2 3 4 5 6 7
   G A|T T A C A
      +-----+
   C T A A T|G T
   1 2 3 4 5 6 7

Primary cut = 2 Complement cut = 5 Horizontal cuts = 3, 4, 5

Methods

Included Modules

CutSymbol StringFormatting

Attributes

circular  [RW]  Set to true if the fragment CalculatedCuts is working on is circular
hc_between_strands  [R]  Array of horizontal cuts between strands in 0-based index notation
size  [R]  Size of the sequence being digested.
strands_for_display_current  [R]  If false the strands_for_display method needs to be called to update the contents of @strands_for_display. Becomes out of date whenever add_cuts_from_cut_ranges is called.
vc_complement  [R]  Array of vertical cuts on the complementary strand in 0-based index notation
vc_primary  [R]  Array of vertical cuts on the primary strand in 0-based index notation

Public Class methods

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 60
60:   def initialize(size=nil, circular=false)
61:     @size = size
62:     @circular = circular
63:     @vc_primary = []
64:     @vc_complement = []
65:     @hc_between_strands = []
66:   end

Public Instance methods

Accepts an Array of CutRange type objects and applies them to @vc_complement, @vc_primary, and @hc_between_strands.


Arguments

Returns:nothing

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 75
75:   def add_cuts_from_cut_ranges(cut_ranges)
76:     @strands_for_display_current = false
77: 
78:     cut_ranges.each do |cut_range|
79:       @vc_primary += [cut_range.p_cut_left, cut_range.p_cut_right]
80:       @vc_complement += [cut_range.c_cut_left, cut_range.c_cut_right]
81: 
82:       # Add horizontal cut ranges.  This may happen from cuts made inbetween a
83:       # VerticalCutRange or may be specifically defined by a HorizontalCutRange.
84:       if cut_range.class == VerticalCutRange
85:         ( cut_range.min + 1 ).upto( cut_range.max ){|i| @hc_between_strands << i} if cut_range.min < cut_range.max
86:       elsif cut_range.class == HorizontalCutRange
87:         ( cut_range.hcuts.first ).upto( cut_range.hcuts.last ){|i| @hc_between_strands << i}
88:       end
89:     end
90:     clean_all
91:     #return
92:   end

There may be incomplete cuts made, this method removes the cuts that don‘t create sub-sequences for easier processing.

For example, stray horizontal cuts that do not end with a left and right separation:

  G A T T A C A
     +--  ---
  C T|A A T G T

Or stray vertical cuts:

  G A T T A C A
     +--   +
  C T|A A T|G T

However note that for non-circular sequences this would be a successful cut which would result in a floating ‘GT’ sub-sequence:

  G A T T A C A
           +---
  C T A A T|G T

Blunt cuts are also complete cuts.


Arguments

  • size: (optional) Size of the sequence being digested. Defined here or during initalization of CalculatedCuts.
Returns:nothing

[Source]

     # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 122
122:   def remove_incomplete_cuts(size=nil)
123:     @strands_for_display_current = false
124:     @size = size if size
125:     raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular
126: 
127:     vcuts = (@vc_primary + @vc_complement).uniq.sort
128:     hcuts = @hc_between_strands
129:     last_index = @size - 1
130:     good_hcuts = []
131:     potential_hcuts = []
132: 
133:     if @circular
134:     # NOTE
135:     # if it's circular we should start at the beginning of a cut for orientation,
136:     # scan for it, hack off the first set of hcuts and move them to the back
137:     else
138:       vcuts.unshift(-1) unless vcuts.include?(-1)
139:       vcuts.push(last_index) unless vcuts.include?(last_index)
140:     end
141: 
142:     hcuts.each do |hcut|
143:       raise IndexError if hcut < -1 or hcut > last_index
144:       # skipped a nucleotide
145:       potential_hcuts.clear if !potential_hcuts.empty? and (hcut - potential_hcuts.last).abs > 1
146: 
147:       if potential_hcuts.empty?
148:         if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 )
149:           good_hcuts += [hcut]
150:         elsif vcuts.include?( hcut - 1 )
151:           potential_hcuts << hcut
152:         end
153:       else
154:         if vcuts.include?( hcut )
155:           good_hcuts += potential_hcuts + [hcut]
156:           potential_hcuts.clear
157:         else
158:           potential_hcuts << hcut
159:         end
160:       end
161:     end
162: 
163:     check_vc = lambda do |vertical_cuts, opposing_vcuts|
164:       # opposing_vcuts is here only to check for blunt cuts, so there shouldn't
165:       # be any out-of-order problems with this
166:       good_vc = []
167:       vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) }
168:       good_vc
169:     end
170: 
171:     @vc_primary = check_vc.call(@vc_primary, @vc_complement)
172:     @vc_complement = check_vc.call(@vc_complement, @vc_primary)
173:     @hc_between_strands = good_hcuts
174: 
175:     clean_all
176:   end

Sets @strands_for_display_current to true and populates @strands_for_display.


Arguments

  • +str1+: (optional) For displaying a primary strand. If nil a numbered sequence will be used in place.
  • +str2+: (optional) For displaying a complementary strand. If nil a numbered sequence will be used in place.
  • vcp: (optional) An array of vertical cut locations on the primary strand. If nil the contents of @vc_primary is used.
  • vcc: (optional) An array of vertical cut locations on the complementary strand. If nil the contents of @vc_complementary is used.
  • hc: (optional) An array of horizontal cut locations between strands. If nil the contents of @hc_between_strands is used.
Returns:Array An array with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts.

[Source]

     # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 189
189:   def strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil)
190:     return @strands_for_display if @strands_for_display_current
191:     vcs = '|'   # Vertical cut symbol
192:     hcs = '-'   # Horizontal cut symbol
193:     vhcs = '+'  # Intersection of vertical and horizontal cut symbol
194:       
195:     num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * ( @size / num_txt.size.to_f ).ceil)[0..@size-1] }
196:     (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
197:     (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup
198: 
199:     vcp = @vc_primary if vcp==nil
200:     vcc = @vc_complement if vcc==nil
201:     hc = @hc_between_strands if hc==nil
202: 
203:     vcuts = (vcp + vcc).uniq.sort
204: 
205:     vcp.reverse.each { |c| a.insert(c+1, vcs) }
206:     vcc.reverse.each { |c| b.insert(c+1, vcs) }
207: 
208:     between = ' ' * @size
209:     hc.each {|hcut| between[hcut,1] = hcs }
210: 
211:     s_a = add_spacing(a, vcs)
212:     s_b = add_spacing(b, vcs)
213:     s_bet = add_spacing(between)
214: 
215:     # NOTE watch this for circular
216:     i = 0
217:     0.upto( s_a.size-1 ) do
218:       if (s_a[i,1] == vcs) or (s_b[i,1] == vcs)
219:         s_bet[i] = vhcs 
220:       elsif i != 0 and s_bet[i-1,1] == hcs and s_bet[i+1,1] == hcs
221:         s_bet[i] = hcs 
222:       end
223:       i+=1
224:     end
225: 
226:     @strands_for_display_current = true
227:     @strands_for_display = [s_a, s_bet, s_b]
228:   end

Protected Instance methods

remove nil values, remove duplicate values, and sort @vc_primary, @vc_complement, and @hc_between_strands

[Source]

     # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 236
236:   def clean_all
237:     [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! }
238:   end

[Validate]