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
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 Becomes out of date whenever add_cuts_from_cut_ranges is called.

Public Class methods

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 86
86:   def initialize(size=nil, circular=false)
87:     @size = size
88:     @circular = circular
89:     @vc_primary = SortedNumArray[]
90:     @vc_complement = SortedNumArray[]
91:     @hc_between_strands = SortedNumArray[]
92:   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 101
101:   def add_cuts_from_cut_ranges(cut_ranges)
102:     @strands_for_display_current = false
103: 
104:     @vc_primary = @vc_primary.dup
105:     @vc_complement = @vc_complement.dup
106: 
107:     cut_ranges.each do |cut_range|
108:       @vc_primary.concat [cut_range.p_cut_left, cut_range.p_cut_right]
109:       @vc_complement.concat [cut_range.c_cut_left, cut_range.c_cut_right]
110: 
111:       # Add horizontal cut ranges.  This may happen from cuts made inbetween a
112:       # VerticalCutRange or may be specifically defined by a HorizontalCutRange.
113:       if cut_range.class == VerticalCutRange
114:         ( cut_range.min + 1 ).upto( cut_range.max ){|i| @hc_between_strands << i} if cut_range.min < cut_range.max
115:       elsif cut_range.class == HorizontalCutRange
116:         ( cut_range.hcuts.first ).upto( cut_range.hcuts.last ){|i| @hc_between_strands << i}
117:       end
118:     end
119:     clean_all
120:     #return
121:   end

Array of horizontal cuts between strands in 0-based index notation

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 60
60:   def hc_between_strands
61:     #$stderr.puts caller[0].inspect ###DEBUG
62:     @hc_between_strands.to_a
63:   end

Returns the same contents as hc_between_strands, but returns original data structure used in the class.

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 67
67:   def hc_between_strands_as_original_class
68:     @hc_between_strands
69:   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 151
151:   def remove_incomplete_cuts(size=nil)
152:     @strands_for_display_current = false
153:     @size = size if size
154:     raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular
155: 
156:     vcuts = @vc_primary + @vc_complement
157:     hcuts = @hc_between_strands
158:     last_index = @size - 1
159:     good_hcuts = SortedNumArray[]
160:     potential_hcuts = []
161: 
162:     if @circular
163:     # NOTE
164:     # if it's circular we should start at the beginning of a cut for orientation,
165:     # scan for it, hack off the first set of hcuts and move them to the back
166:     else
167:       vcuts.unshift(-1) unless vcuts.include?(-1)
168:       vcuts.push(last_index) unless vcuts.include?(last_index)
169:     end
170: 
171:     hcuts.each do |hcut|
172:       raise IndexError if hcut < -1 or hcut > last_index
173:       # skipped a nucleotide
174:       potential_hcuts.clear if !potential_hcuts.empty? and (hcut - potential_hcuts.last).abs > 1
175: 
176:       if potential_hcuts.empty?
177:         if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 )
178:           good_hcuts << hcut
179:         elsif vcuts.include?( hcut - 1 )
180:           potential_hcuts << hcut
181:         end
182:       else
183:         if vcuts.include?( hcut )
184:           good_hcuts.concat(potential_hcuts)
185:           good_hcuts << hcut
186:           potential_hcuts.clear
187:         else
188:           potential_hcuts << hcut
189:         end
190:       end
191:     end
192: 
193:     check_vc = lambda do |vertical_cuts, opposing_vcuts|
194:       # opposing_vcuts is here only to check for blunt cuts, so there shouldn't
195:       # be any out-of-order problems with this
196:       good_vc = SortedNumArray[]
197:       vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) }
198:       good_vc
199:     end
200: 
201:     @vc_primary = check_vc.call(@vc_primary, @vc_complement)
202:     @vc_complement = check_vc.call(@vc_complement, @vc_primary)
203:     @hc_between_strands = good_hcuts
204: 
205:     clean_all
206:   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 219
219:   def strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil)
220:     return @strands_for_display if @strands_for_display_current
221:     vcs = '|'   # Vertical cut symbol
222:     hcs = '-'   # Horizontal cut symbol
223:     vhcs = '+'  # Intersection of vertical and horizontal cut symbol
224:       
225:     num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * (@size.div(num_txt.size) + 1))[0..@size-1] }
226:     (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
227:     (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup
228: 
229:     if vcp and !vcp.is_a?(SortedNumArray) then
230:       vcp = SortedNumArray.new.concat(vcp)
231:     end
232:     if vcc and !vcc.is_a?(SortedNumArray) then
233:       vcc = SortedNumArray.new.concat(vcc)
234:     end
235:     if hc and !hc.is_a?(SortedNumArray) then
236:       hc = SortedNumArray.new.concat(hc)
237:     end
238: 
239:     vcp = @vc_primary if vcp==nil
240:     vcc = @vc_complement if vcc==nil
241:     hc = @hc_between_strands if hc==nil
242: 
243:     vcp.reverse_each { |c| a.insert(c+1, vcs) }
244:     vcc.reverse_each { |c| b.insert(c+1, vcs) }
245: 
246:     between = ' ' * @size
247:     hc.each {|hcut| between[hcut,1] = hcs }
248: 
249:     s_a = add_spacing(a, vcs)
250:     s_b = add_spacing(b, vcs)
251:     s_bet = add_spacing(between)
252: 
253:     # NOTE watch this for circular
254:     i = 0
255:     0.upto( s_a.size-1 ) do
256:       if (s_a[i,1] == vcs) or (s_b[i,1] == vcs)
257:         s_bet[i] = vhcs 
258:       elsif i != 0 and s_bet[i-1,1] == hcs and s_bet[i+1,1] == hcs
259:         s_bet[i] = hcs 
260:       end
261:       i+=1
262:     end
263: 
264:     @strands_for_display_current = true
265:     @strands_for_display = [s_a, s_bet, s_b]
266:   end

Array of vertical cuts on the complementary strand in 0-based index notation

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 48
48:   def vc_complement
49:     #$stderr.puts caller[0].inspect ###DEBUG
50:     @vc_complement.to_a
51:   end

Returns the same contents as vc_complement, but returns original data structure used in the class.

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 55
55:   def vc_complement_as_original_class
56:     @vc_complement
57:   end

Array of vertical cuts on the primary strand in 0-based index notation

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 36
36:   def vc_primary
37:     #$stderr.puts caller[0].inspect ###DEBUG
38:     @vc_primary.to_a
39:   end

Returns the same contents as vc_primary, but returns original data structure used in the class.

[Source]

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 43
43:   def vc_primary_as_original_class
44:     @vc_primary
45:   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 274
274:   def clean_all
275:     [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! }
276:   end

[Validate]