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
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 | [R] | An Array with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts. |
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 Becomes out of date whenever add_cuts_from_cut_ranges is called.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 |
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 58 58: def initialize(size=nil, circular=false) 59: @size = size 60: @circular = circular 61: @vc_primary = [] 62: @vc_complement = [] 63: @hc_between_strands = [] 64: end
Accepts an Array of CutRange type objects and applies them to @vc_complement, @vc_primary, and @hc_between_strands.
Arguments
Returns: | nothing |
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 73 73: def add_cuts_from_cut_ranges(cut_ranges) 74: @strands_for_display_current = false 75: 76: cut_ranges.each do |cut_range| 77: @vc_primary += [cut_range.p_cut_left, cut_range.p_cut_right] 78: @vc_complement += [cut_range.c_cut_left, cut_range.c_cut_right] 79: 80: # Add horizontal cut ranges. This may happen from cuts made inbetween a 81: # VerticalCutRange or may be specifically defined by a HorizontalCutRange. 82: if cut_range.class == VerticalCutRange 83: ( cut_range.min + 1 ).upto( cut_range.max ){|i| @hc_between_strands << i} if cut_range.min < cut_range.max 84: elsif cut_range.class == HorizontalCutRange 85: ( cut_range.hcuts.first ).upto( cut_range.hcuts.last ){|i| @hc_between_strands << i} 86: end 87: end 88: clean_all 89: #return 90: 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
Returns: | nothing |
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 120 120: def remove_incomplete_cuts(size=nil) 121: @strands_for_display_current = false 122: @size = size if size 123: raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular 124: 125: vcuts = (@vc_primary + @vc_complement).uniq.sort 126: hcuts = @hc_between_strands 127: last_index = @size - 1 128: good_hcuts = [] 129: potential_hcuts = [] 130: 131: if @circular 132: # NOTE 133: # if it's circular we should start at the beginning of a cut for orientation, 134: # scan for it, hack off the first set of hcuts and move them to the back 135: else 136: vcuts.unshift(-1) unless vcuts.include?(-1) 137: vcuts.push(last_index) unless vcuts.include?(last_index) 138: end 139: 140: hcuts.each do |hcut| 141: raise IndexError if hcut < -1 or hcut > last_index 142: # skipped a nucleotide 143: potential_hcuts.clear if !potential_hcuts.empty? and (hcut - potential_hcuts.last).abs > 1 144: 145: if potential_hcuts.empty? 146: if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 ) 147: good_hcuts += [hcut] 148: elsif vcuts.include?( hcut - 1 ) 149: potential_hcuts << hcut 150: end 151: else 152: if vcuts.include?( hcut ) 153: good_hcuts += potential_hcuts + [hcut] 154: potential_hcuts.clear 155: else 156: potential_hcuts << hcut 157: end 158: end 159: end 160: 161: check_vc = lambda do |vertical_cuts, opposing_vcuts| 162: # opposing_vcuts is here only to check for blunt cuts, so there shouldn't 163: # be any out-of-order problems with this 164: good_vc = [] 165: vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) } 166: good_vc 167: end 168: 169: @vc_primary = check_vc.call(@vc_primary, @vc_complement) 170: @vc_complement = check_vc.call(@vc_complement, @vc_primary) 171: @hc_between_strands = good_hcuts 172: 173: clean_all 174: end
Sets @strands_for_display_current to true and populates @strands_for_display.
Arguments
Returns: | Array An array with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts. |
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 187 187: def strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil) 188: return @strands_for_display if @strands_for_display_current 189: vcs = '|' # Vertical cut symbol 190: hcs = '-' # Horizontal cut symbol 191: vhcs = '+' # Intersection of vertical and horizontal cut symbol 192: 193: num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * ( @size / num_txt.size.to_f ).ceil)[0..@size-1] } 194: (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup 195: (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup 196: 197: vcp = @vc_primary if vcp==nil 198: vcc = @vc_complement if vcc==nil 199: hc = @hc_between_strands if hc==nil 200: 201: vcuts = (vcp + vcc).uniq.sort 202: 203: vcp.reverse.each { |c| a.insert(c+1, vcs) } 204: vcc.reverse.each { |c| b.insert(c+1, vcs) } 205: 206: between = ' ' * @size 207: hc.each {|hcut| between[hcut,1] = hcs } 208: 209: s_a = add_spacing(a, vcs) 210: s_b = add_spacing(b, vcs) 211: s_bet = add_spacing(between) 212: 213: # NOTE watch this for circular 214: i = 0 215: 0.upto( s_a.size-1 ) do 216: if (s_a[i,1] == vcs) or (s_b[i,1] == vcs) 217: s_bet[i] = vhcs 218: elsif i != 0 and s_bet[i-1,1] == hcs and s_bet[i+1,1] == hcs 219: s_bet[i] = hcs 220: end 221: i+=1 222: end 223: 224: @strands_for_display_current = true 225: @strands_for_display = [s_a, s_bet, s_b] 226: end
remove nil values, remove duplicate values, and sort @vc_primary, @vc_complement, and @hc_between_strands
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 234 234: def clean_all 235: [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! } 236: end