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_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 Becomes out of date whenever add_cuts_from_cut_ranges is called.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 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
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 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
Returns: | nothing |
# 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
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 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
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 236 236: def clean_all 237: [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! } 238: end