class Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
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
Attributes
Set to true
if the fragment CalculatedCuts
is working on is circular
Array
of horizontal cuts between strands in 0-based index notation
Size of the sequence being digested.
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 Becomes out of date whenever add_cuts_from_cut_ranges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.
Array
of vertical cuts on the complementary strand in 0-based index notation
Array
of vertical cuts on the primary strand in 0-based index notation
Public Class Methods
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 52 def initialize(size=nil, circular=false) @size = size @circular = circular @vc_primary = [] @vc_complement = [] @hc_between_strands = [] end
Public Instance Methods
Accepts an Array
of CutRange
type objects and applies them to @vc_complement, @vc_primary, and @hc_between_strands.
Arguments
-
cut_ranges
: AnArray
ofHorizontalCutRange
orVerticalCutRange
objects
- Returns
-
nothing
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 67 def add_cuts_from_cut_ranges(cut_ranges) @strands_for_display_current = false cut_ranges.each do |cut_range| @vc_primary += [cut_range.p_cut_left, cut_range.p_cut_right] @vc_complement += [cut_range.c_cut_left, cut_range.c_cut_right] # Add horizontal cut ranges. This may happen from cuts made inbetween a # VerticalCutRange or may be specifically defined by a HorizontalCutRange. if cut_range.class == VerticalCutRange ( cut_range.min + 1 ).upto( cut_range.max ){|i| @hc_between_strands << i} if cut_range.min < cut_range.max elsif cut_range.class == HorizontalCutRange ( cut_range.hcuts.first ).upto( cut_range.hcuts.last ){|i| @hc_between_strands << i} end end clean_all #return 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 ofCalculatedCuts
.
- Returns
-
nothing
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 114 def remove_incomplete_cuts(size=nil) @strands_for_display_current = false @size = size if size raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular vcuts = (@vc_primary + @vc_complement).uniq.sort hcuts = @hc_between_strands last_index = @size - 1 good_hcuts = [] potential_hcuts = [] if @circular # NOTE # if it's circular we should start at the beginning of a cut for orientation, # scan for it, hack off the first set of hcuts and move them to the back else vcuts.unshift(-1) unless vcuts.include?(-1) vcuts.push(last_index) unless vcuts.include?(last_index) end hcuts.each do |hcut| raise IndexError if hcut < -1 or hcut > last_index # skipped a nucleotide potential_hcuts.clear if !potential_hcuts.empty? and (hcut - potential_hcuts.last).abs > 1 if potential_hcuts.empty? if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 ) good_hcuts += [hcut] elsif vcuts.include?( hcut - 1 ) potential_hcuts << hcut end else if vcuts.include?( hcut ) good_hcuts += potential_hcuts + [hcut] potential_hcuts.clear else potential_hcuts << hcut end end end check_vc = lambda do |vertical_cuts, opposing_vcuts| # opposing_vcuts is here only to check for blunt cuts, so there shouldn't # be any out-of-order problems with this good_vc = [] vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) } good_vc end @vc_primary = check_vc.call(@vc_primary, @vc_complement) @vc_complement = check_vc.call(@vc_complement, @vc_primary) @hc_between_strands = good_hcuts clean_all end
Sets @strands_for_display_current to true
and populates @strands_for_display.
Arguments
-
str1
: (optional) For displaying a primary strand. Ifnil
a numbered sequence will be used in place. -
str2
: (optional) For displaying a complementary strand. Ifnil
a numbered sequence will be used in place. -
vcp
: (optional) An array of vertical cut locations on the primary strand. Ifnil
the contents of @vc_primary is used. -
vcc
: (optional) An array of vertical cut locations on the complementary strand. Ifnil
the contents of @vc_complementary is used. -
hc
: (optional) An array of horizontal cut locations between strands. Ifnil
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.
# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 181 def strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil) return @strands_for_display if @strands_for_display_current vcs = '|' # Vertical cut symbol hcs = '-' # Horizontal cut symbol vhcs = '+' # Intersection of vertical and horizontal cut symbol num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * ( @size / num_txt.size.to_f ).ceil)[0..@size-1] } (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup vcp = @vc_primary if vcp==nil vcc = @vc_complement if vcc==nil hc = @hc_between_strands if hc==nil vcuts = (vcp + vcc).uniq.sort vcp.reverse.each { |c| a.insert(c+1, vcs) } vcc.reverse.each { |c| b.insert(c+1, vcs) } between = ' ' * @size hc.each {|hcut| between[hcut,1] = hcs } s_a = add_spacing(a, vcs) s_b = add_spacing(b, vcs) s_bet = add_spacing(between) # NOTE watch this for circular i = 0 0.upto( s_a.size-1 ) do if (s_a[i,1] == vcs) or (s_b[i,1] == vcs) s_bet[i] = vhcs elsif i != 0 and s_bet[i-1,1] == hcs and s_bet[i+1,1] == hcs s_bet[i] = hcs end i+=1 end @strands_for_display_current = true @strands_for_display = [s_a, s_bet, s_b] end
Protected Instance Methods
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 228 def clean_all [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! } end