Class: Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts

Inherits:
Object
  • Object
show all
Includes:
CutSymbol, StringFormatting
Defined in:
lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb

Overview

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from StringFormatting

#add_spacing, #left_padding, #right_padding, #strip_cuts_and_padding, #strip_padding

Methods included from CutSymbol

#cut_symbol, #escaped_cut_symbol, #re_cut_symbol, #re_cut_symbol_adjacent, #set_cut_symbol

Constructor Details

#initialize(size = nil, circular = false) ⇒ CalculatedCuts

Returns a new instance of CalculatedCuts.



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 86

def initialize(size=nil, circular=false)
  @size = size
  @circular = circular
  @vc_primary = SortedNumArray[]
  @vc_complement = SortedNumArray[]
  @hc_between_strands = SortedNumArray[]
end

Instance Attribute Details

#circular ⇒ Object

Set to true if the fragment CalculatedCuts is working on is circular



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 72

def circular
  @circular
end

#size ⇒ Object (readonly)

Size of the sequence being digested.



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 84

def size
  @size
end

#strands_for_display_current ⇒ Object (readonly)

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 Becomes out of date whenever add_cuts_from_cut_ranges is called.



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 81

def strands_for_display_current
  @strands_for_display_current
end

Instance Method Details

#add_cuts_from_cut_ranges(cut_ranges) ⇒ Object

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

Arguments

  • cut_ranges: An Array of HorizontalCutRange or VerticalCutRange objects

Returns

nothing



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 101

def add_cuts_from_cut_ranges(cut_ranges)
  @strands_for_display_current = false

  @vc_primary = @vc_primary.dup
  @vc_complement = @vc_complement.dup

  cut_ranges.each do |cut_range|
    @vc_primary.concat [cut_range.p_cut_left, cut_range.p_cut_right]
    @vc_complement.concat [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

#hc_between_strands ⇒ Object

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



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 60

def hc_between_strands
  #$stderr.puts caller[0].inspect ###DEBUG
  @hc_between_strands.to_a
end

#hc_between_strands_as_original_class ⇒ Object

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



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 67

def hc_between_strands_as_original_class
  @hc_between_strands
end

#remove_incomplete_cuts(size = nil) ⇒ Object

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

Raises:

  • (IndexError) 


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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 151

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
  hcuts = @hc_between_strands
  last_index = @size - 1
  good_hcuts = SortedNumArray[]
  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.concat(potential_hcuts)
        good_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 = SortedNumArray[]
    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

#strands_for_display(str1 = nil, str2 = nil, vcp = nil, vcc = nil, hc = nil) ⇒ Object

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.



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 219

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.div(num_txt.size) + 1))[0..@size-1] }
  (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
  (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup

  if vcp and !vcp.is_a?(SortedNumArray) then
    vcp = SortedNumArray.new.concat(vcp)
  end
  if vcc and !vcc.is_a?(SortedNumArray) then
    vcc = SortedNumArray.new.concat(vcc)
  end
  if hc and !hc.is_a?(SortedNumArray) then
    hc = SortedNumArray.new.concat(hc)
  end

  vcp = @vc_primary if vcp==nil
  vcc = @vc_complement if vcc==nil
  hc = @hc_between_strands if hc==nil

  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

#vc_complement ⇒ Object

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



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 48

def vc_complement
  #$stderr.puts caller[0].inspect ###DEBUG
  @vc_complement.to_a
end

#vc_complement_as_original_class ⇒ Object

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



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 55

def vc_complement_as_original_class
  @vc_complement
end

#vc_primary ⇒ Object

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



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 36

def vc_primary
  #$stderr.puts caller[0].inspect ###DEBUG
  @vc_primary.to_a
end

#vc_primary_as_original_class ⇒ Object

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



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# File 'lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb', line 43

def vc_primary_as_original_class
  @vc_primary
end