class Bio::RestrictionEnzyme::Range::SequenceRange
A defined range over a nucleotide sequence.
This class accomadates having cuts defined on a sequence and returning the fragments made by those cuts.
Constants
- Bin
-
A
Bio::RestrictionEnzyme::Range::SequenceRange::Binholds anArrayof indexes for the primary and complement strands (pandcaccessors).Example hash with
Binvalues:{0=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[0, 1], p=[0]>, 2=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[], p=[1, 2]>, 3=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[2, 3], p=[]>, 4=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[4, 5], p=[3, 4, 5]>}Note that the bin cannot be easily stored as a range since there may be nucleotides excised in the middle of a range.
TODO: Perhaps store the bins as one-or-many ranges since missing nucleotides due to enzyme cutting is a special case.
Attributes
Left-most index of complementary strand
Right-most index of complementary strand
CutRanges in this SequenceRange
Left-most index of DNA sequence
Left-most index of primary strand
Right-most index of primary strand
Right-most index of DNA sequence
Size of DNA sequence
Public Class Methods
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 55 def initialize( p_left = nil, p_right = nil, c_left = nil, c_right = nil ) 56 raise ArgumentError if p_left == nil and c_left == nil 57 raise ArgumentError if p_right == nil and c_right == nil 58 (raise ArgumentError unless p_left <= p_right) unless p_left == nil or p_right == nil 59 (raise ArgumentError unless c_left <= c_right) unless c_left == nil or c_right == nil 60 61 @p_left, @p_right, @c_left, @c_right = p_left, p_right, c_left, c_right 62 @left = [p_left, c_left].compact.sort.first 63 @right = [p_right, c_right].compact.sort.last 64 @size = (@right - @left) + 1 unless @left == nil or @right == nil 65 @cut_ranges = CutRanges.new 66 @__fragments_current = false 67 end
Public Instance Methods
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 85 def add_cut_range( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil ) 86 @__fragments_current = false 87 if p_cut_left.kind_of? CutRange # shortcut 88 @cut_ranges << p_cut_left 89 else 90 [p_cut_left, p_cut_right, c_cut_left, c_cut_right].each { |n| (raise IndexError unless n >= @left and n <= @right) unless n == nil } 91 @cut_ranges << VerticalCutRange.new( p_cut_left, p_cut_right, c_cut_left, c_cut_right ) 92 end 93 end
If the first object is HorizontalCutRange or VerticalCutRange, that is added to the SequenceRange. Otherwise this method builds a VerticalCutRange object and adds it to the SequenceRange.
Note: Cut occurs immediately after the index supplied. For example, a cut at ‘0’ would mean a cut occurs between bases 0 and 1.
Arguments
-
p_cut_left: (optional) Left-most cut on the primary strand or aCutRangeobject.nilto skip -
p_cut_right: (optional) Right-most cut on the primary strand.nilto skip -
c_cut_left: (optional) Left-most cut on the complementary strand.nilto skip -
c_cut_right: (optional) Right-most cut on the complementary strand.nilto skip
- Returns
-
nothing
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 101 def add_cut_ranges(*cut_ranges) 102 cut_ranges.flatten.each do |cut_range| 103 raise TypeError, "Not of type CutRange" unless cut_range.kind_of? CutRange 104 self.add_cut_range( cut_range ) 105 end 106 end
Add a series of CutRange objects (HorizontalCutRange or VerticalCutRange).
Arguments
-
cut_ranges: A series ofCutRangeobjects
- Returns
-
nothing
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 115 def add_horizontal_cut_range( left, right=left ) 116 @__fragments_current = false 117 @cut_ranges << HorizontalCutRange.new( left, right ) 118 end
Builds a HorizontalCutRange object and adds it to the SequenceRange.
Arguments
-
left: Left-most cut -
right: (optional) Right side - by default this equals the left side, default is recommended.
- Returns
-
nothing
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 157 def fragments 158 return @__fragments if @__fragments_current == true 159 @__fragments_current = true 160 161 num_txt = '0123456789' 162 num_txt_repeat = (num_txt * ( @size.div(num_txt.size) + 1))[0..@size-1] 163 fragments = Fragments.new(num_txt_repeat, num_txt_repeat) 164 165 cc = Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts.new(@size) 166 cc.add_cuts_from_cut_ranges(@cut_ranges) 167 cc.remove_incomplete_cuts 168 169 create_bins(cc).sort.each { |k, bin| fragments << Fragment.new( bin.p, bin.c ) } 170 @__fragments = fragments 171 return fragments 172 end
Calculates the fragments over this sequence range as defined after using the methods add_cut_range, add_cut_ranges, and/or add_horizontal_cut_range
Example return value:
[#<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277bdc @complement_bin=[0, 1], @primary_bin=[0]>, #<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277bc8 @complement_bin=[], @primary_bin=[1, 2]>, #<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277bb4 @complement_bin=[2, 3], @primary_bin=[]>, #<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277ba0 @complement_bin=[4, 5], @primary_bin=[3, 4, 5]>]
Arguments
-
none
Protected Instance Methods
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 194 def create_bins(cc) 195 p_cut = cc.vc_primary_as_original_class 196 c_cut = cc.vc_complement_as_original_class 197 h_cut = cc.hc_between_strands_as_original_class 198 199 if (defined? @circular) && @circular 200 # NOTE 201 # if it's circular we should start at the beginning of a cut for orientation 202 # scan for it, hack off the first set of hcuts and move them to the back 203 204 unique_id = 0 205 else 206 p_cut.unshift(-1) unless p_cut.include?(-1) 207 c_cut.unshift(-1) unless c_cut.include?(-1) 208 unique_id = -1 209 end 210 211 p_bin_id = c_bin_id = unique_id 212 bins = {} 213 setup_new_bin(bins, unique_id) 214 215 -1.upto(@size-1) do |idx| # NOTE - circular, for the future - should '-1' be replace with 'unique_id'? 216 217 # if bin_ids are out of sync but the strands are attached 218 if (p_bin_id != c_bin_id) and !h_cut.include?(idx) 219 min_id, max_id = [p_bin_id, c_bin_id].sort 220 bins.delete(max_id) 221 p_bin_id = c_bin_id = min_id 222 end 223 224 bins[ p_bin_id ].p << idx 225 bins[ c_bin_id ].c << idx 226 227 if p_cut.include? idx 228 p_bin_id = (unique_id += 1) 229 setup_new_bin(bins, p_bin_id) 230 end 231 232 if c_cut.include? idx # repetition 233 c_bin_id = (unique_id += 1) # repetition 234 setup_new_bin(bins, c_bin_id) # repetition 235 end # repetition 236 237 end 238 239 # Bin "-1" is an easy way to indicate the start of a strand just in case 240 # there is a horizontal cut at position 0 241 bins.delete(-1) unless ((defined? @circular) && @circular) 242 bins 243 end
Example:
cc = Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts.new(@size) cc.add_cuts_from_cut_ranges(@cut_ranges) cc.remove_incomplete_cuts bins = create_bins(cc)
Example return value:
{0=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[0, 1], p=[0]>,
2=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[], p=[1, 2]>,
3=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[2, 3], p=[]>,
4=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[4, 5], p=[3, 4, 5]>}
Arguments
- Returns
-
HashKeys are unique, values areBio::RestrictionEnzyme::Range::SequenceRange::Binobjects filled with indexes of the sequence locations they represent.
Source
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb 247 def setup_new_bin(bins, bin_id) 248 bins[ bin_id ] = Bin.new 249 bins[ bin_id ].p = DenseIntArray[] #could be replaced by SortedNumArray[] 250 bins[ bin_id ].c = DenseIntArray[] #could be replaced by SortedNumArray[] 251 end
Modifies bins in place by creating a new element with key bin_id and initializing the bin.