Class | Bio::RestrictionEnzyme::Range::SequenceRange |
In: |
lib/bio/util/restriction_enzyme/range/sequence_range.rb
lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb |
Parent: | Object |
A defined range over a nucleotide sequence.
This class accomadates having cuts defined on a sequence and returning the fragments made by those cuts.
Bin | = | Struct.new(:c, :p) |
A Bio::RestrictionEnzyme::Range::SequenceRange::Bin holds an Array
of indexes for the primary and complement strands (p and
c accessors).
Example hash with Bin values: {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. |
c_left | [R] | Left-most index of complementary strand |
c_right | [R] | Right-most index of complementary strand |
cut_ranges | [R] | CutRanges in this SequenceRange |
left | [R] | Left-most index of DNA sequence |
p_left | [R] | Left-most index of primary strand |
p_right | [R] | Right-most index of primary strand |
right | [R] | Right-most index of DNA sequence |
size | [R] | Size of DNA sequence |
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 55 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
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
Returns: | nothing |
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 85 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
Add a series of CutRange objects (HorizontalCutRange or VerticalCutRange).
Arguments
Returns: | nothing |
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 101 101: 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
Builds a HorizontalCutRange object and adds it to the SequenceRange.
Arguments
Returns: | nothing |
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 115 115: def add_horizontal_cut_range( left, right=left ) 116: @__fragments_current = false 117: @cut_ranges << HorizontalCutRange.new( left, right ) 118: 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
Returns: | Bio::RestrictionEnzyme::Range::SequenceRange::Fragments |
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 157 157: 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
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: | Hash Keys are unique, values are Bio::RestrictionEnzyme::Range::SequenceRange::Bin objects filled with indexes of the sequence locations they represent. |
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 194 194: 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 @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 @circular 242: bins 243: end
Modifies bins in place by creating a new element with key bin_id and initializing the bin.
# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 247 247: 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