Class | Bio::Locations |
In: |
lib/bio/location.rb
|
Parent: | Object |
The Bio::Locations class is a container for Bio::Location objects: creating a Bio::Locations object (based on a GenBank style position string) will spawn an array of Bio::Location objects.
locations = Bio::Locations.new('join(complement(500..550), 600..625)') locations.each do |loc| puts "class = " + loc.class.to_s puts "range = #{loc.from}..#{loc.to} (strand = #{loc.strand})" end # Output would be: # class = Bio::Location # range = 500..550 (strand = -1) # class = Bio::Location # range = 600..625 (strand = 1) # For the following three location strings, print the span and range ['one-of(898,900)..983', 'one-of(5971..6308,5971..6309)', '8050..one-of(10731,10758,10905,11242)'].each do |loc| location = Bio::Locations.new(loc) puts location.span puts location.range end
According to the GenBank manual ‘gbrel.txt’, position notations were classified into 10 patterns - (A) to (J).
3.4.12.2 Feature Location The second column of the feature descriptor line designates the location of the feature in the sequence. The location descriptor begins at position 22. Several conventions are used to indicate sequence location. Base numbers in location descriptors refer to numbering in the entry, which is not necessarily the same as the numbering scheme used in the published report. The first base in the presented sequence is numbered base 1. Sequences are presented in the 5 to 3 direction. Location descriptors can be one of the following: (A) 1. A single base; (B) 2. A contiguous span of bases; (C) 3. A site between two bases; (D) 4. A single base chosen from a range of bases; (E) 5. A single base chosen from among two or more specified bases; (F) 6. A joining of sequence spans; (G) 7. A reference to an entry other than the one to which the feature belongs (i.e., a remote entry), followed by a location descriptor referring to the remote sequence; (H) 8. A literal sequence (a string of bases enclosed in quotation marks).
(C) A site between two residues, such as an endonuclease cleavage site, is indicated by listing the two bases separated by a carat (e.g., 23^24). (D) A single residue chosen from a range of residues is indicated by the number of the first and last bases in the range separated by a single period (e.g., 23.79). The symbols < and > indicate that the end point (I) of the range is beyond the specified base number. (B) A contiguous span of bases is indicated by the number of the first and last bases in the range separated by two periods (e.g., 23..79). The (I) symbols < and > indicate that the end point of the range is beyond the specified base number. Starting and ending positions can be indicated by base number or by one of the operators described below. Operators are prefixes that specify what must be done to the indicated sequence to locate the feature. The following are the operators available, along with their most common format and a description. (J) complement (location): The feature is complementary to the location indicated. Complementary strands are read 5 to 3. (F) join (location, location, .. location): The indicated elements should be placed end to end to form one contiguous sequence. (F) order (location, location, .. location): The elements are found in the specified order in the 5 to 3 direction, but nothing is implied about the rationality of joining them. (F) group (location, location, .. location): The elements are related and should be grouped together, but no order is implied. (E) one-of (location, location, .. location): The element can be any one, but only one, of the items listed.
locations | [RW] | (Array) An Array of Bio::Location objects |
operator | [RW] | (Symbol or nil) Operator. nil (means :join), :order, or :group (obsolete). |
Parses a GenBank style position string and returns a Bio::Locations object, which contains a list of Bio::Location objects.
locations = Bio::Locations.new('join(complement(500..550), 600..625)')
Arguments:
Returns: | Bio::Locations object |
# File lib/bio/location.rb, line 346 346: def initialize(position) 347: @operator = nil 348: if position.is_a? Array 349: @locations = position 350: else 351: position = gbl_cleanup(position) # preprocessing 352: @locations = gbl_pos2loc(position) # create an Array of Bio::Location objects 353: end 354: end
If other is equal with the self, returns true. Otherwise, returns false.
Arguments:
Returns: | true or false |
# File lib/bio/location.rb, line 381 381: def ==(other) 382: return true if super(other) 383: return false unless other.instance_of?(self.class) 384: if self.locations == other.locations and 385: self.operator == other.operator then 386: true 387: else 388: false 389: end 390: end
Returns nth Bio::Location object.
# File lib/bio/location.rb, line 400 400: def [](n) 401: @locations[n] 402: end
Converts relative position in the locus to position in the whole of the DNA sequence.
This method can for example be used to relate positions in a DNA-sequence with those in RNA. In this use, the optional ’:aa’-flag returns the position of the associated amino-acid rather than the nucleotide.
loc = Bio::Locations.new('complement(12838..13533)') puts loc.absolute(10) # => 13524 puts loc.absolute(10, :aa) # => 13506
Arguments:
Returns: | position within the whole of the sequence |
# File lib/bio/location.rb, line 490 490: def absolute(n, type = nil) 491: case type 492: when :location 493: ; 494: when :aa 495: n = (n - 1) * 3 + 1 496: rel2abs(n) 497: else 498: rel2abs(n) 499: end 500: end
Iterates on each Bio::Location object.
# File lib/bio/location.rb, line 393 393: def each 394: @locations.each do |x| 395: yield(x) 396: end 397: end
Evaluate equality of Bio::Locations object.
# File lib/bio/location.rb, line 364 364: def equals?(other) 365: if ! other.kind_of?(Bio::Locations) 366: return nil 367: end 368: if self.sort == other.sort 369: return true 370: else 371: return false 372: end 373: end
Returns first Bio::Location object.
# File lib/bio/location.rb, line 405 405: def first 406: @locations.first 407: end
Returns last Bio::Location object.
# File lib/bio/location.rb, line 410 410: def last 411: @locations.last 412: end
Converts absolute position in the whole of the DNA sequence to relative position in the locus.
This method can for example be used to relate positions in a DNA-sequence with those in RNA. In this use, the optional ’:aa’-flag returns the position of the associated amino-acid rather than the nucleotide.
loc = Bio::Locations.new('complement(12838..13533)') puts loc.relative(13524) # => 10 puts loc.relative(13506, :aa) # => 3
Arguments:
Returns: | position within the location |
# File lib/bio/location.rb, line 458 458: def relative(n, type = nil) 459: case type 460: when :location 461: ; 462: when :aa 463: if n = abs2rel(n) 464: (n - 1) / 3 + 1 465: else 466: nil 467: end 468: else 469: abs2rel(n) 470: end 471: end
Returns an Array containing overall min and max position [min, max] of this Bio::Locations object.
# File lib/bio/location.rb, line 416 416: def span 417: span_min = @locations.min { |a,b| a.from <=> b.from } 418: span_max = @locations.max { |a,b| a.to <=> b.to } 419: return span_min.from, span_max.to 420: end
String representation.
Note: In some cases, it fails to detect whether "complement(join(…))" or "join(complement(..))", and whether "complement(order(…))" or "order(complement(..))".
Returns: | String |
# File lib/bio/location.rb, line 511 511: def to_s 512: return '' if @locations.empty? 513: complement_join = false 514: locs = @locations 515: if locs.size >= 2 and locs.inject(true) do |flag, loc| 516: # check if each location is complement 517: (flag && (loc.strand == -1) && !loc.xref_id) 518: end and locs.inject(locs[0].from) do |pos, loc| 519: if pos then 520: (pos >= loc.from) ? loc.from : false 521: else 522: false 523: end 524: end then 525: locs = locs.reverse 526: complement_join = true 527: end 528: locs = locs.collect do |loc| 529: lt = loc.lt ? '<' : '' 530: gt = loc.gt ? '>' : '' 531: str = if loc.from == loc.to then 532: "#{lt}#{gt}#{loc.from.to_i}" 533: elsif loc.carat then 534: "#{lt}#{loc.from.to_i}^#{gt}#{loc.to.to_i}" 535: else 536: "#{lt}#{loc.from.to_i}..#{gt}#{loc.to.to_i}" 537: end 538: if loc.xref_id and !loc.xref_id.empty? then 539: str = "#{loc.xref_id}:#{str}" 540: end 541: if loc.strand == -1 and !complement_join then 542: str = "complement(#{str})" 543: end 544: if loc.sequence then 545: str = "replace(#{str},\"#{loc.sequence}\")" 546: end 547: str 548: end 549: if locs.size >= 2 then 550: op = (self.operator || 'join').to_s 551: result = "#{op}(#{locs.join(',')})" 552: else 553: result = locs[0] 554: end 555: if complement_join then 556: result = "complement(#{result})" 557: end 558: result 559: end