Class Bio::Locations
In: lib/bio/location.rb  (CVS)
Parent: Object

Description

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.

Usage

  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

GenBank location descriptor classification

Definition of the position notation of the GenBank location format

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).

Description commented with pattern IDs.

  (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.

Reduction strategy of the position notations

Methods

[]   absolute   each   equals?   first   last   length   new   range   relative   size   span  

Included Modules

Enumerable

Attributes

locations  [RW]  An Array of Bio::Location objects

Public Class methods

new(position)

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:

  • (required) str: GenBank style position string
Returns:Bio::Locations object

[Source]

# File lib/bio/location.rb, line 295
  def initialize(position)
    if position.is_a? Array
      @locations = position
    else
      position   = gbl_cleanup(position)        # preprocessing
      @locations = gbl_pos2loc(position)        # create an Array of Bio::Location objects
    end
  end

Public Instance methods

[](n)

Returns nth Bio::Location object.

[Source]

# File lib/bio/location.rb, line 327
  def [](n)
    @locations[n]
  end
absolute(n, type = nil)

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:

  • (required) position: nucleotide position within locus
  • _:aa_: flag to be used if position is a aminoacid position rather than a nucleotide position
Returns:position within the whole of the sequence

[Source]

# File lib/bio/location.rb, line 417
  def absolute(n, type = nil)
    case type
    when :location
      ;
    when :aa
      n = (n - 1) * 3 + 1
      rel2abs(n)
    else
      rel2abs(n)
    end
  end
each() {|x| ...}

Iterates on each Bio::Location object.

[Source]

# File lib/bio/location.rb, line 320
  def each
    @locations.each do |x|
      yield(x)
    end
  end
equals?(other)

Evaluate equality of Bio::Locations object.

[Source]

# File lib/bio/location.rb, line 308
  def equals?(other)
    if ! other.kind_of?(Bio::Locations)
      return nil
    end
    if self.sort == other.sort
      return true
    else
      return false
    end
  end
first()

Returns first Bio::Location object.

[Source]

# File lib/bio/location.rb, line 332
  def first
    @locations.first
  end
last()

Returns last Bio::Location object.

[Source]

# File lib/bio/location.rb, line 337
  def last
    @locations.last
  end
length()

Returns a length of the spliced RNA.

[Source]

# File lib/bio/location.rb, line 356
  def length
    len = 0
    @locations.each do |x|
      if x.sequence
        len += x.sequence.size
      else
        len += (x.to - x.from + 1)
      end
    end
    len
  end
range()

Similar to span, but returns a Range object min..max

[Source]

# File lib/bio/location.rb, line 350
  def range
    min, max = span
    min..max
  end
relative(n, type = nil)

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:

  • (required) position: nucleotide position within whole of the sequence
  • _:aa_: flag that lets method return position in aminoacid coordinates
Returns:position within the location

[Source]

# File lib/bio/location.rb, line 385
  def relative(n, type = nil)
    case type
    when :location
      ;
    when :aa
      if n = abs2rel(n)
        (n - 1) / 3 + 1
      else
        nil
      end
    else
      abs2rel(n)
    end
  end
size()

Alias for length

span()

Returns an Array containing overall min and max position [min, max] of this Bio::Locations object.

[Source]

# File lib/bio/location.rb, line 343
  def span
    span_min = @locations.min { |a,b| a.from <=> b.from }
    span_max = @locations.max { |a,b| a.to   <=> b.to   }
    return span_min.from, span_max.to
  end

[Validate]