class Bio::Location

Description¶ ↑

The Bio::Location class describes the position of a genomic locus. Typically, Bio::Location objects are created automatically when the user creates a Bio::Locations object, instead of initialized directly.

Usage¶ ↑

location = Bio::Location.new('500..550')
puts "start=" + location.from.to_s + ";end=" + location.to.to_s

#, or better: through Bio::Locations
locations = Bio::Locations.new('500..550')
locations.each do |location|
  puts "start=" + location.from.to_s + ";end=" + location.to.to_s
end

Attributes

carat [RW]

(true, false or nil) true if the location indicates the site between two adjoining nucleotides

from [RW]

(Integer) start position of the location

gt [RW]

(true, false or nil) true if the position contains ‘>’

lt [RW]

(true, false or nil) true if the position contains ‘<’

sequence [RW]

(String) literal sequence of the location

strand [RW]

(Integer) strand direction of the location (forward => 1 or complement => -1)

to [RW]

(Integer) end position of the location

xref_id [RW]

(String) link to the external entry as GenBank ID

Public Class Methods

new (location = nil)

Source

   # File lib/bio/location.rb
45   def initialize(location = nil)
46 
47     if location
48       if location =~ /:/                                # (G) ID:location
49         xref_id, location = location.split(':')
50       end
51       if location =~ /</                                # (I) <,>
52         lt = true
53       end
54       if location =~ />/
55         gt = true
56       end
57     end
58 
59     # s : start base, e : end base => from, to
60     case location
61     when /^[<>]?(\d+)$/                                 # (A, I) n
62       s = e = $1.to_i
63     when /^[<>]?(\d+)\.\.[<>]?(\d+)$/                   # (B, I) n..m
64       s = $1.to_i
65       e = $2.to_i
66       if e - s < 0
67 #       raise "Error: invalid range : #{location}"
68         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
69       end
70     when /^[<>]?(\d+)\^[<>]?(\d+)$/                     # (C, I) n^m
71       s = $1.to_i
72       e = $2.to_i
73       carat = true
74       if e - s != 1 or e != 1 # assert n^n+1 or n^1
75 #       raise "Error: invalid range : #{location}"
76         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
77       end
78     when /^"?([ATGCatgc]+)"?$/                  # (H) literal sequence
79       sequence = $1.downcase
80       s = e = nil
81     when nil
82       ;
83     else
84       raise "Error: unknown location format : #{location}"
85     end
86 
87     @from       = s             # start position of the location
88     @to         = e             # end position of the location
89     @strand     = 1             # strand direction of the location
90                                 #   forward => 1 or complement => -1
91     @sequence   = sequence      # literal sequence of the location
92     @lt         = lt            # true if the position contains '<'
93     @gt         = gt            # true if the position contains '>'
94     @xref_id    = xref_id       # link to the external entry as GenBank ID
95     @carat      = carat         # true if the location indicates the site
96                                 # between two adjoining nucleotides
97   end

Parses a’location’ segment, which can be ‘ID:’ + (‘n’ or ‘n..m’ or ‘n^m’ or “seq”) with ‘<’ or ‘>’, and returns a Bio::Location object.

location = Bio::Location.new('500..550')

Arguments:

(required) str: GenBank style position string (see Bio::Locations documentation)

Returns: the Bio::Location object

Public Instance Methods

<=> (other)

Source

    # File lib/bio/location.rb
163 def <=>(other)
164   if ! other.kind_of?(Bio::Location)
165     return nil
166   end
167 
168   if @from.to_f < other.from.to_f
169     return -1
170   elsif @from.to_f > other.from.to_f
171     return 1
172   end
173 
174   if @to.to_f < other.to.to_f
175     return -1
176   elsif @to.to_f > other.to.to_f
177     return 1
178   end
179   return 0
180 end

Check where a Bio::Location object is located compared to another Bio::Location object (mainly to facilitate the use of Comparable). A location A is upstream of location B if the start position of location A is smaller than the start position of location B. If they’re the same, the end positions are checked.

Arguments:

(required) _other location_: a Bio::Location object

Returns

1 if self < other location
-1 if self > other location
0 if both location are the same
nil if the argument is not a Bio::Location object

== (other)

Source

    # File lib/bio/location.rb
188 def ==(other)
189   return true if super(other)
190   return false unless other.instance_of?(self.class)
191   flag = false
192   [ :from, :to, :strand, :sequence, :lt, :gt,
193     :xref_id, :carat ].each do |m|
194     begin
195       flag = (self.__send__(m) == other.__send__(m))
196     rescue NoMethodError, ArgumentError, NameError
197       flag = false
198     end
199     break unless flag
200   end
201   flag
202 end

If other is equal with the self, returns true. Otherwise, returns false.

Arguments:

(required) other: any object

Returns: true or false

Calls superclass method

complement ()

Source

    # File lib/bio/location.rb
129 def complement
130   @strand *= -1
131   self                                        # return Location object
132 end

Complements the sequence location (i.e. alternates the strand). Note that it is destructive method (i.e. modifies itself), but it does not modify the “sequence” attribute.

Returns: the Bio::Location object

range ()

Source

    # File lib/bio/location.rb
146 def range
147   @from..@to
148 end

Returns the range (from..to) of the location as a Range object.

replace (sequence)

Source

    # File lib/bio/location.rb
140 def replace(sequence)
141   @sequence = sequence.downcase
142   self                                        # return Location object
143 end

Replaces the sequence of the location.

Arguments:

(required) sequence: sequence to be used to replace the sequence at the location

Returns: the Bio::Location object