Class: Bio::Location

Inherits:
Object show all
Includes:
Comparable
Defined in:
lib/bio/location.rb

Overview

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(location = nil) ⇒ Location

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



45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
 
# File 'lib/bio/location.rb', line 45

def initialize(location = nil)

  if location
    if location =~ /:/				# (G) ID:location
      xref_id, location = location.split(':')
    end
    if location =~ /</				# (I) <,>
      lt = true
    end
    if location =~ />/
      gt = true
    end
  end

  # s : start base, e : end base => from, to
  case location
  when /^[<>]?(\d+)$/					# (A, I) n
    s = e = $1.to_i
  when /^[<>]?(\d+)\.\.[<>]?(\d+)$/			# (B, I) n..m
    s = $1.to_i
    e = $2.to_i
    if e - s < 0
#       raise "Error: invalid range : #{location}"
      $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
    end
  when /^[<>]?(\d+)\^[<>]?(\d+)$/			# (C, I) n^m
    s = $1.to_i
    e = $2.to_i
    carat = true
    if e - s != 1 or e != 1 # assert n^n+1 or n^1
#       raise "Error: invalid range : #{location}"
      $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
    end
  when /^"?([ATGCatgc]+)"?$/                  # (H) literal sequence
    sequence = $1.downcase
    s = e = nil
  when nil
    ;
  else
    raise "Error: unknown location format : #{location}"
  end

  @from       = s             # start position of the location
  @to         = e             # end position of the location
  @strand     = 1             # strand direction of the location
                              #   forward => 1 or complement => -1
  @sequence   = sequence      # literal sequence of the location
  @lt         = lt            # true if the position contains '<'
  @gt         = gt            # true if the position contains '>'
  @xref_id    = xref_id       # link to the external entry as GenBank ID
  @carat      = carat         # true if the location indicates the site
                              # between two adjoining nucleotides
end

Instance Attribute Details

#carat ⇒ Object

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



122
123
124
 
# File 'lib/bio/location.rb', line 122

def carat
  @carat
end

#from ⇒ Object

(Integer) start position of the location



100
101
102
 
# File 'lib/bio/location.rb', line 100

def from
  @from
end

#gt ⇒ Object

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



115
116
117
 
# File 'lib/bio/location.rb', line 115

def gt
  @gt
end

#lt ⇒ Object

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



112
113
114
 
# File 'lib/bio/location.rb', line 112

def lt
  @lt
end

#sequence ⇒ Object

(String) literal sequence of the location



109
110
111
 
# File 'lib/bio/location.rb', line 109

def sequence
  @sequence
end

#strand ⇒ Object

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



106
107
108
 
# File 'lib/bio/location.rb', line 106

def strand
  @strand
end

#to ⇒ Object

(Integer) end position of the location



102
103
104
 
# File 'lib/bio/location.rb', line 102

def to
  @to
end

#xref_id ⇒ Object

(String) link to the external entry as GenBank ID



118
119
120
 
# File 'lib/bio/location.rb', line 118

def xref_id
  @xref_id
end

Instance Method Details

#<=>(other) ⇒ Object

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



163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
 
# File 'lib/bio/location.rb', line 163

def <=>(other)
  if ! other.kind_of?(Bio::Location)
    return nil
  end

  if @from.to_f < other.from.to_f
    return -1
  elsif @from.to_f > other.from.to_f
    return 1
  end

  if @to.to_f < other.to.to_f
    return -1
  elsif @to.to_f > other.to.to_f
    return 1
  end
  return 0
end

#==(other) ⇒ Object

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

Arguments:

  • (required) other: any object

Returns

true or false



188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
 
# File 'lib/bio/location.rb', line 188

def ==(other)
  return true if super(other)
  return false unless other.instance_of?(self.class)
  flag = false
  [ :from, :to, :strand, :sequence, :lt, :gt,
    :xref_id, :carat ].each do |m|
    begin
      flag = (self.__send__(m) == other.__send__(m))
    rescue NoMethodError, ArgumentError, NameError
      flag = false
    end
    break unless flag
  end
  flag
end

#complement ⇒ Object

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



129
130
131
132
 
# File 'lib/bio/location.rb', line 129

def complement
  @strand *= -1
  self					# return Location object
end

#range ⇒ Object

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



146
147
148
 
# File 'lib/bio/location.rb', line 146

def range
  @from..@to
end

#replace(sequence) ⇒ Object

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



140
141
142
143
 
# File 'lib/bio/location.rb', line 140

def replace(sequence)
  @sequence = sequence.downcase
  self					# return Location object
end