Class Bio::Feature
In: lib/bio/feature.rb
Parent: Object

DESCRIPTION

Container for the sequence annotation.

USAGE

 # Create a Bio::Feature object.
 # For example: the GenBank-formatted entry in genbank for accession M33388
 # contains the following feature:
 #    exon     1532..1799
 #             /gene="CYP2D6"
 #             /note="cytochrome P450 IID6; GOO-132-127"
 #             /number="1"
 feature = Bio::Feature.new('exon','1532..1799')
 feature.append(Bio::Feature::Qualifier.new('gene', 'CYP2D6'))
 feature.append(Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6'))
 feature.append(Bio::Feature::Qualifier.new('number', '1'))

 # or all in one go:
 feature2 = Bio::Feature.new('exon','1532..1799',
   [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
     Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6; GOO-132-127'),
     Bio::Feature::Qualifier.new('number', '1')
   ])

 # Print the feature
 puts feature.feature + "\t" + feature.position
 feature.each do |qualifier|
   puts "- " + qualifier.qualifier + ": " + qualifier.value
 end

REFERENCES

INSD feature table definition:www.ddbj.nig.ac.jp/FT/full_index.html

Methods

[]   append   assoc   each   locations   new   to_hash  

Classes and Modules

Class Bio::Feature::Qualifier

Attributes

feature  [RW]  Returns type of feature in String (e.g ‘CDS’, ‘gene’)
position  [RW]  Returns position of the feature in String (e.g. ‘complement(123..146)’)
qualifiers  [RW]  Returns an Array of Qualifier objects.

Public Class methods

new(feature = '', position = '', qualifiers = [])

Create a new Bio::Feature object. Arguments:

  • (required) feature: type of feature (e.g. "exon")
  • (required) position: position of feature (e.g. "complement(1532..1799)")
  • (opt) qualifiers: list of Bio::Feature::Qualifier objects (default: [])
Returns:Bio::Feature object

[Source]

    # File lib/bio/feature.rb, line 52
52:   def initialize(feature = '', position = '', qualifiers = [])
53:     @feature, @position, @qualifiers = feature, position, qualifiers
54:   end

Public Instance methods

[](key)

Short cut for the Bio::Feature#to_hash[key]

[Source]

     # File lib/bio/feature.rb, line 112
112:   def [](key)
113:     self.to_hash[key]
114:   end
append(a)

Appends a Qualifier object to the Feature.

Arguments:

Returns:Bio::Feature object

[Source]

    # File lib/bio/feature.rb, line 75
75:   def append(a)
76:     @qualifiers.push(a) if a.is_a? Qualifier
77:     return self
78:   end
assoc()

Returns a Hash constructed from qualifier objects.

[Source]

    # File lib/bio/feature.rb, line 92
92:   def assoc
93:     STDERR.puts "Bio::Feature#assoc is deprecated, use Bio::Feature#to_hash instead" if $DEBUG
94:     hash = Hash.new
95:     @qualifiers.each do |x|
96:       hash[x.qualifier] = x.value
97:     end
98:     return hash
99:   end
each(arg = nil) {|x| ...}

Iterates on each qualifier object.

Arguments:

  • (optional) key: if specified, only iterates over qualifiers with this key

[Source]

    # File lib/bio/feature.rb, line 84
84:   def each(arg = nil)
85:     @qualifiers.each do |x|
86:       next if arg and x.qualifier != arg
87:       yield x
88:     end
89:   end
locations()

Returns a Bio::Locations object translated from the position string.

[Source]

    # File lib/bio/feature.rb, line 66
66:   def locations
67:     Locations.new(@position)
68:   end
to_hash()

Returns a Hash constructed from qualifier objects.

[Source]

     # File lib/bio/feature.rb, line 102
102:   def to_hash
103:     hash = Hash.new
104:     @qualifiers.each do |x|
105:       hash[x.qualifier] ||= []
106:       hash[x.qualifier] << x.value
107:     end
108:     return hash
109:   end

[Validate]