Bio::Feature

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

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 = []) click to toggle source

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

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

Public Instance Methods

[](key) click to toggle source

Short cut for the Bio::Feature#to_hash

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

append(a) click to toggle source

Appends a Qualifier object to the Feature.

Arguments:

(required) qualifier: Bio::Feature::Qualifier object

Returns

Bio::Feature object

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

assoc() click to toggle source

Returns a Hash constructed from qualifier objects.

# File lib/bio/feature.rb, line 92
def assoc
  STDERR.puts "Bio::Feature#assoc is deprecated, use Bio::Feature#to_hash instead" if $DEBUG
  hash = Hash.new
  @qualifiers.each do |x|
    hash[x.qualifier] = x.value
  end
  return hash
end

each(arg = nil) click to toggle source

Iterates on each qualifier object.

Arguments:

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

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

locations() click to toggle source

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

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

to_hash() click to toggle source

Returns a Hash constructed from qualifier objects.

# File lib/bio/feature.rb, line 102
def to_hash
  hash = Hash.new
  @qualifiers.each do |x|
    hash[x.qualifier] ||= []
    hash[x.qualifier] << x.value
  end
  return hash
end

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