class 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 51
def initialize(feature = '', position = '', qualifiers = [])
  @feature, @position, @qualifiers = feature, position, qualifiers
end

Public Instance Methods

[](key) click to toggle source

Short cut for the #to_hash

# File lib/bio/feature.rb, line 111
def [](key)
  self.to_hash[key]
end
append(a) click to toggle source

Appends a Qualifier object to the Feature.

Arguments:

Returns

Bio::Feature object

# File lib/bio/feature.rb, line 74
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 91
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) { |x| ... } 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 83
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 65
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 101
def to_hash
  hash = Hash.new
  @qualifiers.each do |x|
    hash[x.qualifier] ||= []
    hash[x.qualifier] << x.value
  end
  return hash
end