DESCRIPTION

Container for a list of Feature objects.

USAGE

 # First, create some Bio::Feature objects
 feature1 = Bio::Feature.new('intron','3627..4059')
 feature2 = Bio::Feature.new('exon','4060..4236')
 feature3 = Bio::Feature.new('intron','4237..4426')
 feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',
                  [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
                    Bio::Feature::Qualifier.new('translation','MGXXTVMHLL...')
                  ])

 # And create a container for them
 feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])

 # Iterate over all features and print
 feature_container.each do |feature|
   puts feature.feature + "\t" + feature.position
   feature.each do |qualifier|
     puts "- " + qualifier.qualifier + ": " + qualifier.value
   end
 end

 # Iterate only over CDS features and extract translated amino acid sequences
 features.each("CDS") do |feature|
   hash = feature.to_hash
   name = hash["gene"] || hash["product"] || hash["note"]
   aaseq  = hash["translation"]
   pos  = feature.position
   if name and seq
     puts ">#{gene} #{feature.position}"
     puts aaseq
   end
 end

Methods

[] append each first last new

Attributes

features [RW] Returns an Array of Feature objects.

Public Class methods

new(ary = [])

Create a new Bio::Features object.

Arguments:

(optional) _list of features_: list of Bio::Feature objects

Returns:

Bio::Features object

[Source]

# File lib/bio/feature.rb, line 180
  def initialize(ary = [])
    @features = ary
  end

Public Instance methods

[](*arg)

Short cut for the Features#features[n]

[Source]

# File lib/bio/feature.rb, line 209
  def [](*arg)
    @features[*arg]
  end

append(a)

Appends a Feature object to Features.

Arguments:

(required) feature: Bio::Feature object

Returns:

Bio::Features object

[Source]

# File lib/bio/feature.rb, line 192
  def append(a)
    @features.push(a) if a.is_a? Feature
    return self
  end

each(arg = nil) {|x| ...}

Iterates on each feature object.

Arguments:

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

[Source]

# File lib/bio/feature.rb, line 201
  def each(arg = nil)
    @features.each do |x|
      next if arg and x.feature != arg
      yield x
    end
  end

first()

Short cut for the Features#features.first

[Source]

# File lib/bio/feature.rb, line 214
  def first
    @features.first
  end

last()

Short cut for the Features#features.last

[Source]

# File lib/bio/feature.rb, line 219
  def last
    @features.last
  end