Class Bio::Features
In: lib/feature.rb
Parent: Object

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

Create a new Bio::Features object.

Arguments:

Returns:Bio::Features object

Public Instance methods

Short cut for the Features#features[n]

Appends a Feature object to Features.

Arguments:

Returns:Bio::Features object

Iterates on each feature object.

Arguments:

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

Short cut for the Features#features.first

Short cut for the Features#features.last

[Validate]