class Bio::Features
DESCRIPTION¶ ↑
This class is OBSOLETED, and will soon be removed. Instead of this class, an array is to be used.
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
Attributes
Returns an Array of Feature objects.
Public Class Methods
This method should not be used. Only for backward compatibility of existing code.
Since Bio::Features is obsoleted, ::new not returns Bio::Features object, but modifies given ary and returns the ary.
Arguments:
-
(optional) __: Array of Bio::Feature objects
- Returns
-
the given array
# File lib/bio/compat/features.rb, line 98 def self.new(ary = []) warn 'Bio::Features is obsoleted. Some methods are added to given array to keep backward compatibility.' ary.extend(BackwardCompatibility) ary end
Normally, users can not call this method.
Create a new Bio::Features object.
Arguments:
-
(optional) _list of features_: list of Bio::Feature objects
- Returns
-
Bio::Features object
# File lib/bio/compat/features.rb, line 111 def initialize(ary = []) @features = ary end
Public Instance Methods
Short cut for the #features
# File lib/bio/compat/features.rb, line 140 def [](*arg) @features[*arg] end
Appends a Feature object to Features.
Arguments:
-
(required) feature: Bio::Feature object
- Returns
-
Bio::Features object
# File lib/bio/compat/features.rb, line 123 def append(a) @features.push(a) if a.is_a? Feature return self end
Iterates on each feature object.
Arguments:
-
(optional) key: if specified, only iterates over features with this key
# File lib/bio/compat/features.rb, line 132 def each(arg = nil) @features.each do |x| next if arg and x.feature != arg yield x end end
Short cut for the #features.first
# File lib/bio/compat/features.rb, line 145 def first @features.first end
Short cut for the #features.last
# File lib/bio/compat/features.rb, line 150 def last @features.last end