Class | Bio::Features |
In: |
lib/bio/compat/features.rb
|
Parent: | Object |
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.
# 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
features | [RW] | Returns an Array of Feature objects. |
Normally, users can not call this method.
Create a new Bio::Features object.
Arguments:
Returns: | Bio::Features object |
# File lib/bio/compat/features.rb, line 111 111: def initialize(ary = []) 112: @features = ary 113: end
This method should not be used. Only for backward compatibility of existing code.
Since Bio::Features is obsoleted, Bio::Features.new not returns Bio::Features object, but modifies given ary and returns the ary.
Arguments:
Returns: | the given array |
# File lib/bio/compat/features.rb, line 98 98: def self.new(ary = []) 99: warn 'Bio::Features is obsoleted. Some methods are added to given array to keep backward compatibility.' 100: ary.extend(BackwardCompatibility) 101: ary 102: end
Short cut for the Features#features[n]
# File lib/bio/compat/features.rb, line 140 140: def [](*arg) 141: @features[*arg] 142: end
Appends a Feature object to Features.
Arguments:
Returns: | Bio::Features object |
# File lib/bio/compat/features.rb, line 123 123: def append(a) 124: @features.push(a) if a.is_a? Feature 125: return self 126: end