Container for the sequence annotation.
# 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
INSD feature table definition |
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
Short cut for the Bio::Feature#to_hash
# File lib/bio/feature.rb, line 111 def [](key) self.to_hash[key] end
Appends a Qualifier object to the Feature.
Arguments:
(required) qualifier: Bio::Feature::Qualifier object
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
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
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
Returns a Bio::Locations object translated from the position string.
# File lib/bio/feature.rb, line 65 def locations Locations.new(@position) end
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
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