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#
# = bio/feature.rb - Features/Feature class (GenBank Feature table)
#
# Copyright:: Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org>
# 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
# License:: The Ruby License
#
module Bio
autoload :Locations, 'bio/location' unless const_defined?(:Locations)
# = DESCRIPTION
# Container for the sequence annotation.
#
# = USAGE
# # 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
#
# = REFERENCES
# INSD feature table definition:: http://www.ddbj.nig.ac.jp/FT/full_index.html
class Feature
# 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
def initialize(feature = '', position = '', qualifiers = [])
@feature, @position, @qualifiers = feature, position, qualifiers
end
# Returns type of feature in String (e.g 'CDS', 'gene')
attr_accessor :feature
# Returns position of the feature in String (e.g. 'complement(123..146)')
attr_accessor :position
# Returns an Array of Qualifier objects.
attr_accessor :qualifiers
# Returns a Bio::Locations object translated from the position string.
def locations
Locations.new(@position)
end
# Appends a Qualifier object to the Feature.
#
# *Arguments*:
# * (required) _qualifier_: Bio::Feature::Qualifier object
# *Returns*:: Bio::Feature object
def append(a)
@qualifiers.push(a) if a.is_a? Qualifier
return self
end
# Iterates on each qualifier object.
#
# *Arguments*:
# * (optional) _key_: if specified, only iterates over qualifiers with this key
def each(arg = nil)
@qualifiers.each do |x|
next if arg and x.qualifier != arg
yield x
end
end
# Returns a Hash constructed from qualifier objects.
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
# Returns a Hash constructed from qualifier objects.
def to_hash
hash = Hash.new
@qualifiers.each do |x|
hash[x.qualifier] ||= []
hash[x.qualifier] << x.value
end
return hash
end
# Short cut for the Bio::Feature#to_hash[key]
def [](key)
self.to_hash[key]
end
# Container for qualifier-value pairs for sequence features.
class Qualifier
# Creates a new Bio::Feature::Qualifier object
#
# *Arguments*:
# * (required) _key_: key of the qualifier (e.g. "gene")
# * (required) _value_: value of the qualifier (e.g. "CYP2D6")
# *Returns*:: Bio::Feature::Qualifier object
def initialize(key, value)
@qualifier, @value = key, value
end
# Qualifier name in String
attr_reader :qualifier
# Qualifier value in String
attr_reader :value
end #Qualifier
end #Feature
end # Bio
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