Class: Bio::Features

Inherits:
Object
  • Object
show all
Defined in:
lib/feature.rb

Overview

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 || hash || hash aaseq = hash pos = feature.position if name and seq puts ">#gene #featurefeature.position" puts aaseq end end

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(ary = []) ⇒ Features

Create a new Bio::Features object.

Arguments:

  • (optional) list of features: list of Bio::Feature objects
Returns

Bio::Features object



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# File 'lib/feature.rb', line 161

def initialize(ary = [])
  @features = ary
end

Instance Attribute Details

#features ⇒ Object

Returns an Array of Feature objects.



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# File 'lib/feature.rb', line 166

def features
  @features
end

Instance Method Details

#[](*arg) ⇒ Object

Short cut for the Features#features



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# File 'lib/feature.rb', line 190

def [](*arg)
  @features[*arg]
end

#append(a) ⇒ Object

Appends a Feature object to Features.

Arguments:

  • (required) feature: Bio::Feature object
Returns

Bio::Features object



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# File 'lib/feature.rb', line 173

def append(a)
  @features.push(a) if a.is_a? Feature
  return self
end

#each(arg = nil) ⇒ Object

Iterates on each feature object.

Arguments:

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


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# File 'lib/feature.rb', line 182

def each(arg = nil)
  @features.each do |x|
    next if arg and x.feature != arg
    yield x
  end
end

#first ⇒ Object

Short cut for the Features#features.first



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# File 'lib/feature.rb', line 195

def first
  @features.first
end

#last ⇒ Object

Short cut for the Features#features.last



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# File 'lib/feature.rb', line 200

def last
  @features.last
end