Class: Scaffolder::Test::Sequence

Inherits:
Object
  • Object
show all
Defined in:
lib/scaffolder/test/sequence.rb

Instance Method Summary collapse

Constructor Details

#initialize(options = {}) ⇒ Sequence

Returns a new instance of Sequence.



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# File 'lib/scaffolder/test/sequence.rb', line 6

def initialize(options = {})
  @options = options
end

Instance Method Details

#initialize_copy(source) ⇒ Object 



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# File 'lib/scaffolder/test/sequence.rb', line 10

def initialize_copy(source)
  super
  @options = @options.dup
end

#inserts(arg = nil) ⇒ Object 



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# File 'lib/scaffolder/test/sequence.rb', line 25

def inserts(arg = nil)
  return @options[:inserts] if arg.nil?
  @options[:inserts] ||= Array.new
  if arg.instance_of?(Array)
   arg.each {|a| @options[:inserts] << a}
  else
    @options[:inserts] << arg
  end
  return self
end

#to_fasta ⇒ Object 



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# File 'lib/scaffolder/test/sequence.rb', line 47

def to_fasta
  fasta = Bio::Sequence.new(sequence).output(:fasta,:header => name)
  inserts.each_with_index do |insert,i|
    fasta << Bio::Sequence.new(insert[:sequence]).output(:fasta,:header => "insert#{i+1}")
  end if inserts
  fasta.strip
end

#to_hash ⇒ Object 



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# File 'lib/scaffolder/test/sequence.rb', line 36

def to_hash
  hash = {'source' => name}.merge stringify_keys(@options)
  if @options[:inserts]
    hash['inserts'] = Array.new
    @options[:inserts].each_with_index do |insert,i|
      hash['inserts'] << {'source' => "insert#{i+1}"}.merge(stringify_keys(insert))
    end
  end
  {'sequence' => hash}
end