Method: Bio::DAS#get_sequence

Defined in:
lib/bio/io/das.rb

#get_sequence(dsn, segments) ⇒ Object

Returns an Array of Bio::DAS::SEQUENCE. The ‘dsn’ can be a String or a Bio::DAS::DSN object. The ‘segments’ can be a Bio::DAS::SEGMENT object or an Array of Bio::DAS::SEGMENT



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# File 'lib/bio/io/das.rb', line 135

def get_sequence(dsn, segments)
  ary = []

  dsn = dsn.source if dsn.instance_of?(DSN)
  segments = [segments] if segments.instance_of?(SEGMENT)

  opts = []
  segments.each do |s|
    opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
  end

  result = Bio::Command.post_form("#{@server}/das/#{dsn}/sequence", opts)
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::SEQUENCE') do |e|
    sequence = SEQUENCE.new
    sequence.entry_id = e.attributes['id']
    sequence.start = e.attributes['start']
    sequence.stop = e.attributes['stop']
    sequence.moltype = e.attributes['moltype']
    sequence.version = e.attributes['version']
    case sequence.moltype
    when /dna|rna/i		# 'DNA', 'ssRNA', 'dsRNA'
      sequence.sequence = Bio::Sequence::NA.new(e.text)
    when /protein/i		# 'Protein
      sequence.sequence = Bio::Sequence::AA.new(e.text)
    else
      sequence.sequence = e.text
    end
    ary << sequence
  end
  ary
end