Method: Bio::DAS#get_features

Defined in:

lib/bio/io/das.rb

#get_features(dsn, segments = [], categorize = false, feature_ids = [], group_ids = []) ⇒ Object

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

# File 'lib/bio/io/das.rb', line 214

def get_features(dsn, segments = [], categorize = false, feature_ids = [], group_ids = [])
  # arguments 'type' and 'category' are deprecated
  gff = GFF.new

  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
  if categorize
    opts << "categorize=yes"  # default is 'no'
  end
  feature_ids.each do |fid|
    opts << "feature_id=#{fid}"
  end
  group_ids.each do |gid|
    opts << "group_id=#{gid}"
  end

  result, = Bio::Command.post_form("#{@server}/das/#{dsn}/features", opts)
  doc = REXML::Document.new(result.body)
  doc.elements.each('/descendant::GFF') do |e|
    gff.version = e.attributes['version']
    gff.href = e.attributes['href']
    e.elements.each('SEGMENT') do |e|
      segment = SEGMENT.new
      segment.entry_id = e.attributes['id']
      segment.start = e.attributes['start']
      segment.stop = e.attributes['stop']
      segment.version = e.attributes['version']
      segment.label = e.attributes['label']
      e.elements.each do |e|
        feature = FEATURE.new
        feature.entry_id = e.attributes['id']
        feature.label = e.attributes['label']
        e.elements.each do |e|
          case e.name
          when 'TYPE'
            type = TYPE.new
            type.entry_id = e.attributes['id']
            type.category = e.attributes['category']
            type.reference = e.attributes['referrence']
            type.label = e.text
            feature.types << type
          when 'METHOD'
            feature.method_id = e.attributes['id']
            feature.method = e.text
          when 'START'
            feature.start = e.text
          when 'STOP', 'END'
            feature.stop = e.text
          when 'SCORE'
            feature.score = e.text
          when 'ORIENTATION'
            feature.orientation = e.text
          when 'PHASE'
            feature.phase = e.text
          when 'NOTE'
            feature.notes << e.text
          when 'LINK'
            link = LINK.new
            link.href = e.attributes['href']
            link.text = e.text
            feature.links << link
          when 'TARGET'
            target = TARGET.new
            target.entry_id = e.attributes['id']
            target.start = e.attributes['start']
            target.stop = e.attributes['stop']
            target.name = e.text
            feature.targets << target
          when 'GROUP'
            group = GROUP.new
            group.entry_id = e.attributes['id']
            group.label = e.attributes['label']
            group.type = e.attributes['type']
            e.elements.each do |e|
              case e.name
              when 'NOTE'   # in GROUP
                group.notes << e.text
              when 'LINK'   # in GROUP
                link = LINK.new
                link.href = e.attributes['href']
                link.text = e.text
                group.links << link
              when 'TARGET'   # in GROUP
                target = TARGET.new
                target.entry_id = e.attributes['id']
                target.start = e.attributes['start']
                target.stop = e.attributes['stop']
                target.name = e.text
                group.targets << target
              end
            end
            feature.groups << group
          end
        end
        segment.features << feature
      end
      gff.segments << segment
    end
  end
  gff
end