[BioRuby-cvs] bioruby/lib/bio/shell/plugin das.rb,NONE,1.1

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory dev.open-bio.org:/tmp/cvs-serv7731/shell/plugin

Added Files:
	das.rb 
Log Message:
* newly added BioDAS client plugin


--- NEW FILE: das.rb ---
#
# = bio/shell/plugin/keggdas.rb - plugin for KEGG DAS
#
# Copyright::   Copyright (C) 2006
#               Toshiaki Katayama <k at bioruby.org>
# License::     Ruby's
#
# $Id: das.rb,v 1.1 2007/03/28 16:52:20 k Exp $
#

module Bio

  class DAS
    def list(serv = nil)
      result = ""
      self.get_dsn.each do |dsn|
        src = dsn.source_id
        self.get_entry_points(src).each do |ep|
          data = [src, ep.entry_id, ep.start.to_i, ep.stop.to_i, "# #{ep.description}"].join("\t") + "\n"
          puts data
          result += data
        end
      end
      return result
    end

    def dna(dsn, entry_point, start, stop)
      seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
      self.get_dna(dsn, seg).first.sequence
    end

    def features(dsn, entry_point, start, stop)
      seg = Bio::DAS::SEGMENT.region(entry_point, start, stop)
      self.get_features(dsn, seg)
    end
  end

end

module Bio::Shell

  private

  # http://www.biodas.org/
  # http://www.dasregistry.org/

  def das(url = nil)
    if url
      @das = Bio::DAS.new(url)
    else
      @das ||= keggdas
    end
  end

  def keggdas(url = "http://das.hgc.jp/cgi-bin/")
    das(url)
  end

  def ensembl(url = "http://das.ensembl.org/")
    das(url)
  end

  def wormbase(url = "http://www.wormbase.org/db/")
    das(url)
  end

end