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Contents
#
# = bio/shell/plugin/keggdas.rb - plugin for KEGG DAS
#
# Copyright:: Copyright (C) 2006
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
#
module Bio
class DAS
def list_sequences
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
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
Version data entries
29 entries across 29 versions & 6 rubygems