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#
# = sample/demo_go.rb - demonstration of Bio::DAS, BioDAS access module
#
# Copyright:: Copyright (C) 2003, 2004, 2007
# Shuichi Kawashima <shuichi@hgc.jp>,
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
#
# == Description
#
# Demonstration of Bio::GO, BioDAS access module.
#
# == Requirements
#
# Internet connection is needed.
#
# == Usage
#
# Simply run this script.
#
# $ ruby demo_das.rb
#
# == Notes
#
# Demo using the WormBase DAS server is temporarily disabled because
# it does not work well possibly because of the server trouble.
#
# == Development information
#
# The code was moved from lib/bio/io/das.rb and modified as below:
#
# * Demo codes using UCSC DAS server is added.
#
require 'bio'
# begin
# require 'pp'
# alias p pp
# rescue LoadError
# end
if false #disabled
puts "### WormBase"
wormbase = Bio::DAS.new('http://www.wormbase.org/db/')
puts ">>> test get_dsn"
p wormbase.get_dsn
puts ">>> create segment obj Bio::DAS::SEGMENT.region('I', 1, 1000)"
seg = Bio::DAS::SEGMENT.region('I', 1, 1000)
p seg
puts ">>> test get_dna"
p wormbase.get_dna('elegans', seg)
puts "### test get_features"
p wormbase.get_features('elegans', seg)
end #if false #disabled
if true #enabled
puts "### UCSC"
ucsc = Bio::DAS.new('http://genome.ucsc.edu/cgi-bin/')
puts ">>> test get_dsn"
p ucsc.get_dsn
puts ">>> test get_entry_points('hg19')"
p ucsc.get_entry_points('hg19')
puts ">>> test get_types('hg19')"
p ucsc.get_types('hg19')
len = rand(50) * 10 + 100
pos = rand(243199373 - len)
puts ">>> create segment obj Bio::DAS::SEGMENT.region('2', #{pos}, #{pos + len - 1})"
seg2 = Bio::DAS::SEGMENT.region('2', pos, pos + len - 1)
p seg2
puts ">>> test get_dna"
p ucsc.get_dna('hg19', seg2)
puts "### test get_features"
p ucsc.get_features('hg19', seg2)
end #if true #enabled
if true #enabled
puts "### KEGG DAS"
kegg_das = Bio::DAS.new("http://das.hgc.jp/cgi-bin/")
dsn_list = kegg_das.get_dsn
org_list = dsn_list.collect {|x| x.source}
puts ">>> dsn : entry_points"
org_list.each do |org|
print "#{org} : "
list = kegg_das.get_entry_points(org)
list.segments.each do |seg|
print " #{seg.entry_id}"
end
puts
end
end #if true #enabled
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