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|
#
# = sample/demo_go.rb - demonstration of Bio::GO, classes for Gene Ontology
#
# Copyright:: Copyright (C) 2003
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
#
# == Description
#
# Demonstration of Bio::GO, classes for Gene Ontology.
#
# == Requirement
#
# Internet connection is needed.
#
# == Usage
#
# Simply run this script.
#
# $ ruby demo_go.rb
#
# == Note
#
# The code was originally written in 2003, and it can only parse GO format
# that is deprecated and no new data is available after August 2009.
#
# == Development information
#
# The code was moved from lib/bio/db/go.rb.
#
require 'bio'
#if __FILE__ == $0
def wget(url)
Bio::Command.read_uri(url)
end
go_c_url = 'http://www.geneontology.org/ontology/component.ontology'
ga_url = 'http://www.geneontology.org/gene-associations/gene_association.sgd.gz'
e2g_url = 'http://www.geneontology.org/external2go/spkw2go'
puts "\n #==> Bio::GO::Ontology"
p go_c_url
component_ontology = wget(go_c_url)
comp = Bio::GO::Ontology.new(component_ontology)
[['0003673', '0005632'],
['0003673', '0005619'],
['0003673', '0004649']].each {|pair|
puts
p pair
p [:pair, pair.map {|i| [comp.id2term[i], comp.goid2term(i)] }]
puts "\n #==> comp.bfs_shortest_path(pair[0], pair[1])"
p comp.bfs_shortest_path(pair[0], pair[1])
}
puts "\n #==> Bio::GO::External2go"
p e2g_url
spkw2go = Bio::GO::External2go.parser(wget(e2g_url))
puts "\n #==> spkw2go.dbs"
p spkw2go.dbs
puts "\n #==> spkw2go[1]"
p spkw2go[1]
require 'zlib'
puts "\n #==> Bio::GO::GeenAssociation"
p ga_url
#
# The workaround (Zlib::MAX_WBITS + 32) is taken from:
# http://d.hatena.ne.jp/ksef-3go/20070924/1190563143
#
ga = Zlib::Inflate.new(Zlib::MAX_WBITS + 32).inflate(wget(ga_url))
#ga = Zlib::Inflate.inflate(wget(ga_url))
ga = Bio::GO::GeneAssociation.parser(ga)
puts "\n #==> ga.size"
p ga.size
puts "\n #==> ga[100]"
p ga[100]
#end
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