See www.genome.jp/kegg/xml/ for more details on KGML.
Most of incompatible attribute names with KGML tags are now deprecated. Use the names of KGML tags instead of old incompatible names that will be removed in the future.
Bio::KGML::Entry#id (entry_id is deprecated)
Bio::KGML::Entry#type (category is deprecated)
Bio::KGML::Relation#entry1 (node1 is deprecated)
Bio::KGML::Relation#entry2 (node2 is deprecated)
Bio::KGML::Relation#type (rel is deprecated)
Bio::KGML::Reaction#name (entry_id is deprecated)
Bio::KGML::Reaction#type (direction is deprecated)
New class Bio::KGML::Graphics and new method Bio::KGML::Entry#graphics. Because two or more graphics elements may exist, following attribute methods in Bio::KGML::Entry are now deprecated and will be removed in the future. See rdoc of these methods for details.
Incompatible changes: Bio::KEGG::KGML::Reaction#substrates now returns an array containing Bio::KEGG::KGML::Substrate objects, and Bio::KEGG::KGML::Reaction#products now returns an array containing Bio::KEGG::KGML::Product objects. The changes enable us to get id of substrates and products.
<entry> :map -> :pathway names() <subtype> edge()
file = File.read("kgml/hsa/hsa00010.xml") kgml = Bio::KEGG::KGML.new(file) # <pathway> attributes puts kgml.name puts kgml.org puts kgml.number puts kgml.title puts kgml.image puts kgml.link kgml.entries.each do |entry| # <entry> attributes puts entry.id puts entry.name puts entry.type puts entry.link puts entry.reaction # <graphics> attributes entry.graphics.each do |graphics| puts graphics.name puts graphics.type puts graphics.x puts graphics.y puts graphics.width puts graphics.height puts graphics.fgcolor puts graphics.bgcolor end # <component> attributes puts entry.components # methood puts entry.names end kgml.relations.each do |relation| # <relation> attributes puts relation.entry1 puts relation.entry2 puts relation.type # <subtype> attributes puts relation.name puts relation.value end kgml.reactions.each do |reaction| # <reaction> attributes puts reaction.name puts reaction.type # <substrate> attributes reaction.substrates.each do |substrate| puts substrate.id puts substrate.name # <alt> attributes altnames = reaction.alt[entry_id] altnames.each do |name| puts name end end # <product> attributes reaction.products.each do |product| puts product.id puts product.name # <alt> attributes altnames = reaction.alt[entry_id] altnames.each do |name| puts name end end end
Creates a new KGML object.
Arguments:
(required) str: String containing xml data
Returns |
Bio::KEGG::KGML object |
# File lib/bio/db/kegg/kgml.rb, line 141 def initialize(xml) dom = REXML::Document.new(xml) parse_root(dom) parse_entry(dom) parse_relation(dom) parse_reaction(dom) end
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