KGML (KEGG XML) parser

See www.genome.jp/kegg/xml/ for more details on KGML.

Incompatible attribute names with KGML tags

<entry>

 :id -> :entry_id
 :type -> :category
 :map -> :pathway
 names()
 <graphics>
 :name -> :label
 :type -> :shape

<relation>

 :entry1 -> :node1
 :entry2 -> :node2
 :type -> :rel
 <subtype>
 edge()

<reaction>

 :name -> :entry_id
 :type -> :direction

Examples

 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.entry_id
   puts entry.name
   puts entry.category
   puts entry.link
   puts entry.reaction
   puts entry.pathway
   # <graphics> attributes
   puts entry.label         # name
   puts entry.shape         # type
   puts entry.x
   puts entry.y
   puts entry.width
   puts entry.height
   puts entry.fgcolor
   puts entry.bgcolor
   # <component> attributes
   puts entry.components
   # methood
   puts entry.names
 end

 kgml.relations.each do |relation|
   # <relation> attributes
   puts relation.node1      # entry1
   puts relation.node2      # entry2
   puts relation.rel        # type
   # method
   puts relation.edge
   # <subtype> attributes
   puts relation.name
   puts relation.value
 end

 kgml.reactions.each do |reaction|
   # <reaction> attributes
   puts reaction.entry_id   # name
   puts reaction.direction  # type
   # <substrate> attributes
   reaction.substrates.each do |entry_id|
     puts entry_id
     # <alt> attributes
     altnames = reaction.alt[entry_id]
     altnames.each do |name|
       puts name
     end
   end
   # <product> attributes
   reaction.products.each do |entry_id|
     puts entry_id
     # <alt> attributes
     altnames = reaction.alt[entry_id]
     altnames.each do |name|
       puts name
     end
   end
 end