Class: Bio::KEGG::KGML
Overview
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
Defined Under Namespace
Classes: Entry, Reaction, Relation
Instance Attribute Summary collapse
-
#entries ⇒ Object
Returns the value of attribute entries.
-
#image ⇒ Object
readonly
Returns the value of attribute image.
-
#link ⇒ Object
readonly
Returns the value of attribute link.
-
#name ⇒ Object
readonly
Returns the value of attribute name.
-
#number ⇒ Object
readonly
Returns the value of attribute number.
-
#org ⇒ Object
readonly
Returns the value of attribute org.
-
#reactions ⇒ Object
Returns the value of attribute reactions.
-
#relations ⇒ Object
Returns the value of attribute relations.
-
#title ⇒ Object
readonly
Returns the value of attribute title.
Instance Method Summary collapse
-
#initialize(xml) ⇒ KGML
constructor
A new instance of KGML.
Constructor Details
#initialize(xml) ⇒ KGML
Returns a new instance of KGML.
114 115 116 117 118 119 120 |
# File 'lib/bio/db/kegg/kgml.rb', line 114 def initialize(xml) dom = REXML::Document.new(xml) parse_root(dom) parse_entry(dom) parse_relation(dom) parse_reaction(dom) end |
Instance Attribute Details
#entries ⇒ Object
Returns the value of attribute entries.
122 123 124 |
# File 'lib/bio/db/kegg/kgml.rb', line 122 def entries @entries end |
#image ⇒ Object (readonly)
Returns the value of attribute image.
121 122 123 |
# File 'lib/bio/db/kegg/kgml.rb', line 121 def image @image end |
#link ⇒ Object (readonly)
Returns the value of attribute link.
121 122 123 |
# File 'lib/bio/db/kegg/kgml.rb', line 121 def link @link end |
#name ⇒ Object (readonly)
Returns the value of attribute name.
121 122 123 |
# File 'lib/bio/db/kegg/kgml.rb', line 121 def name @name end |
#number ⇒ Object (readonly)
Returns the value of attribute number.
121 122 123 |
# File 'lib/bio/db/kegg/kgml.rb', line 121 def number @number end |
#org ⇒ Object (readonly)
Returns the value of attribute org.
121 122 123 |
# File 'lib/bio/db/kegg/kgml.rb', line 121 def org @org end |
#reactions ⇒ Object
Returns the value of attribute reactions.
122 123 124 |
# File 'lib/bio/db/kegg/kgml.rb', line 122 def reactions @reactions end |
#relations ⇒ Object
Returns the value of attribute relations.
122 123 124 |
# File 'lib/bio/db/kegg/kgml.rb', line 122 def relations @relations end |
#title ⇒ Object (readonly)
Returns the value of attribute title.
121 122 123 |
# File 'lib/bio/db/kegg/kgml.rb', line 121 def title @title end |