class Bio::KEGG::KGML
KGML
(KEGG
XML) parser¶ ↑
See www.genome.jp/kegg/xml/ for more details on KGML
.
Note for older version users¶ ↑
-
Most of incompatible attribute names with
KGML
tags are now deprecated. Use the names ofKGML
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 containingBio::KEGG::KGML::Substrate
objects, andBio::KEGG::KGML::Reaction#products
now returns an array containingBio::KEGG::KGML::Product
objects. The changes enable us to get id of substrates and products.
Incompatible attribute names with KGML
tags¶ ↑
<entry> :map -> :pathway names() <subtype> edge()
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.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
References
¶ ↑
Attributes
entry elements (Array containing KGML::Entry
objects, or nil)
image URL of this pathway map (String or nil) (‘pathway’ element)
information URL of this pathway map (String or nil) (‘pathway’ element)
KEGG-style ID string of this pathway map (String or nil) (‘pathway’ element)
map number (String or nil) (‘pathway’ element)
reaction elements (Array containing KGML::Reactions objects, or nil)
relation elements (Array containing KGML::Relations objects, or nil)
title (String or nil) (‘pathway’ element)
Public Class Methods
Creates a new KGML
object.
Arguments:
-
(required) str: String containing xml data
- Returns
-
Bio::KEGG::KGML
object
# File lib/bio/db/kegg/kgml.rb 141 def initialize(xml) 142 dom = REXML::Document.new(xml) 143 parse_root(dom) 144 parse_entry(dom) 145 parse_relation(dom) 146 parse_reaction(dom) 147 end