Class: Bio::KEGG::KGML

Inherits:
Object show all
Defined in:
lib/bio/db/kegg/kgml.rb

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

Instance Method Summary collapse

Constructor Details

#initialize(xml) ⇒ KGML

Returns a new instance of KGML.



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# 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.



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# File 'lib/bio/db/kegg/kgml.rb', line 122

def entries
  @entries
end

#image ⇒ Object (readonly)

Returns the value of attribute image.



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# File 'lib/bio/db/kegg/kgml.rb', line 121

def image
  @image
end

#link ⇒ Object (readonly)

Returns the value of attribute link.



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# File 'lib/bio/db/kegg/kgml.rb', line 121

def link
  @link
end

#name ⇒ Object (readonly)

Returns the value of attribute name.



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# File 'lib/bio/db/kegg/kgml.rb', line 121

def name
  @name
end

#number ⇒ Object (readonly)

Returns the value of attribute number.



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# File 'lib/bio/db/kegg/kgml.rb', line 121

def number
  @number
end

#org ⇒ Object (readonly)

Returns the value of attribute org.



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# File 'lib/bio/db/kegg/kgml.rb', line 121

def org
  @org
end

#reactions ⇒ Object

Returns the value of attribute reactions.



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# File 'lib/bio/db/kegg/kgml.rb', line 122

def reactions
  @reactions
end

#relations ⇒ Object

Returns the value of attribute relations.



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# File 'lib/bio/db/kegg/kgml.rb', line 122

def relations
  @relations
end

#title ⇒ Object (readonly)

Returns the value of attribute title.



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# File 'lib/bio/db/kegg/kgml.rb', line 121

def title
  @title
end