class Bio::KEGG::ORTHOLOGY

Description

KO (KEGG Orthology) entry parser.

References

Constants

DELIMITER
TAGSIZE

Public Class Methods

new(entry) click to toggle source

Reads a flat file format entry of the KO database.

Calls superclass method Bio::NCBIDB::new
   # File lib/bio/db/kegg/orthology.rb
63 def initialize(entry)
64   super(entry, TAGSIZE)
65 end

Public Instance Methods

definition() click to toggle source

Returns DEFINITION field of the entry.

   # File lib/bio/db/kegg/orthology.rb
83 def definition
84   field_fetch('DEFINITION')
85 end
entry_id() click to toggle source

Returns ID of the entry.

   # File lib/bio/db/kegg/orthology.rb
68 def entry_id
69   field_fetch('ENTRY')[/\S+/]
70 end
genes()
Alias for: genes_as_hash
genes_as_hash() click to toggle source

Returns a Hash of the organism ID and an Array of entry IDs in GENES field.

   # File lib/bio/db/kegg/orthology.rb
38 def genes_as_hash; super; end
Also aliased as: genes
genes_as_strings() click to toggle source

Returns an Array of the organism ID and entry IDs in GENES field.

    # File lib/bio/db/kegg/orthology.rb
126 def genes_as_strings
127   lines_fetch('GENES')
128 end
keggclass() click to toggle source

Returns CLASS field of the entry.

   # File lib/bio/db/kegg/orthology.rb
88 def keggclass
89   field_fetch('CLASS')
90 end
keggclasses() click to toggle source

Returns an Array of biological classes in CLASS field.

   # File lib/bio/db/kegg/orthology.rb
93 def keggclasses
94   keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
95 end
modules()
Alias for: modules_as_hash
modules_as_hash() click to toggle source

Returns MODULE field as a Hash. Each key of the hash is KEGG MODULE ID, and each value is the name of the Pathway Module.


Returns

Hash

   # File lib/bio/db/kegg/orthology.rb
52 def modules_as_hash; super; end
Also aliased as: modules
modules_as_strings() click to toggle source

Returns MODULE field of the entry.


Returns

Array containing String objects

    # File lib/bio/db/kegg/orthology.rb
116 def modules_as_strings
117   lines_fetch('MODULE')
118 end
name() click to toggle source

Returns NAME field of the entry.

   # File lib/bio/db/kegg/orthology.rb
73 def name
74   field_fetch('NAME')
75 end
names() click to toggle source

Returns an Array of names in NAME field.

   # File lib/bio/db/kegg/orthology.rb
78 def names
79   name.split(', ')
80 end
pathways()
Alias for: pathways_as_hash
pathways_as_hash() click to toggle source

Returns a Hash of the pathway ID and name in PATHWAY field.

   # File lib/bio/db/kegg/orthology.rb
43 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathways described in the PATHWAY field.


Returns

Array containing String

    # File lib/bio/db/kegg/orthology.rb
100 def pathways_as_strings
101   lines_fetch('PATHWAY')
102 end
pathways_in_keggclass() click to toggle source

OBSOLETE Do not use this method. Because KEGG ORTHOLOGY format is changed and PATHWAY field is added, older “pathways” method is renamed and remain only for compatibility.

Returns an Array of KEGG/PATHWAY ID in CLASS field.

    # File lib/bio/db/kegg/orthology.rb
109 def pathways_in_keggclass
110   keggclass.scan(/\[PATH:(.*?)\]/).flatten
111 end
references() click to toggle source

REFERENCE – Returns contents of the REFERENCE records as an Array of Bio::Reference objects.


Returns

an Array containing Bio::Reference objects

   # File lib/bio/db/kegg/orthology.rb
60 def references; super; end