class Bio::KEGG::ORTHOLOGY
Description¶ ↑
KO (KEGG
Orthology) entry parser.
References
¶ ↑
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
Reads a flat file format entry of the KO database.
Bio::NCBIDB::new
# File lib/bio/db/kegg/orthology.rb 63 def initialize(entry) 64 super(entry, TAGSIZE) 65 end
Public Instance Methods
Returns a Hash of the DB
name and an Array of entry IDs in DBLINKS field.
Bio::KEGG::Common::DblinksAsHash#dblinks_as_hash
# File lib/bio/db/kegg/orthology.rb 33 def dblinks_as_hash; super; end
Returns an Array of a database name and entry IDs in DBLINKS field.
# File lib/bio/db/kegg/orthology.rb 121 def dblinks_as_strings 122 lines_fetch('DBLINKS') 123 end
Returns DEFINITION field of the entry.
# File lib/bio/db/kegg/orthology.rb 83 def definition 84 field_fetch('DEFINITION') 85 end
Returns ID of the entry.
# File lib/bio/db/kegg/orthology.rb 68 def entry_id 69 field_fetch('ENTRY')[/\S+/] 70 end
Returns a Hash of the organism ID and an Array of entry IDs in GENES
field.
Bio::KEGG::Common::GenesAsHash#genes_as_hash
# File lib/bio/db/kegg/orthology.rb 38 def genes_as_hash; super; end
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
Returns CLASS field of the entry.
# File lib/bio/db/kegg/orthology.rb 88 def keggclass 89 field_fetch('CLASS') 90 end
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
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
Bio::KEGG::Common::ModulesAsHash#modules_as_hash
# File lib/bio/db/kegg/orthology.rb 52 def modules_as_hash; super; end
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
Returns NAME field of the entry.
# File lib/bio/db/kegg/orthology.rb 73 def name 74 field_fetch('NAME') 75 end
Returns an Array of names in NAME field.
# File lib/bio/db/kegg/orthology.rb 78 def names 79 name.split(', ') 80 end
Returns a Hash of the pathway ID and name in PATHWAY
field.
Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash
# File lib/bio/db/kegg/orthology.rb 43 def pathways_as_hash; super; end
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
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
REFERENCE – Returns contents of the REFERENCE records as an Array of Bio::Reference
objects.
- Returns
-
an Array containing
Bio::Reference
objects
Bio::KEGG::Common::References#references
# File lib/bio/db/kegg/orthology.rb 60 def references; super; end