Class | Bio::KEGG::ORTHOLOGY |
In: |
lib/bio/db/kegg/orthology.rb
|
Parent: | KEGGDB |
DELIMITER | = | RS = "\n///\n" |
TAGSIZE | = | 12 |
Reads a flat file format entry of the KO database.
# File lib/bio/db/kegg/orthology.rb, line 63 63: def initialize(entry) 64: super(entry, TAGSIZE) 65: end
Returns DEFINITION field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 83 83: def definition 84: field_fetch('DEFINITION') 85: end
Returns ID of the entry.
# File lib/bio/db/kegg/orthology.rb, line 68 68: def entry_id 69: field_fetch('ENTRY')[/\S+/] 70: end
Returns CLASS field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 88 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, line 93 93: def keggclasses 94: keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/) 95: end
Returns NAME field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 73 73: def name 74: field_fetch('NAME') 75: 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, line 109 109: 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 |
# File lib/bio/db/kegg/orthology.rb, line 60 60: def references; super; end