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 31 31: def initialize(entry) 32: super(entry, TAGSIZE) 33: end
Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.
# File lib/bio/db/kegg/orthology.rb, line 79 79: def dblinks_as_hash 80: hash = {} 81: dblinks.each do |line| 82: name, *list = line.split(/\s+/) 83: db = name.downcase.sub(/:/, '') 84: hash[db] = list 85: end 86: return hash 87: end
Returns DEFINITION field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 51 51: def definition 52: field_fetch('DEFINITION') 53: end
Returns ID of the entry.
# File lib/bio/db/kegg/orthology.rb, line 36 36: def entry_id 37: field_fetch('ENTRY')[/\S+/] 38: end
Returns a Hash of the organism ID and an Array of entry IDs in GENES field.
# File lib/bio/db/kegg/orthology.rb, line 98 98: def genes_as_hash 99: hash = {} 100: genes.each do |line| 101: name, *list = line.split(/\s+/) 102: org = name.downcase.sub(/:/, '') 103: genes = list.map {|x| x.sub(/\(.*\)/, '')} 104: #names = list.map {|x| x.scan(/.*\((.*)\)/)} 105: hash[org] = genes 106: end 107: return hash 108: end
Returns CLASS field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 56 56: def keggclass 57: field_fetch('CLASS') 58: end
Returns an Array of biological classes in CLASS field.
# File lib/bio/db/kegg/orthology.rb, line 61 61: def keggclasses 62: keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/) 63: end
Returns NAME field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 41 41: def name 42: field_fetch('NAME') 43: end