Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.
# File lib/bio/db/kegg/orthology.rb, line 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, line 121 def dblinks_as_strings lines_fetch('DBLINKS') end
Returns DEFINITION field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 83 def definition field_fetch('DEFINITION') end
Returns ID of the entry.
# File lib/bio/db/kegg/orthology.rb, line 68 def entry_id field_fetch('ENTRY')[/\S+/] 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 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, line 126 def genes_as_strings lines_fetch('GENES') end
Returns CLASS field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 88 def keggclass field_fetch('CLASS') end
Returns an Array of biological classes in CLASS field.
# File lib/bio/db/kegg/orthology.rb, line 93 def keggclasses keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/) 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 |
# File lib/bio/db/kegg/orthology.rb, line 52 def modules_as_hash; super; end
Returns NAME field of the entry.
# File lib/bio/db/kegg/orthology.rb, line 73 def name field_fetch('NAME') end
Returns an Array of names in NAME field.
# File lib/bio/db/kegg/orthology.rb, line 78 def names name.split(', ') end
Returns a Hash of the pathway ID and name in PATHWAY field.
# File lib/bio/db/kegg/orthology.rb, line 43 def pathways_as_hash; super; 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 def pathways_in_keggclass keggclass.scan(/\[PATH:(.*?)\]/).flatten 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 def references; super; end
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