KEGGDB
Creates a new Bio::KEGG::MODULE object.
Arguments:
(required) entry: (String) single entry as a string
Returns |
Bio::KEGG::MODULE object |
# File lib/bio/db/kegg/module.rb, line 41 def initialize(entry) super(entry, TAGSIZE) end
Compounds described in the COMPOUND lines.
Returns |
Hash of compound ID and its definition |
# File lib/bio/db/kegg/module.rb, line 147 def compounds_as_hash unless @compounds_as_hash @compounds_as_hash = strings_as_hash(compounds_as_strings) end @compounds_as_hash end
Definition of the module, described in the DEFINITION line.
Returns |
# File lib/bio/db/kegg/module.rb, line 62 def definition field_fetch('DEFINITION') end
Return the ID, described in the ENTRY line.
Returns |
# File lib/bio/db/kegg/module.rb, line 48 def entry_id field_fetch('ENTRY')[/\S+/] end
Name of the module, described in the NAME line.
Returns |
# File lib/bio/db/kegg/module.rb, line 55 def name field_fetch('NAME') end
All KO IDs in the ORTHOLOGY lines.
Returns |
Array of orthology IDs |
# File lib/bio/db/kegg/module.rb, line 113 def orthologs_as_array orthologs_as_hash.keys.map{|x| x.split(/\+|\-|,/)}.flatten.sort.uniq end
Orthologs described in the ORTHOLOGY lines.
Returns |
Hash of orthology ID and its definition |
# File lib/bio/db/kegg/module.rb, line 102 def orthologs_as_hash unless @orthologs_as_hash @orthologs_as_hash = strings_as_hash(orthologs_as_strings) end @orthologs_as_hash end
Pathways described in the PATHWAY lines.
Returns |
Hash of pathway ID and its definition |
# File lib/bio/db/kegg/module.rb, line 83 def pathways_as_hash unless @pathways_as_hash @pathways_as_hash = strings_as_hash(pathways_as_strings) end @pathways_as_hash end
Reactions described in the REACTION lines.
Returns |
Hash of reaction ID and its definition |
# File lib/bio/db/kegg/module.rb, line 128 def reactions_as_hash unless @reactions_as_hash @reactions_as_hash = strings_as_hash(reactions_as_strings) end @reactions_as_hash end
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