# genes.rb

Path: | lib/bio/db/kegg/genes.rb
Last Update: | Sat Sep 29 00:26:22 +0000 2012

# bio/db/kegg/genes.rb - KEGG/GENES database class

Copyright: | Copyright (C) 2001, 2002, 2006, 2010 Toshiaki Katayama <k@bioruby.org>
License: | The Ruby License

$Id:$

## KEGG GENES parser

See www.genome.jp/kegg/genes.html

### Examples

     require 'bio/io/fetch'
     entry_string = Bio::Fetch.query('genes', 'b0002')

     entry = Bio::KEGG::GENES.new(entry_string)

     # ENTRY
     p entry.entry       # => Hash

     p entry.entry_id    # => String
     p entry.division    # => String
     p entry.organism    # => String

     # NAME
     p entry.name        # => String
     p entry.names       # => Array

     # DEFINITION
     p entry.definition  # => String
     p entry.eclinks     # => Array

     # PATHWAY
     p entry.pathway     # => String
     p entry.pathways    # => Hash

     # POSITION
     p entry.position    # => String
     p entry.chromosome  # => String
     p entry.gbposition  # => String
     p entry.locations   # => Bio::Locations

     # MOTIF
     p entry.motifs      # => Hash of Array

     # DBLINKS
     p entry.dblinks     # => Hash of Array

     # STRUCTURE
     p entry.structure   # => Array

     # CODON_USAGE
     p entry.codon_usage # => Hash
     p entry.cu_list     # => Array

     # AASEQ
     p entry.aaseq       # => Bio::Sequence::AA
     p entry.aalen       # => Fixnum

     # NTSEQ
     p entry.ntseq       # => Bio::Sequence::NA
     p entry.naseq       # => Bio::Sequence::NA
     p entry.ntlen       # => Fixnum
     p entry.nalen       # => Fixnum

### Required files

bio/db bio/db/kegg/common

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