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

$Id: genes.rb,v 0.26 2007/12/14 16:20:38 k Exp $

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.genes       # => Array
 p entry.gene        # => String

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

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

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

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

 # DBLINKS
 p entry.dblinks     # => Hash of 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