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#!/usr/bin/env ruby
#
# genes2tab.rb - convert KEGG/GENES into tab delimited data for MySQL
#
# Usage:
#
# % genes2tab.rb /bio/db/kegg/genes/e.coli > genes_eco.tab
#
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# $Id: genes2tab.rb,v 0.5 2002/06/23 20:21:56 k Exp $
#
require 'bio/db/kegg/genes'
include Bio
while entry = gets(KEGG::GENES::DELIMITER)
genes = KEGG::GENES.new(entry)
db = genes.dblinks.inspect
if genes.codon_usage.length == 64
cu = genes.codon_usage.join(' ')
else
cu = '\N'
end
ary = [
genes.entry_id,
genes.division,
genes.organism,
genes.name,
genes.definition,
genes.keggclass,
genes.position,
db,
cu,
genes.aalen,
genes.aaseq,
genes.nalen,
genes.naseq
]
puts ary.join("\t")
end
=begin
CREATE DATABASE IF NOT EXISTS db_name;
CREATE TABLE IF NOT EXISTS db_name.genes (
id varchar(30) not NULL, # ENTRY ID
division varchar(30), # CDS, tRNA etc.
organism varchar(255),
gene varchar(255),
definition varchar(255),
keggclass varchar(255),
position varchar(255),
dblinks varchar(255),
codon_usage text,
aalen integer,
aaseq text,
nalen integer,
naseq text
);
LOAD DATA LOCAL INFILE 'genes.tab' INTO TABLE db_name.genes;
=end
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