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#!/usr/bin/env ruby
#
# genome2tab.rb - convert KEGG/GENOME into tab delimited data for MySQL
#
# Usage:
#
# % genome2tab.rb /bio/db/kegg/genome/genome > genome.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: genome2tab.rb,v 0.5 2002/06/23 20:21:56 k Exp $
#
require 'bio/db/kegg/genome'
include Bio
while entry = gets(KEGG::GENOME::DELIMITER)
genome = KEGG::GENOME.new(entry)
ref = genome.references.inspect
chr = genome.chromosomes.inspect
ary = [
genome.entry_id,
genome.name,
genome.definition,
genome.taxid,
genome.taxonomy,
genome.comment,
ref,
chr,
genome.nalen,
genome.num_gene,
genome.num_rna,
genome.gc,
genome.genomemap,
]
puts ary.join("\t")
end
=begin
CREATE DATABASE IF NOT EXISTS db_name;
CREATE TABLE IF NOT EXISTS db_name.genome (
id varchar(30) not NULL,
name varchar(80),
definition varchar(255),
taxid varchar(30),
taxonomy varchar(255),
comment varchar(255),
reference text,
chromosome text,
nalen integer,
num_gene integer,
num_rna integer,
gc float,
genomemap varchar(30),
);
LOAD DATA LOCAL INFILE 'genome.tab' INTO TABLE db_name.genome;
=end
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