RubyGems - bio - Versions diffs - 0.7.0 - Mend

bio 0.7.0

Files changed (201) hide show

data/bin/bioruby +107 -0
data/bin/br_biofetch.rb +59 -0
data/bin/br_bioflat.rb +294 -0
data/bin/br_biogetseq.rb +57 -0
data/bin/br_pmfetch.rb +431 -0
data/doc/BioRuby.rd.ja +225 -0
data/doc/Changes-0.7.rd +236 -0
data/doc/Design.rd.ja +341 -0
data/doc/KEGG_API.rd +1437 -0
data/doc/KEGG_API.rd.ja +1399 -0
data/doc/TODO.rd.ja +138 -0
data/doc/Tutorial.rd +1138 -0
data/doc/Tutorial.rd.ja +2110 -0
data/etc/bioinformatics/seqdatabase.ini +210 -0
data/lib/bio.rb +256 -0
data/lib/bio/alignment.rb +1906 -0
data/lib/bio/appl/bl2seq/report.rb +350 -0
data/lib/bio/appl/blast.rb +269 -0
data/lib/bio/appl/blast/format0.rb +1402 -0
data/lib/bio/appl/blast/format8.rb +95 -0
data/lib/bio/appl/blast/report.rb +652 -0
data/lib/bio/appl/blast/rexml.rb +151 -0
data/lib/bio/appl/blast/wublast.rb +553 -0
data/lib/bio/appl/blast/xmlparser.rb +222 -0
data/lib/bio/appl/blat/report.rb +392 -0
data/lib/bio/appl/clustalw.rb +191 -0
data/lib/bio/appl/clustalw/report.rb +154 -0
data/lib/bio/appl/emboss.rb +68 -0
data/lib/bio/appl/fasta.rb +262 -0
data/lib/bio/appl/fasta/format10.rb +428 -0
data/lib/bio/appl/fasta/format6.rb +37 -0
data/lib/bio/appl/genscan/report.rb +570 -0
data/lib/bio/appl/hmmer.rb +129 -0
data/lib/bio/appl/hmmer/report.rb +556 -0
data/lib/bio/appl/mafft.rb +222 -0
data/lib/bio/appl/mafft/report.rb +119 -0
data/lib/bio/appl/psort.rb +555 -0
data/lib/bio/appl/psort/report.rb +473 -0
data/lib/bio/appl/sim4.rb +134 -0
data/lib/bio/appl/sim4/report.rb +501 -0
data/lib/bio/appl/sosui/report.rb +166 -0
data/lib/bio/appl/spidey/report.rb +604 -0
data/lib/bio/appl/targetp/report.rb +283 -0
data/lib/bio/appl/tmhmm/report.rb +238 -0
data/lib/bio/command.rb +166 -0
data/lib/bio/data/aa.rb +354 -0
data/lib/bio/data/codontable.rb +740 -0
data/lib/bio/data/na.rb +226 -0
data/lib/bio/db.rb +340 -0
data/lib/bio/db/aaindex.rb +280 -0
data/lib/bio/db/embl/common.rb +332 -0
data/lib/bio/db/embl/embl.rb +446 -0
data/lib/bio/db/embl/sptr.rb +954 -0
data/lib/bio/db/embl/swissprot.rb +32 -0
data/lib/bio/db/embl/trembl.rb +31 -0
data/lib/bio/db/embl/uniprot.rb +32 -0
data/lib/bio/db/fantom.rb +604 -0
data/lib/bio/db/fasta.rb +869 -0
data/lib/bio/db/genbank/common.rb +299 -0
data/lib/bio/db/genbank/ddbj.rb +34 -0
data/lib/bio/db/genbank/genbank.rb +354 -0
data/lib/bio/db/genbank/genpept.rb +73 -0
data/lib/bio/db/genbank/refseq.rb +31 -0
data/lib/bio/db/gff.rb +106 -0
data/lib/bio/db/go.rb +497 -0
data/lib/bio/db/kegg/brite.rb +51 -0
data/lib/bio/db/kegg/cell.rb +88 -0
data/lib/bio/db/kegg/compound.rb +130 -0
data/lib/bio/db/kegg/enzyme.rb +125 -0
data/lib/bio/db/kegg/expression.rb +173 -0
data/lib/bio/db/kegg/genes.rb +293 -0
data/lib/bio/db/kegg/genome.rb +362 -0
data/lib/bio/db/kegg/glycan.rb +213 -0
data/lib/bio/db/kegg/keggtab.rb +418 -0
data/lib/bio/db/kegg/kgml.rb +299 -0
data/lib/bio/db/kegg/ko.rb +178 -0
data/lib/bio/db/kegg/reaction.rb +97 -0
data/lib/bio/db/litdb.rb +131 -0
data/lib/bio/db/medline.rb +317 -0
data/lib/bio/db/nbrf.rb +199 -0
data/lib/bio/db/pdb.rb +38 -0
data/lib/bio/db/pdb/atom.rb +60 -0
data/lib/bio/db/pdb/chain.rb +117 -0
data/lib/bio/db/pdb/model.rb +106 -0
data/lib/bio/db/pdb/pdb.rb +1682 -0
data/lib/bio/db/pdb/residue.rb +122 -0
data/lib/bio/db/pdb/utils.rb +234 -0
data/lib/bio/db/prosite.rb +616 -0
data/lib/bio/db/rebase.rb +417 -0
data/lib/bio/db/transfac.rb +387 -0
data/lib/bio/feature.rb +201 -0
data/lib/bio/io/brdb.rb +103 -0
data/lib/bio/io/das.rb +471 -0
data/lib/bio/io/dbget.rb +212 -0
data/lib/bio/io/ddbjxml.rb +614 -0
data/lib/bio/io/fastacmd.rb +123 -0
data/lib/bio/io/fetch.rb +114 -0
data/lib/bio/io/flatfile.rb +496 -0
data/lib/bio/io/flatfile/bdb.rb +266 -0
data/lib/bio/io/flatfile/index.rb +1308 -0
data/lib/bio/io/flatfile/indexer.rb +778 -0
data/lib/bio/io/higet.rb +92 -0
data/lib/bio/io/keggapi.rb +863 -0
data/lib/bio/io/pubmed.rb +189 -0
data/lib/bio/io/registry.rb +308 -0
data/lib/bio/io/soapwsdl.rb +114 -0
data/lib/bio/io/sql.rb +428 -0
data/lib/bio/location.rb +650 -0
data/lib/bio/pathway.rb +991 -0
data/lib/bio/reference.rb +308 -0
data/lib/bio/sequence.rb +593 -0
data/lib/bio/shell.rb +51 -0
data/lib/bio/shell/core.rb +512 -0
data/lib/bio/shell/plugin/codon.rb +228 -0
data/lib/bio/shell/plugin/entry.rb +85 -0
data/lib/bio/shell/plugin/flatfile.rb +119 -0
data/lib/bio/shell/plugin/keggapi.rb +187 -0
data/lib/bio/shell/plugin/midi.rb +448 -0
data/lib/bio/shell/plugin/obda.rb +63 -0
data/lib/bio/shell/plugin/seq.rb +238 -0
data/lib/bio/shell/session.rb +214 -0
data/lib/bio/util/color_scheme.rb +214 -0
data/lib/bio/util/color_scheme/buried.rb +78 -0
data/lib/bio/util/color_scheme/helix.rb +78 -0
data/lib/bio/util/color_scheme/hydropathy.rb +83 -0
data/lib/bio/util/color_scheme/nucleotide.rb +50 -0
data/lib/bio/util/color_scheme/strand.rb +78 -0
data/lib/bio/util/color_scheme/taylor.rb +69 -0
data/lib/bio/util/color_scheme/turn.rb +78 -0
data/lib/bio/util/color_scheme/zappo.rb +69 -0
data/lib/bio/util/contingency_table.rb +337 -0
data/lib/bio/util/sirna.rb +306 -0
data/lib/bioruby.rb +34 -0
data/sample/biofetch.rb +475 -0
data/sample/color_scheme_na.rb +99 -0
data/sample/dbget +37 -0
data/sample/fasta2tab.rb +99 -0
data/sample/fsplit.rb +51 -0
data/sample/gb2fasta.rb +31 -0
data/sample/gb2tab.rb +325 -0
data/sample/gbtab2mysql.rb +161 -0
data/sample/genes2nuc.rb +33 -0
data/sample/genes2pep.rb +33 -0
data/sample/genes2tab.rb +81 -0
data/sample/genome2rb.rb +29 -0
data/sample/genome2tab.rb +76 -0
data/sample/goslim.rb +311 -0
data/sample/gt2fasta.rb +47 -0
data/sample/pmfetch.rb +42 -0
data/sample/pmsearch.rb +42 -0
data/sample/psortplot_html.rb +222 -0
data/sample/ssearch2tab.rb +96 -0
data/sample/tdiary.rb +158 -0
data/sample/tfastx2tab.rb +100 -0
data/sample/vs-genes.rb +212 -0
data/test/data/SOSUI/sample.report +11 -0
data/test/data/TMHMM/sample.report +21 -0
data/test/data/blast/eco:b0002.faa +15 -0
data/test/data/blast/eco:b0002.faa.m0 +128 -0
data/test/data/blast/eco:b0002.faa.m7 +65 -0
data/test/data/blast/eco:b0002.faa.m8 +1 -0
data/test/data/embl/AB090716.embl +65 -0
data/test/data/genscan/sample.report +63 -0
data/test/data/prosite/prosite.dat +2233 -0
data/test/data/refseq/nm_126355.entret +64 -0
data/test/data/uniprot/p53_human.uniprot +1456 -0
data/test/runner.rb +10 -0
data/test/unit/bio/appl/blast/test_report.rb +427 -0
data/test/unit/bio/appl/blast/test_xmlparser.rb +400 -0
data/test/unit/bio/appl/genscan/test_report.rb +195 -0
data/test/unit/bio/appl/sosui/test_report.rb +94 -0
data/test/unit/bio/appl/targetp/test_report.rb +159 -0
data/test/unit/bio/appl/test_blast.rb +159 -0
data/test/unit/bio/appl/test_fasta.rb +142 -0
data/test/unit/bio/appl/tmhmm/test_report.rb +139 -0
data/test/unit/bio/data/test_aa.rb +103 -0
data/test/unit/bio/data/test_codontable.rb +120 -0
data/test/unit/bio/data/test_na.rb +89 -0
data/test/unit/bio/db/embl/test_common.rb +130 -0
data/test/unit/bio/db/embl/test_embl.rb +227 -0
data/test/unit/bio/db/embl/test_sptr.rb +268 -0
data/test/unit/bio/db/embl/test_uniprot.rb +44 -0
data/test/unit/bio/db/kegg/test_genes.rb +58 -0
data/test/unit/bio/db/test_fasta.rb +263 -0
data/test/unit/bio/db/test_gff.rb +140 -0
data/test/unit/bio/db/test_prosite.rb +1450 -0
data/test/unit/bio/io/test_ddbjxml.rb +87 -0
data/test/unit/bio/io/test_soapwsdl.rb +45 -0
data/test/unit/bio/shell/plugin/test_seq.rb +175 -0
data/test/unit/bio/test_alignment.rb +1028 -0
data/test/unit/bio/test_command.rb +71 -0
data/test/unit/bio/test_db.rb +109 -0
data/test/unit/bio/test_feature.rb +128 -0
data/test/unit/bio/test_location.rb +51 -0
data/test/unit/bio/test_pathway.rb +485 -0
data/test/unit/bio/test_sequence.rb +386 -0
data/test/unit/bio/test_shell.rb +31 -0
data/test/unit/bio/util/test_color_scheme.rb +45 -0
data/test/unit/bio/util/test_contingency_table.rb +106 -0
data/test/unit/bio/util/test_sirna.rb +258 -0
metadata +295 -0

data/sample/color_scheme_na.rb ADDED Viewed

@@ -0,0 +1,99 @@
+#!/usr/bin/env ruby
+#
+# color_scheme_na.rb - A Bio::ColorScheme demo script for Nucleic Acids
+#                      sequences.
+#
+#  Usage:
+#
+#   % ruby color_scheme_na.rb > cs-seq-fna.html
+#
+#   % cat seq.fna
+#   >DNA_sequence
+#   acgtgtgtcatgctagtcgatcgtactagtcgtagctagtca
+#   % ruby color_scheme_na.rb seq.fna > colored-seq-fna.html
+#
+#
+# Copyright (C) 2005 Mitsuteru C. Nakao <n@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: color_scheme_na.rb,v 1.1 2005/10/31 07:39:13 nakao Exp $
+#
+require 'bio'
+# returns folded sequence with <br>.
+def br(i, width = 80)
+  return "<br\n>"  if i % width == 0
+  ""
+end
+# returns sequence html doc
+def display(seq, cs)
+  html = '<p style="font-family: monospace">'
+  postfix = '</span>'
+  i = 0
+  seq.each_byte do |c|
+    color = cs[c.chr]
+    prefix = %Q(<span style="background:\##{color};">)
+    html += prefix + c.chr + postfix
+    html += br(i += 1)
+  end
+  html + '</p>'
+end
+# returns scheme wise html doc
+def display_scheme(scheme, naseq, aaseq)
+  html = ''
+  cs = eval("Bio::ColorScheme::#{scheme}")
+  [naseq, aaseq].each do |seq|
+    html += display(seq, cs)
+  end
+  return  ['<div>', "<h3>#{cs}</h3>", html, '</div>']
+end
+if fna = ARGV.shift
+  naseq = Bio::FastaFormat.new(File.open(fna, 'r').read).naseq
+  aaseq = naseq.translate
+else
+  naseq = Bio::Sequence::NA.new('acgtu' * 20).randomize
+  aaseq = naseq.translate
+end
+title =  'Bio::ColorScheme for DNA sequences'
+doc = ['<html>',
+       '<header>', '<title>', title, '</title>', '</header>',
+       '<body>',  '<h1>', title, '</h1>']
+doc << ['<div>', '<h2>', 'Simple colors', '</h2>']
+['Nucleotide'].each do |scheme|
+  doc << display_scheme(scheme, naseq, "")
+end
+doc << ['</div>']
+['Zappo', 'Taylor' ].each do |scheme|
+  doc << display_scheme(scheme, "", aaseq)
+end
+doc << ['</div>']
+doc << ['<div>', '<h2>', 'Score colors', '</h2>']
+['Buried', 'Helix', 'Hydropathy', 'Strand', 'Turn'].each do |score|
+  doc << display_scheme(score, "", aaseq)
+end
+doc << ['</div>']
+puts doc + ['</body>','</html>']

data/sample/dbget ADDED Viewed

@@ -0,0 +1,37 @@
+#!/usr/bin/env ruby
+#
+# dbget - DBGET client
+#
+#  Interface to GenomeNet DBGET system - http://www.genome.jp/dbget/
+#
+#   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.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#  $Id: dbget,v 1.7 2004/08/24 00:09:24 k Exp $
+#
+require "bio/io/dbget"
+# DBGET command
+com = File.basename($0)			# e.g. $PATH/bget db entry
+com = ARGV.shift if com == "dbget"	# e.g. $PATH/dbget bget db entry
+# DBGET query strings
+arg = ARGV.join(" ")
+# DBGET result
+print Bio::DBGET.dbget(com, arg)

data/sample/fasta2tab.rb ADDED Viewed

@@ -0,0 +1,99 @@
+#!/usr/bin/env ruby
+#
+# fasta2tab.rb - convert FASTA (-m 6) output into tab delimited data for MySQL
+#
+#  Usage:
+#
+#    % fasta2tab.rb FASTA-output-file[s] > fasta_results.tab
+#    % mysql < fasta_results.sql  (use sample at the end of this file)
+#
+#  Format accepted:
+#
+#    % fasta3[3][_t] -Q -H -m 6 query.f target.f ktup > FASTA-output-file
+#
+#   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: fasta2tab.rb,v 0.1 2001/06/21 08:21:58 katayama Exp $
+#
+while gets
+  # query
+  if /^\S+: (\d+) aa$/
+    q_len = $1
+  end
+  # each hit
+  if /^>>([^>]\S+).*\((\d+) aa\)$/
+    target = $1
+    t_len = $2
+    # d = dummy variable
+    d, d, initn, d, init1, d, opt, d, zscore, d, bits, d, evalue =
+      gets.split(/\s+/)
+    d, d, sw, ident, d, ugident, d, d, overlap, d, d, lap =
+      gets.split(/\s+/)
+    # query-hit pair
+    print "#{$FILENAME}\t#{q_len}\t#{target}\t#{t_len}"
+    # pick up values
+    ary = [
+      initn,
+      init1,
+      opt,
+      zscore,
+      bits,
+      evalue,
+      sw,
+      ident,
+      ugident,
+      overlap,
+      lap
+    ]
+    # print values
+    for i in ary
+      i.tr!('^0-9.:e\-','')
+      print "\t#{i}"
+    end
+    print "\n"
+  end
+end
+=begin MySQL fasta_results.sql sample
+CREATE DATABASE IF NOT EXISTS db_name;
+CREATE TABLE IF NOT EXISTS db_name.table_name (
+	query	varchar(25)	not NULL,
+	q_len	integer		unsigned default 0,
+	target	varchar(25)	not NULL,
+	t_len	integer		unsigned default 0,
+	initn	integer		unsigned default 0,
+	init1	integer		unsigned default 0,
+	opt	integer		unsigned default 0,
+	zscore	float		default 0.0,
+	bits	float		default 0.0,
+	evalue	float		default 0.0,
+	sw	integer		unsigned default 0,
+	ident	float		default 0.0,
+	ugident	float		default 0.0,
+	overlap	integer		unsigned default 0,
+	lap_at	varchar(25)	default NULL
+);
+LOAD DATA LOCAL INFILE 'fasta_results.tab' INTO TABLE db_name.table_name;
+=end

data/sample/fsplit.rb ADDED Viewed

@@ -0,0 +1,51 @@
+#!/usr/bin/env ruby
+#
+# fsplit.rb - split FASTA file by each n entries
+#
+#   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: fsplit.rb,v 0.1 2001/06/21 08:22:29 katayama Exp $
+#
+if ARGV.length != 2
+  print <<-USAGE
+  fsplit.rb - split FASTA file by each n entries
+   Usage :
+     % ./fsplit.rb 2000 seq.f
+     This will produce seq.f.1, seq.f.2, ... with containing 2000 sequences
+     in each file.
+  USAGE
+  exit 1
+end
+count = ARGV.shift.to_i
+i = -1
+while gets
+  if /^>/
+    i += 1
+    if i % count == 0
+      n = i / count
+      out = File.new("#{$FILENAME}.#{n+1}", "w+")
+    end
+  end
+  out.print
+end

data/sample/gb2fasta.rb ADDED Viewed

@@ -0,0 +1,31 @@
+#!/usr/bin/env ruby
+#
+# gb2fasta.rb - convert GenBank entry into FASTA format (nuc)
+#
+#   Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
+#   Copyright (C) 2002 Yoshinori K. Okuji <o@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: gb2fasta.rb,v 0.5 2002/07/23 04:51:24 k Exp $
+#
+require 'bio/io/flatfile'
+require 'bio/db/genbank'
+include Bio
+ff = FlatFile.new(GenBank, ARGF)
+while gb = ff.next_entry
+  print gb.seq.to_fasta("gb:#{gb.entry_id} #{gb.definition}", 70)
+end

data/sample/gb2tab.rb ADDED Viewed

@@ -0,0 +1,325 @@
+#!/usr/bin/env ruby
+#
+# gb2tab.rb - convert GenBank into tab delimited data for MySQL
+#
+#  Usage:
+#
+#    % gb2tab.rb gb*.seq
+#
+#   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: gb2tab.rb,v 0.11 2002/04/22 09:10:10 k Exp $
+#
+require 'bio'
+$stderr.puts Time.now
+ARGV.each do |gbkfile|
+  gbk = open("#{gbkfile}")
+  ent = open("#{gbkfile}.ent.tab", "w")
+  ft  = open("#{gbkfile}.ft.tab", "w")
+  ref = open("#{gbkfile}.ref.tab", "w")
+  seq = open("#{gbkfile}.seq.tab", "w")
+  while entry = gbk.gets(Bio::GenBank::DELIMITER)
+    gb = Bio::GenBank.new(entry)
+    ### MAIN BODY
+    ary = [
+      gb.entry_id,
+      gb.nalen,
+      gb.strand,
+      gb.natype,
+      gb.circular,
+      gb.division,
+      gb.date,
+      gb.definition,
+      gb.accession,
+      gb.versions.inspect,
+      gb.keywords.inspect,
+      gb.segment.inspect,
+      gb.common_name,
+      gb.organism,
+      gb.taxonomy,
+      gb.comment,
+      gb.basecount.inspect,
+      gb.origin,
+    ]
+    ent.puts ary.join("\t")
+    ### FEATURES
+    num = 0
+    gb.features.each do |f|
+      num += 1
+      span_min, span_max = f.locations.span
+      if f.qualifiers.empty?
+	ary = [
+	    gb.entry_id,
+	    num,
+	    f.feature,
+	    f.position,
+	    span_min,
+	    span_max,
+	    '',
+	    '',
+	]
+	ft.puts ary.join("\t")
+      else
+	f.each do |q|
+	  ary = [
+	    gb.entry_id,
+	    num,
+	    f.feature,
+	    f.position,
+	    span_min,
+	    span_max,
+	    q.qualifier,
+	    q.value,
+	  ]
+	  ft.puts ary.join("\t")
+	end
+      end
+    end
+    ### REFERENCE
+    num = 0
+    gb.references.each do |r|
+      num += 1
+      ary = [
+	gb.entry_id,
+	num,
+	r.authors.inspect,
+	r.title,
+	r.journal,
+	r.medline,
+	r.pubmed,
+      ]
+      ref.puts ary.join("\t")
+    end
+    ### SEQUENCE
+    maxlen = 16 * 10 ** 6
+    num = 0
+    0.step(gb.nalen, maxlen) do |i|
+      num += 1
+      ary = [
+	gb.entry_id,
+	num,
+	gb.naseq[i, maxlen]
+      ]
+      seq.puts ary.join("\t")
+    end
+  end
+  gbk.close
+  ent.close
+  ft.close
+  ref.close
+  seq.close
+end
+$stderr.puts Time.now
+=begin
+Example usage in zsh:
+  % gb2tab.rb *.seq
+  % for i in *.seq
+  > do
+  >   base=`basename $i .seq`
+  >   ruby -pe "gsub(/%HOGE%/,'$base')" gb2tab.sql | mysql
+  > done
+gb2tab.sql:
+CREATE DATABASE IF NOT EXISTS genbank;
+USE genbank;
+CREATE TABLE IF NOT EXISTS %HOGE% (
+	id		varchar(16)	NOT NULL PRIMARY KEY,
+	nalen		integer,
+	strand		varchar(5),
+	natype		varchar(5),
+	circular	varchar(10),
+	division	varchar(5),
+	date		varchar(12),
+	definition	varchar(255),
+	accession	varchar(30),
+	versions	varchar(30),
+	keywords	varchar(255),
+	segment		varchar(255),
+	source		varchar(255),
+	organism	varchar(255),
+	taxonomy	varchar(255),
+	comment		text,
+	basecount	varchar(255),
+	origin		varchar(255),
+	KEY (nalen),
+	KEY (division),
+	KEY (accession),
+	KEY (organism),
+	KEY (taxonomy)
+);
+LOAD DATA LOCAL INFILE '%HOGE%.seq.ent.tab' INTO TABLE %HOGE%;
+CREATE TABLE IF NOT EXISTS %HOGE%ft (
+	id		varchar(16)	NOT NULL,
+	num		integer,
+	feature		varchar(30),
+	position	text,
+	span_min	integer,
+	span_max	integer,
+	qualifier	varchar(30),
+	value		text,
+	KEY (id),
+	KEY (num),
+	KEY (feature),
+	KEY (span_min),
+	KEY (span_max),
+	KEY (qualifier)
+);
+LOAD DATA LOCAL INFILE '%HOGE%.seq.ft.tab' INTO TABLE %HOGE%ft;
+CREATE TABLE IF NOT EXISTS %HOGE%ref (
+	id		varchar(16)	NOT NULL,
+	num		integer,
+	authors		text,
+	title		text,
+	journal		text,
+	medline		varchar(255),
+	pubmed		varchar(255),
+	KEY (id),
+	KEY (medline),
+	KEY (pubmed)
+);
+LOAD DATA LOCAL INFILE '%HOGE%.seq.ref.tab' INTO TABLE %HOGE%ref;
+CREATE TABLE IF NOT EXISTS %HOGE%seq (
+	id		varchar(16)	NOT NULL,
+	num		integer,
+	naseq		mediumtext,
+	KEY (id)
+);
+LOAD DATA LOCAL INFILE '%HOGE%.seq.seq.tab' INTO TABLE %HOGE%seq;
+gbmerge.sql sample:
+CREATE TABLE IF NOT EXISTS ent (
+	id		varchar(16)	NOT NULL PRIMARY KEY,
+	nalen		integer,
+	strand		varchar(5),
+	natype		varchar(5),
+	circular	varchar(10),
+	division	varchar(5),
+	date		varchar(12),
+	definition	varchar(255),
+	accession	varchar(30),
+	versions	varchar(30),
+	keywords	varchar(255),
+	segment		varchar(255),
+	source		varchar(255),
+	organism	varchar(255),
+	taxonomy	varchar(255),
+	comment		text,
+	basecount	varchar(255),
+	origin		varchar(255),
+	KEY (nalen),
+	KEY (division),
+	KEY (accession),
+	KEY (organism),
+	KEY (taxonomy)
+) TYPE=MERGE UNION=(
+	gbbct1,
+	gbbct2,
+	...,		# list up all tables by yourself
+	gbvrt
+);
+CREATE TABLE IF NOT EXISTS ft (
+	id		varchar(16)	NOT NULL,
+	num		integer,
+	feature		varchar(30),
+	position	text,
+	span_min	integer,
+	span_max	integer,
+	qualifier	varchar(30),
+	value		text,
+	KEY (id),
+	KEY (num),
+	KEY (feature),
+	KEY (span_min),
+	KEY (span_max),
+	KEY (qualifier)
+) TYPE=MERGE UNION=(
+	gbbct1ft,
+	gbbct2ft,
+	...,		# list up all ft tables by yourself
+	gbvrtft
+);
+CREATE TABLE IF NOT EXISTS ref (
+	id		varchar(16)	NOT NULL,
+	num		integer,
+	authors		text,
+	title		text,
+	journal		text,
+	medline		varchar(255),
+	pubmed		varchar(255),
+	KEY (id),
+	KEY (medline),
+	KEY (pubmed)
+) TYPE=MERGE UNION=(
+	gbbct1ref,
+	gbbct2ref,
+	...,		# list up all ref tables by yourself
+	gbvrtref
+);
+CREATE TABLE IF NOT EXISTS seq (
+	id		varchar(16)	NOT NULL,
+	num		integer,
+	naseq		mediumtext,
+	KEY (id)
+) TYPE=MERGE UNION=(
+	gbbct1seq,
+	gbbct2seq,
+	...,		# list up all seq tables by yourself
+	gbvrtseq
+);
+=end