ngoto-bio 1.2.9.9001

data/sample/biofetch.rb

@@ -0,0 +1,475 @@
+#!/usr/proj/bioruby/bin/ruby
+#
+# biofetch.rb : BioFetch server (interface to GenomeNet/DBGET via KEGG API)
+#
+#   Copyright (C) 2002-2004 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: biofetch.rb,v 1.16 2005/08/07 10:02:41 k Exp $
+#
+
+require 'cgi'
+require 'html/template'
+require 'bio/io/keggapi'
+
+MAX_ID_NUM = 50
+
+
+module BioFetchError
+
+  def print_text_page(str)
+    print "Content-type: text/plain; charset=UTF-8\n\n"
+    puts str
+    exit
+  end
+
+  def error1(db)
+    str = "ERROR 1 Unknown database [#{db}]."
+    print_text_page(str)
+  end
+
+  def error2(style)
+    str = "ERROR 2 Unknown style [#{style}]."
+    print_text_page(str)
+  end
+
+  def error3(format, db)
+    str = "ERROR 3 Format [#{format}] not known for database [#{db}]."
+    print_text_page(str)
+  end
+
+  def error4(entry_id, db)
+    str = "ERROR 4 ID [#{entry_id}] not found in database [#{db}]."
+    print_text_page(str)
+  end
+
+  def error5(count)
+    str = "ERROR 5 Too many IDs [#{count}]. Max [#{MAX_ID_NUM}] allowed."
+    print_text_page(str)
+  end
+
+  def error6(info)
+    str = "ERROR 6 Illegal information request [#{info}]."
+    print_text_page(str)
+  end
+
+end
+
+
+
+module KeggAPI
+
+  include BioFetchError
+
+  def list_databases
+    serv = Bio::KEGG::API.new
+    results = serv.list_databases
+    results.collect {|x| x.entry_id}
+  end
+
+  def bget(db, id_list, format)
+    serv = Bio::KEGG::API.new
+    results = ''
+    id_list.each do |query_id|
+      entry_id = "#{db}:#{query_id}"
+      result = serv.get_entries([entry_id])
+      if result.empty?
+        error4(query_id, db)
+      else
+        results << result
+      end
+    end
+    return results
+  end
+
+end
+
+
+
+
+class BioFetch
+
+  include BioFetchError
+  include KeggAPI
+
+  def initialize(db, id_list, style, format)
+    check_style(style)
+    check_format(format, db)
+    check_number_of_id(id_list.length)
+    check_dbname(db)
+
+    if /html/.match(style)
+      goto_html_style_page(db, id_list, format)
+    end
+
+    entries = bget(db, id_list, format)
+
+    if /fasta/.match(format) and entries
+      entries = convert_to_fasta_format(entries, db)
+    end
+
+    print_text_page(entries)
+  end
+
+  private
+
+  def convert_to_fasta_format(str, db)
+    require 'bio'
+    require 'stringio'
+
+    fasta = Array.new
+
+    entries = StringIO.new(str)
+    Bio::FlatFile.auto(entries) do |ff|
+      ff.each do |entry|
+        seq = nil
+        if entry.respond_to?(:seq)
+          seq = entry.seq
+        elsif entry.respond_to?(:aaseq)
+          seq = entry.aaseq
+        elsif entry.respond_to?(:naseq)
+          seq = entry.naseq
+        end
+        if seq
+          entry_id   = entry.respond_to?(:entry_id)   ? entry.entry_id   : ''
+          definition = entry.respond_to?(:definition) ? entry.definition : ''
+          fasta << seq.to_fasta("#{db}:#{entry_id} #{definition}", 60)
+        end
+      end
+    end
+    return fasta.join
+  end
+
+  def goto_html_style_page(db, id_list, format)
+    url = "http://www.genome.jp/dbget-bin/www_bget"
+    opt = '-f+' if /fasta/.match(format)
+    ids = id_list.join('%2B')
+    print "Location: #{url}?#{opt}#{db}+#{ids}\n\n"
+    exit
+  end
+
+  def check_style(style)
+    error2(style) unless /html|raw/.match(style)
+  end
+
+  def check_format(format, db)
+    error3(format, db) if format && ! /fasta|default/.match(format)
+  end
+
+  def check_number_of_id(num)
+    error5(num) if num > MAX_ID_NUM
+  end
+
+  def check_dbname(db)
+    error1(db) unless list_databases.include?(db)
+  end
+
+end
+
+
+
+class BioFetchInfo
+
+  include BioFetchError
+  include KeggAPI
+
+  def initialize(info, db)
+    @db = db
+    begin
+      send(info)
+    rescue
+      error6(info)
+    end
+  end
+
+  private
+
+  def dbs
+    str = list_databases.sort.join(' ')
+    print_text_page(str)
+  end
+
+  def formats
+    fasta = " fasta" if check_fasta_ok
+    str = "default#{fasta}"
+    print_text_page(str)
+  end
+
+  def maxids
+    str = MAX_ID_NUM.to_s
+    print_text_page(str)
+  end
+
+  def check_fasta_ok
+    # sequence databases supported by Bio::FlatFile.auto
+    /genes|gb|genbank|genpept|rs|refseq|emb|sp|swiss|pir/.match(@db)
+  end
+
+end
+
+
+
+class BioFetchCGI
+
+  def initialize(cgi)
+    @cgi = cgi
+    show_page
+  end
+
+  private
+
+  def show_page
+    if info.empty?
+      if id_list.empty?
+        show_query_page
+      else
+        show_result_page(db, id_list, style, format)
+      end
+    else
+      show_info_page(info, db)
+    end
+  end
+
+  def show_query_page
+    html = HTML::Template.new
+    html.set_html(DATA.read)
+    html.param('max_id_num' => MAX_ID_NUM)
+    @cgi.out do
+      html.output
+    end
+  end
+
+  def show_result_page(db, id_list, style, format)
+    BioFetch.new(db, id_list, style, format)
+  end
+
+  def show_info_page(info, db)
+    BioFetchInfo.new(info, db)
+  end
+
+  def info
+    @cgi['info'].downcase
+  end
+
+  def db
+    @cgi['db'].downcase
+  end
+
+  def id_list
+    @cgi['id'].split(/\W/)		# not only ','
+  end
+
+  def style
+    s = @cgi['style'].downcase
+    return s.empty? ? "html" : s
+  end
+
+  def format
+    f = @cgi['format'].downcase
+    return f.empty? ? "default" : f
+  end
+
+end
+
+
+
+BioFetchCGI.new(CGI.new)
+
+
+
+=begin
+
+This program was created during BioHackathon 2002, Tucson and updated
+in Cape Town :)
+
+Rewrited in 2004 to use KEGG API as the bioruby.org server left from Kyoto
+University (where DBGET runs) and the old version could not run without
+having internally accessible DBGET server.
+
+=end
+
+
+__END__
+
+<HTML>
+<HEAD>
+  <LINK href="http://bioruby.org/img/favicon.png" rel="icon" type="image/png">
+  <LINK href="http://bioruby.org/css/bioruby.css" rel="stylesheet" type="text/css">
+  <TITLE>BioFetch interface to GenomeNet/DBGET</TITLE>
+</HEAD>
+
+<BODY bgcolor="#ffffff">
+
+<H1>
+<IMG src="http://bioruby.org/img/ruby.png" align="middle">
+BioFetch interface to
+<A href="http://www.genome.jp/dbget/">GenomeNet/DBGET</A>
+</H1>
+
+<P>This page allows you to retrieve up to <!var:max_id_num> entries at a time from various up-to-date biological databases.</P>
+
+<HR>
+
+<FORM METHOD="post" ENCTYPE="application/x-www-form-urlencoded" action="biofetch.rb">
+
+<SELECT name="db">
+<OPTION value="genbank">GenBank</OPTION>
+<OPTION value="refseq">RefSeq</OPTION>
+<OPTION value="embl">EMBL</OPTION>
+<OPTION value="swissprot">Swiss-Prot</OPTION>
+<OPTION value="pir">PIR</OPTION>
+<OPTION value="prf">PRF</OPTION>
+<OPTION value="pdb">PDB</OPTION>
+<OPTION value="pdbstr">PDBSTR</OPTION>
+<OPTION value="epd">EPD</OPTION>
+<OPTION value="transfac">TRANSFAC</OPTION>
+<OPTION value="prosite">PROSITE</OPTION>
+<OPTION value="pmd">PMD</OPTION>
+<OPTION value="litdb">LITDB</OPTION>
+<OPTION value="omim">OMIM</OPTION>
+<OPTION value="ligand">KEGG/LIGAND</OPTION>
+<OPTION value="pathway">KEGG/PATHWAY</OPTION>
+<OPTION value="brite">KEGG/BRITE</OPTION>
+<OPTION value="genes">KEGG/GENES</OPTION>
+<OPTION value="genome">KEGG/GENOME</OPTION>
+<OPTION value="linkdb">LinkDB</OPTION>
+<OPTION value="aaindex">AAindex</OPTION>
+</SELECT>
+
+<INPUT name="id" size="40" type="text" maxlength="1000">
+
+<SELECT name="format">
+<OPTION value="default">Default</OPTION>
+<OPTION value="fasta">Fasta</OPTION>
+</SELECT>
+
+<SELECT name="style">
+<OPTION value="raw">Raw</OPTION>
+<OPTION value="html">HTML</OPTION>
+</SELECT>
+
+<INPUT type="submit">
+
+</FORM>
+
+<HR>
+
+<H2>Direct access</H2>
+
+<P>http://bioruby.org/cgi-bin/biofetch.rb?format=(default|fasta|...);style=(html|raw);db=(genbank|embl|...);id=ID[,ID,ID,...]</P>
+<P>(NOTE: the option separator ';' can be '&')</P>
+
+<DL>
+  <DT> <U>format</U> (optional)
+  <DD> default|fasta|...
+
+  <DT> <U>style</U> (required)
+  <DD> html|raw
+
+  <DT> <U>db</U> (required)
+  <DD> genbank|refseq|embl|swissprot|pir|prf|pdb|pdbstr|epd|transfac|prosite|pmd|litdb|omim|ligand|pathway|brite|genes|genome|linkdb|aaindex|...
+
+  <DT> <U>id</U> (required)
+  <DD> comma separated list of IDs
+</DL>
+
+<P>See the <A href="http://obda.open-bio.org/">BioFetch specification</A> for more details.</P>
+
+<H2>Server informations</H2>
+
+<DL>
+  <DT> <A href="?info=dbs">What databases are available?</A>
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=dbs
+
+  <DT> <A href="?info=formats;db=embl">What formats does the database X have?</A>
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=formats;db=embl
+
+  <DT> <A href="?info=maxids">How many entries can be retrieved simultaneously?</A>
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=maxids
+</DL>
+
+<H2>Examples</H2>
+
+<DL>
+  <DT> <A href="?format=default;style=raw;db=genbank;id=AJ617376">gb:AJ617376</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=AJ617376
+
+  <DT> <A href="?format=fasta;style=raw;db=genbank;id=AJ617376">gb:AJ617376</A> (fasta/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=fasta;style=raw;db=genbank;id=AJ617376
+
+  <DT> <A href="?format=default;style=html;db=genbank;id=AJ617376">gb:AJ617376</A> (default/html)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=html;db=genbank;id=AJ617376
+
+  <DT> <A href="?format=default;style=raw;db=genbank;id=AJ617376,AJ617377">gb:AJ617376,AJ617377</A> (default/raw, multiple)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=AJ617376,AJ617377
+
+  <DT> <A href="?format=default;style=raw;db=embl;id=BUM">embl:BUM</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=embl;id=BUM
+
+  <DT> <A href="?format=default;style=raw;db=swissprot;id=CYC_BOVIN">sp:CYC_BOVIN</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=swissprot;id=CYC_BOVIN
+
+  <DT> <A href="?format=fasta;style=raw;db=swissprot;id=CYC_BOVIN">sp:CYC_BOVIN</A> (fasta/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=fasta;style=raw;db=swissprot;id=CYC_BOVIN
+
+  <DT> <A href="?format=default;style=raw;db=genes;id=b0015">genes:b0015</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genes;id=b0015
+
+  <DT> <A href="?format=default;style=raw;db=prosite;id=PS00028">ps:PS00028</A> (default/raw)
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=prosite;id=PS00028
+</DL>
+
+<H2>Errors</H2>
+
+<DL>
+  <DT> <A href="?format=default;style=raw;db=nonexistent;id=AJ617376">Error1</A> sample : DB not found
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=nonexistent;id=AJ617376"
+
+  <DT> <A href="?format=default;style=nonexistent;db=genbank;id=AJ617376">Error2</A> sample : unknown style
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=nonexistent;db=genbank;id=AJ617376"
+
+  <DT> <A href="?format=nonexistent;style=raw;db=genbank;id=AJ617376">Error3</A> sample : unknown format
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=nonexistent;style=raw;db=genbank;id=AJ617376"
+
+  <DT> <A href="?format=default;style=raw;db=genbank;id=nonexistent">Error4</A> sample : ID not found
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?format=default;style=raw;db=genbank;id=nonexistent"
+
+  <DT> <A href="?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51">Error5</A> sample : too many IDs
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?style=raw;db=genes;id=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51
+
+  <DT> <A href="?info=nonexistent">Error6</A> sample : unknown info
+  <DD> http://bioruby.org/cgi-bin/biofetch.rb?info=nonexistent"
+</DL>
+
+<H2>Other BioFetch implementations</H2>
+
+<UL>
+  <LI> <A href="http://www.ebi.ac.uk/cgi-bin/dbfetch">dbfetch at EBI</A>
+</UL>
+
+<HR>
+
+<DIV align=right>
+<I>
+staff@Bio<span class="ruby">Ruby</span>.org
+</I>
+<BR>
+<BR>
+<A href="http://bioruby.org/"><IMG border=0 src="/img/banner.gif"></A>
+</DIV>
+
+</BODY>
+</HTML>

data/sample/color_scheme_na.rb

@@ -0,0 +1,91 @@
+#!/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::  Copyright (C) 2005
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
+#
+#  $Id: color_scheme_na.rb,v 1.3 2007/04/05 23:35:42 trevor 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

@@ -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)
+