bio 1.0.0 → 1.1.0

data/lib/bio/appl/clustalw/report.rb

@@ -2,25 +2,9 @@
 # = bio/appl/clustalw/report.rb - CLUSTAL W format data (*.aln) class
 #
 # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
-# License::   LGPL
+# License::   The Ruby License
 #
-#--
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library 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
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#++
-#
-#  $Id: report.rb,v 1.9 2005/12/18 15:58:40 k Exp $
+#  $Id: report.rb,v 1.13 2007/07/18 08:47:39 ngoto Exp $
 #
 # Bio::ClustalW::Report is a CLUSTAL W report (*.aln file) parser.
 # CLUSTAL W is a very popular software for multiple sequence alignment.
@@ -97,22 +81,36 @@ module Bio
 
       # Gets an multiple alignment.
       # Returns a Bio::Alignment object.
-      def align
+      def alignment
         do_parse() unless @align
         @align
       end
-      alias alignment align
 
+      # This will be deprecated. Instead, please use alignment.
+      #
+      # Gets an multiple alignment.
+      # Returns a Bio::Alignment object.
+      def align
+        warn "Bio::ClustalW#align will be deprecated. Please use \'alignment\'."
+        alignment
+      end
+
+      # This will be deprecated. Instead, please use alignment.output_fasta.
+      #
       # Gets an fasta-format string of the sequences.
       # Returns a string.
       def to_fasta(*arg)
-        align.to_fasta(*arg)
+        warn "Bio::ClustalW::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
+        alignment.output_fasta(*arg)
       end
 
+      # Compatibility note: Behavior of the method will be changed
+      # in the future.
+      #
       # Gets an array of the sequences.
       # Returns an array of Bio::FastaFormat objects.
       def to_a
-        align.to_fastaformat_array
+        alignment.to_fastaformat_array
       end
 
       private

data/lib/bio/appl/emboss.rb

@@ -1,37 +1,131 @@
 #
 # = bio/appl/emboss.rb - EMBOSS wrapper
 # 
-# Copyright::	Copyright (C) 2002, 2005
-#		KATAYAMA Toshiaki <k@bioruby.org>
-# License::	Ruby's
+# Copyright::  Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org>
+# Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::    The Ruby License
 #
-# $Id: emboss.rb,v 1.4 2006/02/27 09:14:30 k Exp $
-#
-# == References
-#
-# * http://www.emboss.org
+# $Id: emboss.rb,v 1.8 2007/04/05 23:35:39 trevor Exp $
 #
 
 module Bio
 
-autoload :Command, 'bio/command'
-
+# == Description
+#
+# This file holds classes pertaining to the EMBOSS software suite.
+#
+# This class provides a wrapper for the applications of the EMBOSS suite, which 
+# is a mature and stable collection of open-source applications that can handle
+# a huge range of sequence formats.
+# Applications include:
+# * Sequence alignment
+# * Rapid database searching with sequence patterns
+# * Protein motif identification, including domain analysis
+# * Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats
+# * Codon usage analysis for small genomes
+# * Rapid identification of sequence patterns in large scale sequence sets
+# * Presentation tools for publication
+#
+# See the emboss website for more information: http://emboss.sourceforge.net.
+#
+#
+# == Usage
+#
+#  require 'bio'
+#
+#  # Suppose that you could get the sequence for XLRHODOP by running
+#  # the EMBOSS command +seqret embl:xlrhodop+ on the command line.
+#  # Then you can get the output of that command in a Bio::EMBOSS object
+#  # by creating a new Bio::EMBOSS object and subsequently executing it.
+#  xlrhodop = Bio::EMBOSS.new('seqret embl:xlrhodop')
+#  puts xlrhodop.exec
+#
+#  # Or all in one go:
+#  puts Bio::EMBOSS.new('seqret embl:xlrhodop').exec
+#
+#  # Similarly:
+#  puts Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop')
+#  puts Bio::EMBOSS.new('showfeat embl:xlrhodop').exec
+#  puts Bio::EMBOSS.new('seqret embl:xlrhodop -osformat acedb').exec
+#
+#  # A shortcut exists for this two-step process for +seqret+ and +entret+.
+#  puts Bio::EMBOSS.seqret('embl:xlrhodop')
+#  puts Bio::EMBOSS.entret('embl:xlrhodop')
+#
+# == Pre-requisites
+#
+# You must have the EMBOSS suite installed locally. You can download from the
+# project website (see References below).
+#
+# = Rereferences
+#
+# * http://emboss.sourceforge.net
+# * Rice P, Longden I and Bleasby A. \
+#    EMBOSS: the European Molecular Biology Open Software Suite. \
+#    Trends Genet. 2000 Jun ; 16(6): 276-7 
+#
 class EMBOSS
 
-  extend Bio::Command::Tools
-
+  # Combines the initialization and execution for the emboss +seqret+ command.
+  #
+  #  puts Bio::EMBOSS.seqret('embl:xlrhodop')
+  #
+  # is equivalent to:
+  #
+  #  object = Bio::EMBOSS.new('seqret embl:xlrhodop')
+  #  puts object.exec
+  # ---
+  # *Arguments*:
+  # * (required) _command_: emboss command
+  # *Returns*:: Bio::EMBOSS object
   def self.seqret(arg)
     str = self.retrieve('seqret', arg)
   end
 
+  # Combines the initialization and execution for the emboss +entret+ command.
+  #
+  #  puts Bio::EMBOSS.entret('embl:xlrhodop')
+  #
+  # is equivalent to:
+  #
+  #  object = Bio::EMBOSS.new('entret embl:xlrhodop')
+  #  puts object.exec
+  # ---
+  # *Arguments*:
+  # * (required) _command_: emboss command
+  # *Returns*:: Bio::EMBOSS object
   def self.entret(arg)
     str = self.retrieve('entret', arg)
   end
 
+  # Initializes a new Bio::EMBOSS object. This provides a holder that can
+  # subsequently be executed (see Bio::EMBOSS.exec). The object does _not_
+  # hold any actual data when initialized.
+  #
+  #   e = Bio::EMBOSS.new('seqret embl:xlrhodop')
+  #
+  # For e to actually hold data, it has to be executed:
+  #   puts e.exec
+  #
+  # For an overview of commands that can be used with this method, see the
+  # emboss website.
+  # ---
+  # *Arguments*:
+  # * (required) _command_: emboss command
+  # *Returns*:: Bio::EMBOSS object
   def initialize(cmd_line)
     @cmd_line = cmd_line + ' -stdout -auto'
   end
 
+  # A Bio::EMBOSS object has to be executed before it can return any result.
+  #   obj_A = Bio::EMBOSS.new('transeq -sbegin 110 -send 1171 embl:xlrhodop')
+  #   puts obj_A.result                   #=> nil
+  #   obj_A.exec
+  #   puts obj_A.result                   #=> a FASTA-formatted sequence
+  #
+  #   obj_B = Bio::EMBOSS.new('showfeat embl:xlrhodop')
+  #   obj_B.exec
+  #   puts obj_B.result
   def exec
     begin
       @io = IO.popen(@cmd_line, "w+")
@@ -41,21 +135,20 @@ class EMBOSS
       @io.close
     end
   end
-  attr_reader :io, :result
+  
+  # Pipe for the command
+  attr_reader :io
+  
+  # Result of the executed command
+  attr_reader :result
 
   private
 
   def self.retrieve(cmd, arg)
     cmd = [ cmd, arg, '-auto', '-stdout' ]
-    str = ''
-    call_command_local(cmd) do |inn, out|
-      inn.close_write
-      str = out.read
-    end
-    return str
+    return Bio::Command.query_command(cmd)
   end
 
 end # EMBOSS
 
 end # Bio
-

data/lib/bio/appl/fasta.rb

@@ -1,23 +1,10 @@
 #
-# bio/appl/fasta.rb - FASTA wrapper
+# = bio/appl/fasta.rb - FASTA wrapper
 #
-#   Copyright (C) 2001,2002 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library 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
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: fasta.rb,v 1.20 2005/09/26 13:00:04 k Exp $
+# $Id: fasta.rb,v 1.25 2007/05/18 15:22:52 k Exp $
 #
 
 require 'net/http'
@@ -27,154 +14,208 @@ require 'shellwords'
 
 module Bio
 
-  class Fasta
-
-    autoload :Report, 'bio/appl/fasta/format10'
-    #autoload :?????,  'bio/appl/fasta/format6'
+class Fasta
 
-    include Bio::Command::Tools
+  #autoload :Report, 'bio/appl/fasta/format10'
+  #autoload :?????,  'bio/appl/fasta/format6'
 
-    def initialize(program, db, opt = [], server = 'local')
-      @format	= 10
+  # Returns a FASTA factory object (Bio::Fasta).
+  def initialize(program, db, opt = [], server = 'local')
+    @format	= 10
 
-      @program	= program
-      @db	= db
-      @server	= server
+    @program	= program
+    @db	= db
+    @server	= server
 
-      @ktup	= nil
-      @matrix	= nil
-
-      @output	= ''
-
-      begin
-        a = opt.to_ary
-      rescue NameError #NoMethodError
-        # backward compatibility
-        a = Shellwords.shellwords(opt)
-      end
-      @options	= [ '-Q', '-H', '-m', @format.to_s, *a ] # need -a ?
-    end
-    attr_accessor :program, :db, :options, :server, :ktup, :matrix
-    attr_reader :output
+    @ktup	= nil
+    @matrix	= nil
 
-    def option
-      # backward compatibility
-      make_command_line(@options)
-    end
+    @output	= ''
 
-    def option=(str)
+    begin
+      a = opt.to_ary
+    rescue NameError #NoMethodError
       # backward compatibility
-      @options = Shellwords.shellwords(str)
+      a = Shellwords.shellwords(opt)
     end
+    @options	= [ '-Q', '-H', '-m', @format.to_s, *a ] # need -a ?
+  end
+  attr_accessor :program, :db, :options, :server, :ktup, :matrix
 
-    def format=(num)
-      @format = num.to_i
-      if i = @options.index('-m') then
-        @options[i+1, 1] = @format.to_s
-      else
-        @options << '-m' << @format.to_s
-      end
-    end
-    attr_reader :format
+  # Returns a String containing fasta execution output in as is format.
+  attr_reader :output
 
-    def self.parser(parser)
-      require "bio/appl/fasta/#{parser}"
-    end
+  def option
+    # backward compatibility
+    Bio::Command.make_command_line(@options)
+  end
 
-    def self.local(program, db, option = '')
-      self.new(program, db, option, 'local')
-    end
+  def option=(str)
+    # backward compatibility
+    @options = Shellwords.shellwords(str)
+  end
 
-    def self.remote(program, db, option = '', server = 'genomenet')
-      self.new(program, db, option, server)
+  # Accessors for the -m option.
+  def format=(num)
+    @format = num.to_i
+    if i = @options.index('-m') then
+      @options[i+1, 1] = @format.to_s
+    else
+      @options << '-m' << @format.to_s
     end
+  end
+  attr_reader :format
+
+  # Select parser to use ('format6' and 'format10' is acceptable for now)
+  #
+  # This method will import Bio::Fasta::Report class by requiring specified
+  # parser and will be useful when you already have fasta output files and
+  # want to use appropriate Report class for parsing.
+  #
+  def self.parser(parser)
+    require "bio/appl/fasta/#{parser}"
+  end
 
-    def query(query)
-      return self.send("exec_#{@server}", query.to_s)
-    end
+  # Returns a FASTA factory object (Bio::Fasta) to run FASTA search on
+  # local computer.
+  def self.local(program, db, option = '')
+    self.new(program, db, option, 'local')
+  end
 
+  # Returns a FASTA factory object (Bio::Fasta) to execute FASTA search on
+  # remote server.
+  #
+  # For the develpper, you can add server 'hoge' by adding
+  # exec_hoge(query) method.
+  #
+  def self.remote(program, db, option = '', server = 'genomenet')
+    self.new(program, db, option, server)
+  end
 
-    private
+  # Execute FASTA search and returns Report object (Bio::Fasta::Report).
+  def query(query)
+    return self.send("exec_#{@server}", query.to_s)
+  end
 
 
-    def parse_result(data)
-      case @format
-      when 6
-        require 'bio/appl/fasta/format6'
-      when 10
-        require 'bio/appl/fasta/format10'
-      end
-      Report.new(data)
-    end
+  private
 
 
-    def exec_local(query)
-      cmd = [ @program, *@options ]
-      cmd.concat([ '@', @db, @ktup ])
+  def parse_result(data)
+    case @format
+    when 6
+      require 'bio/appl/fasta/format6'
+    when 10
+      require 'bio/appl/fasta/format10'
+    end
+    Report.new(data)
+  end
 
-      report = nil
 
-      @output = call_command_local(cmd, query)
-      report = parse_result(@output)
+  def exec_local(query)
+    cmd = [ @program, *@options ]
+    cmd.concat([ '@', @db ])
+    cmd.push(@ktup) if @ktup
 
-      return report
-    end
+    report = nil
 
+    @output = Bio::Command.query_command(cmd, query)
+    report = parse_result(@output)
 
-    def exec_genomenet(query)
-      host = "fasta.genome.jp"
-      #path = "/sit-bin/nph-fasta"
-      path = "/sit-bin/fasta" #2005.08.12
+    return report
+  end
 
-      form = {
-        'style'		=> 'raw',
-        'prog'		=> @program,
-        'dbname'	=> @db,
-        'sequence'	=> CGI.escape(query),
-        'other_param'	=> CGI.escape(make_command_line_unix(@options)),
-        'ktup_value'	=> @ktup,
-        'matrix'	=> @matrix,
-      }
 
-      data = []
+  # == Available databases for Fasta.remote(@program, @db, option, 'genomenet')
+  #
+  # See http://fasta.genome.jp/ideas/ideas.html#fasta for more details.
+  #
+  #   ----------+-------+---------------------------------------------------
+  #    @program | query | @db (supported in GenomeNet)
+  #   ----------+-------+---------------------------------------------------
+  #    fasta    | AA    | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
+  #             |       | pir, prf, pdbstr
+  #             +-------+---------------------------------------------------
+  #             | NA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
+  #             |       | htgs, dbsts, embl-nonst, embnonst-upd, epd,
+  #             |       | genes-nt, genome, vgenes.nuc
+  #   ----------+-------+---------------------------------------------------
+  #    tfasta   | AA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
+  #             |       | htgs, dbsts, embl-nonst, embnonst-upd,
+  #             |       | genes-nt, genome, vgenes.nuc
+  #   ----------+-------+---------------------------------------------------
+  #
+  def exec_genomenet(query)
+    host = "fasta.genome.jp"
+    #path = "/sit-bin/nph-fasta"
+    path = "/sit-bin/fasta"  # 2005.08.12
+
+    form = {
+      'style'        => 'raw',
+      'prog'         => @program,
+      'dbname'       => @db,
+      'sequence'     => CGI.escape(query),
+      'other_param'  => CGI.escape(Bio::Command.make_command_line_unix(@options)),
+      'ktup_value'   => @ktup,
+      'matrix'       => @matrix,
+    }
+
+    data = []
+
+    form.each do |k, v|
+      data.push("#{k}=#{v}") if v
+    end
 
-      form.each do |k, v|
-        data.push("#{k}=#{v}") if v
+    report = nil
+
+    begin
+      http = Bio::Command.new_http(host)
+      http.open_timeout = 3000
+      http.read_timeout = 6000
+      result, = http.post(path, data.join('&'))
+      # workaround 2006.8.1 - fixed for new batch queuing system
+      case result.code
+      when "302"
+        result_location = result.header['location']
+        result_uri = URI.parse(result_location)
+        result_path = result_uri.path
+        done = false
+        until done
+          result = http.get(result_path)
+          if result.body[/Your job ID is/]
+            sleep 15
+          else
+            done = true
+          end
+        end
       end
-
-      report = nil
-
-      begin
-        http = Net::HTTP.new(host)
-        http.open_timeout = 300
-        http.read_timeout = 600
-        result, = http.post(path, data.join('&'))
+      @output = result.body.to_s
+      # workaround 2005.08.12
+      re = %r{<A HREF="http://#{host}(/tmp/[^"]+)">Show all result</A>} # "
+      if path = @output[re, 1]
+        result, = http.get(path)
         @output = result.body
-        # workaround 2005.08.12
-        if /\<A +HREF=\"(http\:\/\/fasta\.genome\.jp(\/tmp\/[^\"]+))\"\>Show all result\<\/A\>/i =~ @output.to_s then
-          result, = http.get($2)
-          @output = result.body
-          txt = @output.to_s.split(/\<pre\>/)[1]
-          raise 'cannot understand response' unless txt
-          txt.sub!(/\<\/pre\>.*\z/m, '')
-          txt.sub!(/.*^((T?FASTA|SSEARCH) (searches|compares))/m, '\1')
-          txt.sub!(/^\<form method\=\"POST\" name\=\"clust_check\"\>.*\n/, '')
-          txt.gsub!(/\<input[^\>]+value\=\"[^\"]*\"[^\>]*\>/i, '')
-          txt.gsub!(/\<(a|form|select|input|option|img)\s+[^\>]+\>/i, '')
-          txt.gsub!(/\<\/(a|form|select|input|option|img)\>/i, '')
-          @output = txt.gsub(/\&lt\;/, '<')
-          report = parse_result(@output.dup)
-        else
-          raise 'cannot understand response'
-        end
+        txt = @output.to_s.split(/\<pre\>/)[1]
+        raise 'cannot understand response' unless txt
+        txt.sub!(/\<\/pre\>.*\z/m, '')
+        txt.sub!(/.*^((T?FASTA|SSEARCH) (searches|compares))/m, '\1')
+        txt.sub!(/^\<form method\=\"POST\" name\=\"clust_check\"\>.*\n/, '')
+        txt.gsub!(/\<input[^\>]+value\=\"[^\"]*\"[^\>]*\>/i, '')
+        txt.gsub!(/\<(a|form|select|input|option|img)\s+[^\>]+\>/i, '')
+        txt.gsub!(/\<\/(a|form|select|input|option|img)\>/i, '')
+        @output = txt.gsub(/\&lt\;/, '<')
+        report = parse_result(@output.dup)
+      else
+        raise 'cannot understand response'
       end
-
-      return report
     end
 
+    return report
   end
 
-end
+end # Fasta
+
+end # Bio
 
 
 if __FILE__ == $0
@@ -187,76 +228,10 @@ if __FILE__ == $0
 # serv = Bio::Fasta.local('fasta34', 'hoge.nuc')
 # serv = Bio::Fasta.local('fasta34', 'hoge.pep')
 # serv = Bio::Fasta.local('ssearch34', 'hoge.pep')
+
+  # This may take 3 minutes or so.
   serv = Bio::Fasta.remote('fasta', 'genes')
   p serv.query(ARGF.read)
 end
 
 
-=begin
-
-= Bio::Fasta
-
---- Bio::Fasta.new(program, db, option = '', server = 'local')
---- Bio::Fasta.local(program, db, option = '')
---- Bio::Fasta.remote(program, db, option = '', server = 'genomenet')
-
-      Returns a fasta factory object (Bio::Fasta).
-
-      For the develpper, you can add server 'hoge' by adding
-      exec_hoge(query) method.
-
---- Bio::Fasta#query(query)
-
-      Execute fasta search and returns Report object (Bio::Fasta::Report).
-
---- Bio::Fasta#output
-
-      Returns a String containing fasta execution output in as is format.
-
---- Bio::Fasta#program
---- Bio::Fasta#db
---- Bio::Fasta#options
---- Bio::Fasta#server
---- Bio::Fasta#ktup
-
-      Accessors for the factory parameters.
-
---- Bio::Fasta#option
---- Bio::Fasta#option=(str)
-
-      Get/set options by string.
-
---- Bio::Fasta#format
---- Bio::Fasta#format=(number)
-
-      Accessors for the -m option.
-
---- Bio::Fasta.parser(parser)
-
-      Import Bio::Fasta::Report class by requiring specified parser.
-
-      This class method will be useful when you already have fasta
-      output files and want to use appropriate Report class for parsing.
-
-
-== Available databases for Fasta.remote(@program, @db, option, 'genomenet')
-
-  # ----------+-------+---------------------------------------------------
-  #  @program | query | @db (supported in GenomeNet)
-  # ----------+-------+---------------------------------------------------
-  #  fasta    | AA    | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
-  #           |       | pir, prf, pdbstr
-  #           +-------+---------------------------------------------------
-  #           | NA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
-  #           |       | htgs, dbsts, embl-nonst, embnonst-upd, epd,
-  #           |       | genes-nt, genome, vgenes.nuc
-  # ----------+-------+---------------------------------------------------
-  #  tfasta   | AA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
-  #           |       | htgs, dbsts, embl-nonst, embnonst-upd,
-  #           |       | genes-nt, genome, vgenes.nuc
-  # ----------+-------+---------------------------------------------------
-
-See http://fasta.genome.jp/ideas/ideas.html#fasta for more details.
-
-=end
-