bio 0.7.0

data/lib/bio/appl/clustalw.rb

@@ -0,0 +1,191 @@
+#
+# = bio/appl/clustalw.rb - CLUSTAL W wrapper class
+#
+# Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+# License::   LGPL
+#
+#--
+#  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: clustalw.rb,v 1.10 2005/12/18 15:58:40 k Exp $
+#
+# Bio::ClustalW is a CLUSTAL W execution wrapper class.
+# Its object is also called an alignment factory.
+# CLUSTAL W is a very popular software for multiple sequence alignment.
+#
+# == References
+#
+# * Thompson,J.D., Higgins,D.G. and Gibson,T.J..
+#   CLUSTAL W: improving the sensitivity of progressive multiple sequence
+#   alignment through sequence weighting, position-specific gap penalties
+#   and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
+#   http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673
+# * http://www.ebi.ac.uk/clustalw/
+# * ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+#
+
+
+require 'tempfile'
+require 'open3'
+
+require 'bio/sequence'
+require 'bio/alignment'
+
+module Bio
+
+  # Bio::ClustalW is a CLUSTAL W execution wrapper class.
+  # Its object is also called an alignment factory.
+  # CLUSTAL W is a very popular software for multiple sequence alignment.
+  class ClustalW
+
+    autoload :Report, 'bio/appl/clustalw/report'
+
+    # Creates a new CLUSTAL W execution wrapper object (alignment factory).
+    def initialize(program = 'clustalw', option = [])
+      @program = program
+      @option = option
+      @command = nil
+      @output = nil
+      @report = nil
+      @log = nil
+    end
+
+    # name of the program (usually 'clustalw' in UNIX)
+    attr_accessor :program
+
+    # options
+    attr_accessor :option
+
+    # Returns last command-line strings executed by this factory.
+    # Note that filenames described in the command-line may already
+    # be removed because they are temporary files.
+    # Returns an array.
+    attr_reader :command
+
+    # Returns last messages of CLUSTAL W execution.
+    attr_reader :log
+
+    # Returns last raw alignment result (String).
+    attr_reader :output
+
+    # Returns last alignment result.
+    # Returns a Bio::ClustalW::Report object.
+    attr_reader :report
+
+    # Executes the program(clustalw).
+    # If +seqs+ is not nil, perform alignment for seqs.
+    # If +seqs+ is nil, simply executes CLUSTAL W.
+    def query(seqs)
+      if seqs then
+        query_align(seqs)
+      else
+        exec_local(@option)
+      end
+    end
+
+    # Performs alignment for +seqs+.
+    # +seqs+ should be Bio::Alignment or Array of sequences or nil.
+    def query_align(seqs)
+      seqtype = nil
+      unless seqs.is_a?(Bio::Alignment)
+        seqs = Bio::Alignment.new(seqs)
+      end
+      seqs.each do |s|
+        if    s.is_a?(Bio::Sequence::AA) then
+          seqtype = 'PROTEIN'
+        elsif s.is_a?(Bio::Sequence::NA) then
+          seqtype = 'DNA'
+        end
+        break if seqtype
+      end
+      query_string(seqs.to_fasta(70, :avoid_same_name => true), seqtype)
+    end
+
+    # Performs alignment for +str+.
+    # +str+ should be a string that can be recognized by CLUSTAL W.
+    def query_string(str, *arg)
+      begin
+        tf_in = Tempfile.open('align')
+        tf_in.print str
+      ensure
+        tf_in.close(false)
+      end
+      r = query_by_filename(tf_in.path, *arg)
+      tf_in.close(true)
+      r
+    end
+
+    # Performs alignment of sequences in the file named +path+.
+    def query_by_filename(path, seqtype = nil)
+      require 'bio/appl/clustalw/report'
+
+      tf_out = Tempfile.open('clustalout')
+      tf_out.close(false)
+      tf_dnd = Tempfile.open('clustaldnd')
+      tf_dnd.close(false)
+
+      opt = [ "-align",
+        "-infile=#{path}",
+        "-outfile=#{tf_out.path}",
+        "-newtree=#{tf_dnd.path}",
+        "-outorder=input"
+      ]
+      opt << "-type=#{seqtype}" if seqtype
+      opt.concat(@option)
+      exec_local(opt)
+      tf_out.open
+      @output = tf_out.read
+      tf_out.close(true)
+      tf_dnd.open
+      @output_dnd = tf_dnd.read
+      tf_dnd.close(true)
+      @report = Report.new(@output, seqtype)
+      @report
+    end
+
+    # Returns last alignment guild-tree (file.dnd).
+    attr_reader :output_dnd
+
+    # Returns last error messages (to stderr) of CLUSTAL W execution.
+    attr_reader :errorlog
+
+    private
+    # Executes the program in the local machine.
+    def exec_local(opt)
+      @command = [ @program,  *opt ]
+      #STDERR.print "DEBUG: ", @command.join(" "), "\n"
+      @log = nil
+
+      Open3.popen3(*@command) do |din, dout, derr|
+        din.close
+        t = Thread.start do
+          @errorlog = derr.read
+        end
+        @log = dout.read
+        t.join
+      end
+#      @command_string = @command.join(" ")
+#      IO.popen(@command, "r") do |io|
+#	io.sync = true
+#	@log = io.read
+#      end
+      @log
+    end
+
+  end #class ClustalW
+
+end #module Bio
+

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

@@ -0,0 +1,154 @@
+#
+# = 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
+#
+#--
+#  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 $
+#
+# Bio::ClustalW::Report is a CLUSTAL W report (*.aln file) parser.
+# CLUSTAL W is a very popular software for multiple sequence alignment.
+#
+# == References
+#
+# * Thompson,J.D., Higgins,D.G. and Gibson,T.J..
+#   CLUSTAL W: improving the sensitivity of progressive multiple sequence
+#   alignment through sequence weighting, position-specific gap penalties
+#   and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
+#   http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673
+# * http://www.ebi.ac.uk/clustalw/
+# * ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+#
+
+require 'bio/sequence'
+require 'bio/db'
+require 'bio/alignment'
+require 'bio/appl/clustalw'
+
+module Bio
+  class ClustalW
+
+    # CLUSTAL W result data (*.aln file) parser class.
+    class Report < Bio::DB
+
+      # Delimiter of each entry. Bio::FlatFile uses it.
+      # In Bio::ClustalW::Report, it it nil (1 entry 1 file).
+      DELIMITER = nil
+
+      # Creates new instance.
+      # +str+ should be a CLUSTAL format string.
+      # +seqclass+ should on of following:
+      # * Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
+      # * String: 'PROTEIN', 'DNA', ...
+      def initialize(str, seqclass = nil)
+        @raw = str
+        @align = nil
+        @match_line = nil
+        @header = nil
+        case seqclass
+        when /PROTEIN/i
+          @seqclass = Bio::Sequence::AA
+        when /[DR]NA/i
+          @seqclass = Bio::Sequence::NA
+        else
+          if seqclass.is_a?(Module) then
+            @seqclass = seqclass
+          else
+            @seqclass = Bio::Sequence
+          end
+        end
+      end
+      # string of whole result
+      attr_reader :raw
+
+      # sequence class (one of Bio::Sequence, Bio::Sequence::NA,
+      # Bio::Sequence::AA, ...)
+      attr_reader :seqclass
+
+      # Shows first line of the result data, for example,
+      # 'CLUSTAL W (1.82) multiple sequence alignment'.
+      # Returns a string.
+      def header
+        @header or (do_parse or @header)
+      end
+
+      # Shows "match line" of CLUSTAL's alignment result, for example,
+      # ':* :* .*   *       .*::*.   ** :* . *    .        '.
+      # Returns a string.
+      def match_line
+        @match_line or (do_parse or @match_line)
+      end
+
+      # Gets an multiple alignment.
+      # Returns a Bio::Alignment object.
+      def align
+        do_parse() unless @align
+        @align
+      end
+      alias alignment align
+
+      # Gets an fasta-format string of the sequences.
+      # Returns a string.
+      def to_fasta(*arg)
+        align.to_fasta(*arg)
+      end
+
+      # Gets an array of the sequences.
+      # Returns an array of Bio::FastaFormat objects.
+      def to_a
+        align.to_fastaformat_array
+      end
+
+      private
+      # Parses Clustal W result text.
+      def do_parse
+        return nil if @align
+        a = @raw.split(/\r?\n\r?\n/)
+        @header = a.shift.to_s
+        xalign = Bio::Alignment.new
+        @match_line = ''
+        if a.size > 0 then
+          a[0].gsub!(/\A(\r?\n)+/, '')
+          a.collect! { |x| x.split(/\r?\n/) }
+          a.each { |x|
+            x.each { |y| y.sub!(/ +\d+\s*$/, '') }} #for -SEQNOS=on option
+          @tagsize = ( a[0][0].rindex(/\s/) or -1 ) + 1
+          a.each do |x|
+            @match_line << x.pop.to_s[@tagsize..-1]
+          end
+          a[0].each do |y|
+            xalign.store(y[0, @tagsize].sub(/\s+\z/, ''), '')
+          end
+          a.each do |x|
+            x.each do |y|
+              name = y[0, @tagsize].sub(/\s+\z/, '')
+              seq = y[@tagsize..-1]
+              xalign[name] << seq
+            end
+          end
+          xalign.collect! { |x| @seqclass.new(x) }
+        end
+        @align = xalign
+        nil
+      end
+
+    end #class Report
+  end #class ClustalW
+end #module Bio
+

data/lib/bio/appl/emboss.rb

@@ -0,0 +1,68 @@
+#
+# bio/appl/emboss.rb - EMBOSS wrapper
+# 
+#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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: emboss.rb,v 1.2 2005/09/08 01:22:08 k Exp $
+#
+
+module Bio
+
+  class EMBOSS
+
+    def initialize(cmd_line)
+      @cmd_line = cmd_line + ' -stdout'
+    end
+
+    def exec
+      begin
+        @io = IO.popen(@cmd_line, "w+")
+        @result = @io.read
+        return @result
+      ensure
+        @io.close
+      end
+    end
+    attr_reader :io, :result
+
+  end
+
+end
+
+=begin
+
+= Bio::EMBOSS
+
+EMBOSS wrapper.
+
+  #!/usr/bin/env ruby
+  require 'bio'
+
+  emboss = Bio::EMBOSS.new("getorf -sequence ~/xlrhodop -outseq stdout")
+  puts emboss.exec
+
+--- Bio::EMBOSS.new(command_line)
+
+--- Bio::EMBOSS#exec
+--- Bio::EMBOSS#io
+--- Bio::EMBOSS#result
+
+=== SEE ALSO
+
+* http://www.emboss.org
+
+=end

data/lib/bio/appl/fasta.rb

@@ -0,0 +1,262 @@
+#
+# bio/appl/fasta.rb - FASTA wrapper
+#
+#   Copyright (C) 2001,2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  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 $
+#
+
+require 'net/http'
+require 'cgi' unless defined?(CGI)
+require 'bio/command'
+require 'shellwords'
+
+module Bio
+
+  class Fasta
+
+    autoload :Report, 'bio/appl/fasta/format10'
+    #autoload :?????,  'bio/appl/fasta/format6'
+
+    include Bio::Command::Tools
+
+    def initialize(program, db, opt = [], server = 'local')
+      @format	= 10
+
+      @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
+
+    def option
+      # backward compatibility
+      make_command_line(@options)
+    end
+
+    def option=(str)
+      # backward compatibility
+      @options = Shellwords.shellwords(str)
+    end
+
+    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
+
+    def self.parser(parser)
+      require "bio/appl/fasta/#{parser}"
+    end
+
+    def self.local(program, db, option = '')
+      self.new(program, db, option, 'local')
+    end
+
+    def self.remote(program, db, option = '', server = 'genomenet')
+      self.new(program, db, option, server)
+    end
+
+    def query(query)
+      return self.send("exec_#{@server}", query.to_s)
+    end
+
+
+    private
+
+
+    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
+
+
+    def exec_local(query)
+      cmd = [ @program, *@options ]
+      cmd.concat([ '@', @db, @ktup ])
+
+      report = nil
+
+      @output = call_command_local(cmd, query)
+      report = parse_result(@output)
+
+      return report
+    end
+
+
+    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(make_command_line_unix(@options)),
+        'ktup_value'	=> @ktup,
+        'matrix'	=> @matrix,
+      }
+
+      data = []
+
+      form.each do |k, v|
+        data.push("#{k}=#{v}") if v
+      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
+        # 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
+      end
+
+      return report
+    end
+
+  end
+
+end
+
+
+if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue
+  end
+
+# serv = Bio::Fasta.local('fasta34', 'hoge.nuc')
+# serv = Bio::Fasta.local('fasta34', 'hoge.pep')
+# serv = Bio::Fasta.local('ssearch34', 'hoge.pep')
+  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
+