bio 0.7.0

data/lib/bio/appl/bl2seq/report.rb

@@ -0,0 +1,350 @@
+#
+# = bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
+# 
+# Copyright:: Copyright (C) 2005 GOTO Naohisa <ng@bioruby.org>
+# 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 1.6 2005/12/18 15:58:39 k Exp $
+#
+# Bio::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
+#
+# = Acknowledgements
+#
+# Thanks to Tomoaki NISHIYAMA <tomoakin __at__ kenroku.kanazawa-u.ac.jp> 
+# for providing bl2seq parser patches based on
+# lib/bio/appl/blast/format0.rb.
+#
+
+require 'bio/appl/blast/format0'
+
+module Bio
+class Blast
+
+  class Bl2seq
+
+    # Bio::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
+    # It inherits Bio::Blast::Default::Report.
+    # Most of its methods are the same as Bio::Blast::Default::Report,
+    # but it lacks many methods.
+    class Report < Bio::Blast::Default::Report
+
+      # Delimiter of each entry. Bio::FlatFile uses it.
+      # In Bio::Bl2seq::Report, it it nil (1 entry 1 file).
+      DELIMITER = RS = nil
+
+      undef format0_parse_header
+      undef program, version, version_number, version_date,
+        message, converged?, reference, db
+
+      # Splits headers.
+      def format0_split_headers(data)
+        @f0query = data.shift
+      end
+      private :format0_split_headers
+
+      # Splits the search results.
+      def format0_split_search(data)
+        iterations = []
+        while r = data[0] and /^\>/ =~ r
+          iterations << Iteration.new(data)
+        end
+        if iterations.size <= 0 then
+          iterations << Iteration.new(data)
+        end
+        iterations
+      end
+      private :format0_split_search
+
+      # Stores format0 database statistics.
+      # Internal use only. Users must not use the class.
+      class F0dbstat < Bio::Blast::Default::Report::F0dbstat #:nodoc:
+        # Returns number of sequences in database.
+        def db_num
+          unless defined?(@db_num)
+            parse_params
+            @db_num = @hash['Number of Sequences'].to_i
+          end
+          @db_num
+        end
+
+        # Returns number of letters in database.
+        def db_len
+          unless defined?(@db_len)
+            parse_params
+            @db_len = @hash['length of database'].to_i
+          end
+          @db_len
+        end
+      end #class F0dbstat
+
+      # Bio::Bl2seq::Report::Iteration stores information about
+      # a iteration.
+      # Normally, it may contain some Bio::Bl2seq::Report::Hit objects.
+      #
+      # Note that its main existance reason is to keep complatibility
+      # between Bio::Blast::Default::Report::* classes.
+      class Iteration < Bio::Blast::Default::Report::Iteration
+        # Creates a new Iteration object.
+        # It is designed to be called only internally from
+        # the Bio::Blast::Default::Report class.
+        # Users shall not use the method directly.
+        def initialize(data)
+          @f0stat = []
+          @f0dbstat = Bio::Blast::Default::Report::AlwaysNil.instance
+          @hits = []
+          @num = 1
+          while r = data[0] and /^\>/ =~ r
+            @hits << Hit.new(data)
+          end
+        end
+
+        # Returns the hits of the iteration.
+        # It returns an array of Bio::Bl2seq::Report::Hit objects.
+        def hits; @hits; end
+
+        undef message, pattern_in_database, 
+          pattern, pattern_positions, hits_found_again,
+          hits_newly_found, hits_for_pattern, parse_hitlist,
+          converged?
+      end #class Iteration
+
+      # Bio::Bl2seq::Report::Hit contains information about a hit.
+      # It may contain some Bio::Blast::Default::Report::HSP objects.
+      # All methods are the same as Bio::Blast::Default::Report::Hit class.
+      # Please refer to Bio::Blast::Default::Report::Hit.
+      class Hit < Bio::Blast::Default::Report::Hit
+      end #class Hit
+
+      # Bio::Bl2seq::Report::HSP holds information about the hsp
+      # (high-scoring segment pair).
+      # NOTE that the HSP class below is NOT used because
+      # Ruby's constants namespace are normally statically determined
+      # and HSP object is created in Bio::Blast::Default::Report::Hit class.
+      # Please refer to Bio::Blast::Default::Report::HSP.
+      class HSP < Bio::Blast::Default::Report::HSP
+      end #class HSP
+
+    end #class Report
+  end #class Bl2seq
+
+end #class Blast
+end #module Bio
+
+######################################################################
+
+if __FILE__ == $0
+
+  Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, ARGF) do |ff|
+  ff.each do |rep|
+
+  print "# === Bio::Blast::Bl2seq::Report\n"
+  puts
+  #@#print "  rep.program           #=> "; p rep.program
+  #@#print "  rep.version           #=> "; p rep.version
+  #@#print "  rep.reference         #=> "; p rep.reference
+  #@#print "  rep.db                #=> "; p rep.db
+  #print "  rep.query_id          #=> "; p rep.query_id
+  print "  rep.query_def         #=> "; p rep.query_def
+  print "  rep.query_len         #=> "; p rep.query_len
+  #puts
+  #@#print "  rep.version_number    #=> "; p rep.version_number
+  #@#print "  rep.version_date      #=> "; p rep.version_date
+  puts
+
+  print "# === Parameters\n"
+  #puts
+  #print "  rep.parameters        #=> "; p rep.parameters
+  puts
+  print "  rep.matrix            #=> "; p rep.matrix
+  print "  rep.expect            #=> "; p rep.expect
+  #print "  rep.inclusion         #=> "; p rep.inclusion
+  print "  rep.sc_match          #=> "; p rep.sc_match
+  print "  rep.sc_mismatch       #=> "; p rep.sc_mismatch
+  print "  rep.gap_open          #=> "; p rep.gap_open
+  print "  rep.gap_extend        #=> "; p rep.gap_extend
+  #print "  rep.filter            #=> "; p rep.filter
+  #@#print "  rep.pattern           #=> "; p rep.pattern
+  #print "  rep.entrez_query      #=> "; p rep.entrez_query
+  #puts
+  #@#print "  rep.pattern_positions  #=> "; p rep.pattern_positions
+  puts
+
+  print "# === Statistics (last iteration's)\n"
+  #puts
+  #print "  rep.statistics        #=> "; p rep.statistics
+  puts
+  print "  rep.db_num            #=> "; p rep.db_num
+  print "  rep.db_len            #=> "; p rep.db_len
+  #print "  rep.hsp_len           #=> "; p rep.hsp_len
+  print "  rep.eff_space         #=> "; p rep.eff_space
+  print "  rep.kappa             #=> "; p rep.kappa
+  print "  rep.lambda            #=> "; p rep.lambda
+  print "  rep.entropy           #=> "; p rep.entropy
+  puts
+  print "  rep.num_hits          #=> "; p rep.num_hits
+  print "  rep.gapped_kappa      #=> "; p rep.gapped_kappa
+  print "  rep.gapped_lambda     #=> "; p rep.gapped_lambda
+  print "  rep.gapped_entropy    #=> "; p rep.gapped_entropy
+  print "  rep.posted_date       #=> "; p rep.posted_date
+  puts
+
+  #@#print "# === Message (last iteration's)\n"
+  #@#puts
+  #@#print "  rep.message           #=> "; p rep.message
+  #puts
+  #@#print "  rep.converged?        #=> "; p rep.converged?
+  #@#puts
+
+  print "# === Iterations\n"
+  puts
+  print "  rep.itrerations.each do |itr|\n"
+  puts
+
+  rep.iterations.each do |itr|
+      
+  print "# --- Bio::Blast::Bl2seq::Report::Iteration\n"
+  puts
+
+  print "    itr.num             #=> "; p itr.num
+  #print "    itr.statistics      #=> "; p itr.statistics
+  #@#print "    itr.message         #=> "; p itr.message
+  print "    itr.hits.size       #=> "; p itr.hits.size
+  #puts
+  #@#print "    itr.hits_newly_found.size    #=> "; p itr.hits_newly_found.size;
+  #@#print "    itr.hits_found_again.size    #=> "; p itr.hits_found_again.size;
+  #@#if itr.hits_for_pattern then
+  #@#itr.hits_for_pattern.each_with_index do |hp, hpi|
+  #@#print "    itr.hits_for_pattern[#{hpi}].size #=> "; p hp.size;
+  #@#end
+  #@#end
+  #@#print "    itr.converged?      #=> "; p itr.converged?
+  puts
+
+  print "    itr.hits.each do |hit|\n"
+  puts
+
+  itr.hits.each_with_index do |hit, i|
+
+  print "# --- Bio::Blast::Bl2seq::Default::Report::Hit"
+  print " ([#{i}])\n"
+  puts
+
+  #print "      hit.num           #=> "; p hit.num
+  #print "      hit.hit_id        #=> "; p hit.hit_id
+  print "      hit.len           #=> "; p hit.len
+  print "      hit.definition    #=> "; p hit.definition
+  #print "      hit.accession     #=> "; p hit.accession
+  #puts
+  print "      hit.found_again?  #=> "; p hit.found_again?
+
+  print "        --- compatible/shortcut ---\n"
+  #print "      hit.query_id      #=> "; p hit.query_id
+  #print "      hit.query_def     #=> "; p hit.query_def
+  #print "      hit.query_len     #=> "; p hit.query_len
+  #print "      hit.target_id     #=> "; p hit.target_id
+  print "      hit.target_def    #=> "; p hit.target_def
+  print "      hit.target_len    #=> "; p hit.target_len
+
+  print "            --- first HSP's values (shortcut) ---\n"
+  print "      hit.evalue        #=> "; p hit.evalue
+  print "      hit.bit_score     #=> "; p hit.bit_score
+  print "      hit.identity      #=> "; p hit.identity
+  #print "      hit.overlap       #=> "; p hit.overlap
+
+  print "      hit.query_seq     #=> "; p hit.query_seq
+  print "      hit.midline       #=> "; p hit.midline
+  print "      hit.target_seq    #=> "; p hit.target_seq
+
+  print "      hit.query_start   #=> "; p hit.query_start
+  print "      hit.query_end     #=> "; p hit.query_end
+  print "      hit.target_start  #=> "; p hit.target_start
+  print "      hit.target_end    #=> "; p hit.target_end
+  print "      hit.lap_at        #=> "; p hit.lap_at
+  print "            --- first HSP's vaules (shortcut) ---\n"
+  print "        --- compatible/shortcut ---\n"
+
+  puts
+  print "      hit.hsps.size     #=> "; p hit.hsps.size
+  if hit.hsps.size == 0 then
+  puts  "          (HSP not found: please see blastall's -b and -v options)"
+  puts
+  else
+
+  puts
+  print "      hit.hsps.each do |hsp|\n"
+  puts
+
+  hit.hsps.each_with_index do |hsp, j|
+
+  print "# --- Bio::Blast::Default::Report::HSP (Bio::Blast::Bl2seq::Report::HSP)"
+  print " ([#{j}])\n"
+  puts
+  #print "        hsp.num         #=> "; p hsp.num
+  print "        hsp.bit_score   #=> "; p hsp.bit_score 
+  print "        hsp.score       #=> "; p hsp.score
+  print "        hsp.evalue      #=> "; p hsp.evalue
+  print "        hsp.identity    #=> "; p hsp.identity
+  print "        hsp.gaps        #=> "; p hsp.gaps
+  print "        hsp.positive    #=> "; p hsp.positive
+  print "        hsp.align_len   #=> "; p hsp.align_len
+  #print "        hsp.density     #=> "; p hsp.density
+
+  print "        hsp.query_frame #=> "; p hsp.query_frame
+  print "        hsp.query_from  #=> "; p hsp.query_from
+  print "        hsp.query_to    #=> "; p hsp.query_to
+
+  print "        hsp.hit_frame   #=> "; p hsp.hit_frame
+  print "        hsp.hit_from    #=> "; p hsp.hit_from
+  print "        hsp.hit_to      #=> "; p hsp.hit_to
+
+  #print "        hsp.pattern_from#=> "; p hsp.pattern_from
+  #print "        hsp.pattern_to  #=> "; p hsp.pattern_to
+
+  print "        hsp.qseq        #=> "; p hsp.qseq
+  print "        hsp.midline     #=> "; p hsp.midline
+  print "        hsp.hseq        #=> "; p hsp.hseq
+  puts
+  print "        hsp.percent_identity  #=> "; p hsp.percent_identity
+  #print "        hsp.mismatch_count    #=> "; p hsp.mismatch_count
+  #
+  print "        hsp.query_strand      #=> "; p hsp.query_strand
+  print "        hsp.hit_strand        #=> "; p hsp.hit_strand
+  print "        hsp.percent_positive  #=> "; p hsp.percent_positive
+  print "        hsp.percent_gaps      #=> "; p hsp.percent_gaps
+  puts
+
+  end #each
+  end #if hit.hsps.size == 0
+  end
+  end
+  end #ff.each
+  end #FlatFile.open
+
+end #if __FILE__ == $0
+
+######################################################################
+
+=begin
+
+= Bio::Blast::Bl2seq::Report
+
+    NCBI bl2seq (BLAST 2 sequences) output parser
+
+=end
+

data/lib/bio/appl/blast.rb

@@ -0,0 +1,269 @@
+#
+# bio/appl/blast.rb - BLAST wrapper
+# 
+#   Copyright (C) 2001 Mitsuteru C. Nakao <n@bioruby.org>
+#   Copyright (C) 2002,2003 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: blast.rb,v 1.27 2005/12/18 17:28:55 nakao Exp $
+#
+
+require 'net/http'
+require 'cgi' unless defined?(CGI)
+require 'bio/command'
+require 'shellwords'
+
+module Bio
+
+  class Blast
+
+    autoload :Fastacmd,     'bio/io/fastacmd'
+    autoload :Report,       'bio/appl/blast/report'
+    autoload :Default,      'bio/appl/blast/format0'
+    autoload :WU,           'bio/appl/blast/wublast'
+    autoload :Bl2seq,       'bio/appl/bl2seq/report'
+
+    include Bio::Command::Tools
+
+    def initialize(program, db, opt = [], server = 'local')
+      @program  = program
+      @db       = db
+      @server   = server
+
+      @blastall = 'blastall'
+      @matrix   = nil
+      @filter   = nil
+
+      @output   = ''
+      @parser   = nil
+
+      begin
+        a = opt.to_ary
+      rescue NameError #NoMethodError
+        # backward compatibility
+        a = Shellwords.shellwords(opt)
+      end
+      unless a.find { |x| /\A\-m/ =~ x.to_s } then
+        if defined?(XMLParser) or defined?(REXML)
+          @format = 7
+        else
+          @format = 8
+        end
+      end
+      @options = [ *a ]
+    end
+    attr_accessor :program, :db, :options, :server, :blastall, :matrix, :filter
+    attr_reader :output, :format
+    attr_writer :parser  # to change :xmlparser, :rexml, :tab
+
+    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
+
+    def option
+      # backward compatibility
+      make_command_line(@options)
+    end
+
+    def option=(str)
+      # backward compatibility
+      @options = Shellwords.shellwords(str)
+    end
+
+    # the method Bio::Blast.report is moved from bio/appl/blast/report.rb.
+    # only for xml format
+    def self.reports(input, parser = nil)
+      ary = []
+      input.each("</BlastOutput>\n") do |xml|
+        xml.sub!(/[^<]*(<?)/, '\1') # skip before <?xml> tag
+        next if xml.empty?          # skip trailing no hits
+        if block_given?
+          yield Report.new(xml, parser)
+        else
+          ary << Report.new(xml, parser)
+        end
+      end
+      return ary
+    end
+
+
+    private
+
+
+    def parse_result(data)
+      Report.new(data, @parser)
+    end
+
+
+    def exec_local(query)
+      cmd = [ @blastall, '-p', @program, '-d', @db ]
+      cmd.concat([ '-M', @matrix ]) if @matrix
+      cmd.concat([ '-F', @filter ]) if @filter
+      cmd.concat([ '-m', @format.to_s ]) if @format
+      cmd.concat(@options) if @options
+
+      report = nil
+
+      @output = call_command_local(cmd, query)
+      report = parse_result(@output)
+
+      return report
+    end
+
+
+    def exec_genomenet(query)
+      host = "blast.genome.jp"
+      #path = "/sit-bin/nph-blast"
+      path = "/sit-bin/blast" #2005.08.12
+
+      matrix = @matrix ? @matrix : 'blosum62'
+      filter = @filter ? @filter : 'T'
+
+      opt = []
+      opt.concat([ '-m', @format.to_s ]) if @format
+      opt.concat(@options) if @options
+
+      form = {
+        'style'          => 'raw',
+        'prog'           => @program,
+        'dbname'         => @db,
+        'sequence'       => CGI.escape(query),
+        'other_param'    => CGI.escape(make_command_line_unix(opt)),
+        'matrix'         => matrix,
+        'filter'         => filter,
+        'V_value'        => 500, # default value for GenomeNet
+        'B_value'        => 250, # default value for GenomeNet
+        'alignment_view' => 0,
+      }
+
+      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\:\/\/blast\.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!(/.*^ \-{20,}\s*/m, '')
+          @output = txt.gsub(/\&lt\;/, '<')
+          report = parse_result(@output)
+        else
+          raise 'cannot understand response'
+        end
+      end
+
+      return report
+    end
+
+
+    def exec_ncbi(query)
+      raise NotImplementedError
+    end
+  end
+
+end
+
+
+if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue
+  end
+
+# serv = Bio::Blast.local('blastn', 'hoge.nuc')
+# serv = Bio::Blast.local('blastp', 'hoge.pep')
+  serv = Bio::Blast.remote('blastp', 'genes')
+
+  query = ARGF.read
+  p serv.query(query)
+end
+
+
+=begin
+
+= Bio::Blast
+
+--- Bio::Blast.new(program, db, option = '', server = 'local')
+--- Bio::Blast.local(program, db, option = '')
+--- Bio::Blast.remote(program, db, option = '', server = 'genomenet')
+
+      Returns a blast factory object (Bio::Blast).
+
+      For the develpper, you can add server 'hoge' by adding
+      exec_hoge(query) method.
+
+--- Bio::Blast#query(query)
+
+      Execute blast search and returns Report object (Bio::Blast::Report).
+
+--- Bio::Blast#output
+
+      Returns a String containing blast execution output in as is format.
+
+--- Bio::Blast#program
+--- Bio::Blast#db
+--- Bio::Blast#options
+--- Bio::Blast#server
+--- Bio::Blast#blastall
+--- Bio::Blast#filter
+
+      Accessors for the factory parameters.
+
+--- Bio::Blast#option
+--- Bio::Blast#option=(str)
+
+      Get/set options by string.
+
+== Available databases for Blast.remote(@program, @db, option, 'genomenet')
+
+  # ----------+-------+---------------------------------------------------
+  #  @program | query | @db (supported in GenomeNet)
+  # ----------+-------+---------------------------------------------------
+  #  blastp   | AA    | nr-aa, genes, vgenes.pep, swissprot, swissprot-upd,
+  # ----------+-------+ pir, prf, pdbstr
+  #  blastx   | NA    | 
+  # ----------+-------+---------------------------------------------------
+  #  blastn   | NA    | nr-nt, genbank-nonst, gbnonst-upd, dbest, dbgss,
+  # ----------+-------+ htgs, dbsts, embl-nonst, embnonst-upd, epd,
+  #  tblastn  | AA    | genes-nt, genome, vgenes.nuc
+  # ----------+-------+---------------------------------------------------
+
+See http://blast.genome.jp/ideas/ideas.html#blast for more details.
+
+=end
+