ngoto-bio 1.2.9.9001

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

@@ -0,0 +1,334 @@
+#
+# = bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
+# 
+# Copyright:: Copyright (C) 2005 GOTO Naohisa <ng@bioruby.org>
+# License::   The Ruby License
+#
+#  $Id: report.rb,v 1.8 2007/04/05 23:35:39 trevor 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/ddbj.rb

@@ -0,0 +1,142 @@
+#
+# = bio/appl/blast/ddbj.rb - Remote BLAST wrapper using DDBJ web service
+# 
+# Copyright::  Copyright (C) 2008       Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/appl/blast/remote'
+require 'bio/io/ddbjxml'
+
+module Bio::Blast::Remote
+
+  # Remote BLAST factory using DDBJ Web API for Biology
+  # (http://xml.nig.ac.jp/).
+  #
+  module DDBJ
+
+    # Creates a remote BLAST factory using DDBJ.
+    # Returns Bio::Blast object.
+    #
+    # Note for future improvement: In the future, it might return
+    # Bio::Blast::Remote::DDBJ or other object. 
+    #
+    def self.new(program, db, options = [])
+      Bio::Blast.new(program, db, options, 'ddbj')
+    end
+
+    # Information about DDBJ BLAST.
+    module Information
+
+      include Bio::Blast::Remote::Information
+
+      # (private) parse database information
+      def _parse_databases
+        if defined? @parse_databases
+          return nil if @parse_databases
+        end
+        drv = Bio::DDBJ::XML::Blast.new
+        str = drv.getSupportDatabaseList
+
+        databases = {}
+        dbdescs = {}
+        key = 'blastn'
+        prefix = ''
+        databases[key] ||= []
+        dbdescs[key] ||= {}
+        str.each_line do |line|
+          a = line.strip.split(/\s*\-\s*/, 2)
+          case a.size
+          when 1
+            prefix = a[0].to_s.strip
+            prefix += ': ' unless prefix.empty?
+            key = 'blastn'
+            next #each_line
+          when 0
+            prefix = ''
+            key = 'blastp'
+            databases[key] ||= []
+            dbdescs[key] ||= {}
+            next #each_line
+          end
+          name = a[0].to_s.strip.freeze
+          desc = (prefix + a[1].to_s.strip).freeze
+          databases[key].push name
+          dbdescs[key][name] = desc
+        end
+
+        databases['blastp'] ||= []
+        dbdescs['blastp'] ||= []
+
+        databases['blastn'].freeze
+        databases['blastp'].freeze
+
+        databases['blastx']  = databases['blastp']
+        dbdescs['blastx']    = dbdescs['blastp']
+        databases['tblastn'] = databases['blastn']
+        dbdescs['tblastn']   = dbdescs['blastn']
+        databases['tblastx'] = databases['blastn']
+        dbdescs['tblastx']   = dbdescs['blastn']
+
+        @databases = databases
+        @database_descriptions = dbdescs
+        @parse_databases = true
+        true
+      end
+      private :_parse_databases
+
+    end #module Information
+
+    extend Information
+
+    # executes BLAST and returns result as a string
+    def exec_ddbj(query)
+      options = make_command_line_options
+      opt = Bio::Blast::NCBIOptions.new(options)
+
+      # SOAP objects are cached
+      @ddbj_remote_blast ||= Bio::DDBJ::XML::Blast.new
+      #@ddbj_request_manager ||= Bio::DDBJ::XML::RequestManager.new
+      # always use REST version to prevent warning messages
+      @ddbj_request_manager ||= Bio::DDBJ::XML::RequestManager::REST.new
+
+      program = opt.delete('-p')
+      db = opt.delete('-d')
+      optstr = Bio::Command.make_command_line_unix(opt.options)
+
+      # using searchParamAsync 
+      qid = @ddbj_remote_blast.searchParamAsync(program, db, query, optstr)
+      @output = qid
+
+      sleeptime = 2
+      flag = true
+      while flag
+        if $VERBOSE then
+          $stderr.puts "DDBJ BLAST: ID: #{qid} -- waitng #{sleeptime} sec."
+        end
+        sleep(sleeptime)
+
+        result = @ddbj_request_manager.getAsyncResult(qid)
+        case result.to_s
+        when /The search and analysis service by WWW is very busy now/
+          raise result.to_s.strip + '(Alternatively, wrong options may be given.)'
+        when /Your job has not completed yet/
+          sleeptime = 5
+        else
+          flag = false
+        end
+      end while flag
+
+      @output = result
+      return @output
+    end
+
+  end #module DDBJ
+
+  # for lazy load DDBJ module
+  Ddbj = DDBJ
+
+end #module Bio::Blast::Remote
+