bio 1.0.0 → 1.1.0

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

@@ -2,25 +2,9 @@
 # = bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
 # 
 # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng@bioruby.org>
-# 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 1.6 2005/12/18 15:58:39 k Exp $
+#  $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.
 #

data/lib/bio/appl/blast.rb

@@ -1,31 +1,12 @@
 #
 # = bio/appl/blast.rb - BLAST wrapper
 # 
-# Copyright::  Copyright (C) 2001
-#              Mitsuteru C. Nakao <n@bioruby.org>
-# Copyrigth::  Copyright (C) 2002,2003
-#              KATAYAMA Toshiaki <k@bioruby.org>
-# License::    Ruby's
+# Copyright::  Copyright (C) 2001       Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k@bioruby.org>
+# Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::    The Ruby License
 #
-# $Id: blast.rb,v 1.28 2006/02/18 16:08:10 nakao Exp $
-#
-# = Description
-#
-# = Examples
-#
-#   program = 'blastp'
-#   database = 'SWISS'
-#   options = '-e 0.0001'
-#   serv = Bio::Blast.new(program, database, options)
-#   server = 'genomenet'
-#   genomenet = Bio::Blast.remote(program, database, options, server)
-#   report = serv.query(sequence_text)
-#
-# = References
-#
-# * http://www.ncbi.nlm.nih.gov/blast/
-#
-# * http://blast.genome.jp/ideas/ideas.html#blast
+# $Id: blast.rb,v 1.33 2007/04/05 23:35:39 trevor Exp $
 #
 
 require 'net/http'
@@ -35,39 +16,54 @@ require 'shellwords'
 
 module Bio
 
-  # BLAST wrapper
-  #
   # == Description
+  # 
+  # The Bio::Blast class contains methods for running local or remote BLAST
+  # searches, as well as for parsing of the output of such BLASTs (i.e. the
+  # BLAST reports). For more information on similarity searches and the BLAST
+  # program, see http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html.
   #
-  # A blastall program wrapper.
-  #
-  # == Examples
+  # == Usage
   #
-  #   program = 'blastp'
-  #   database = 'SWISS'
-  #   options = '-e 0.0001'
-  #   serv = Bio::Blast.new(program, database, options)
+  #   require 'bio'
   #   
-  #   server = 'genomenet'
-  #   genomenet = Bio::Blast.remote(program, database, options, server)
-  #   
-  #   report = serv.query(sequence_text)
+  #   # To run an actual BLAST analysis:
+  #   #   1. create a BLAST factory
+  #   remote_blast_factory = Bio::Blast.remote('blastp', 'SWISS',
+  #                                            '-e 0.0001', 'genomenet')
+  #   #or:
+  #   local_blast_factory = Bio::Blast.local('blastn','/path/to/db')
+  #
+  #   #   2. run the actual BLAST by querying the factory
+  #   report = remote_blast_factory.query(sequence_text)
+  #
+  #   # Then, to parse the report, see Bio::Blast::Report
+  #
+  # === Available databases for Bio::Blast.remote
   #
-  # == 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
+  #  ----------+-------+---------------------------------------------------
   #
-  # ----------+-------+---------------------------------------------------
-  #  @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 also
   #
-  # * See http://blast.genome.jp/ideas/ideas.html#blast for more details.
+  # * Bio::Blast::Report
+  # * Bio::Blast::Report::Hit
+  # * Bio::Blast::Report::Hsp
+  #
+  # == References
+  # 
+  # * http://www.ncbi.nlm.nih.gov/blast/
+  # * http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html
+  # * http://blast.genome.jp/ideas/ideas.html#blast
   #
   class Blast
 
@@ -77,14 +73,31 @@ module Bio
     autoload :WU,           'bio/appl/blast/wublast'
     autoload :Bl2seq,       'bio/appl/bl2seq/report'
 
-    include Bio::Command::Tools
-
-    # Sets up the blast program at the localhost
+    # This is a shortcut for Bio::Blast.new:
+    #  Bio::Blast.local(program, database, options)
+    # is equivalent to
+    #  Bio::Blast.new(program, database, options, 'local')
+    # ---
+    # *Arguments*:
+    # * _program_ (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'
+    # * _db_ (required): name of the local database
+    # * _options_: blastall options \
+    # (see http://www.genome.jp/dbget-bin/show_man?blast2)
+    # *Returns*:: Bio::Blast factory object
     def self.local(program, db, option = '')
       self.new(program, db, option, 'local')
     end
 
-    # Sets up the blast program at the remote host (server)
+    # Bio::Blast.remote does exactly the same as Bio::Blast.new, but sets
+    # the remote server 'genomenet' as its default.
+    # ---
+    # *Arguments*:
+    # * _program_ (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'
+    # * _db_ (required): name of the remote database
+    # * _options_: blastall options \
+    # (see http://www.genome.jp/dbget-bin/show_man?blast2)
+    # * _server_: server to use (DEFAULT = 'genomenet')
+    # *Returns*:: Bio::Blast factory object
     def self.remote(program, db, option = '', server = 'genomenet')
       self.new(program, db, option, server)
     end
@@ -106,16 +119,17 @@ module Bio
     end
 
 
-    # Program name for blastall -p (blastp, blastn, blastx, tblastn or tblastx).
+    # Program name (_-p_ option for blastall): blastp, blastn, blastx, tblastn
+    # or tblastx
     attr_accessor :program
 
-    # Database name for blastall -d
+    # Database name (_-d_ option for blastall)
     attr_accessor :db
     
-    # Options for blastall 
+    # Options for blastall
     attr_accessor :options
 
-    # 
+    # Server to submit the BLASTs to
     attr_accessor :server
 
     # Full path for blastall. (default: 'blastall').
@@ -140,15 +154,22 @@ module Bio
     attr_writer :parser  # to change :xmlparser, :rexml, :tab
 
 
-    # Returns a blast factory object (Bio::Blast).
-    #
-    # --- Bio::Blast.new(program, db, option = '', server = 'local')
-    # --- Bio::Blast.local(program, db, option = '')
-    # --- Bio::Blast.remote(program, db, option = '', server = 'genomenet')
-    #
-    # For the develpper, you can add server 'hoge' by adding
-    # exec_hoge(query) method.
-    #
+    # Creates a Bio::Blast factory object.
+    # 
+    # To run any BLAST searches, a factory has to be created that describes a
+    # certain BLAST pipeline: the program to use, the database to search, any
+    # options and the server to use. E.g.
+    # 
+    #   blast_factory = Bio::Blast.new('blastn','dbsts', '-e 0.0001 -r 4', 'genomenet')
+    # 
+    # ---
+    # *Arguments*:
+    # * _program_ (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'
+    # * _db_ (required): name of the (local or remote) database
+    # * _options_: blastall options \
+    # (see http://www.genome.jp/dbget-bin/show_man?blast2)
+    # * _server_: server to use (e.g. 'genomenet'; DEFAULT = 'local')
+    # *Returns*:: Bio::Blast factory object
     def initialize(program, db, opt = [], server = 'local')
       @program  = program
       @db       = db
@@ -177,18 +198,27 @@ module Bio
       @options = [ *a ]
     end
 
-    # Execute blast search and returns Report object (Bio::Blast::Report).
+    # This method submits a sequence to a BLAST factory, which performs the
+    # actual BLAST.
+    # 
+    #   fasta_sequences = Bio::FlatFile.open(Bio::FastaFormat, 'my_sequences.fa')
+    #   report = blast_factory.query(fasta_sequences)
+    # 
+    # ---
+    # *Arguments*:
+    # * _query_ (required): single- or multiple-FASTA formatted sequence(s)
+    # *Returns*:: a Bio::Blast::Report object
     def query(query)
       return self.send("exec_#{@server}", query.to_s)
     end
 
-    # option reader
+    # Returns options of blastall
     def option
       # backward compatibility
-      make_command_line(@options)
+      Bio::Command.make_command_line(@options)
     end
 
-    # option setter
+    # Set options for blastall
     def option=(str)
       # backward compatibility
       @options = Shellwords.shellwords(str)
@@ -212,12 +242,16 @@ module Bio
 
       report = nil
 
-      @output = call_command_local(cmd, query)
+      @output = Bio::Command.query_command(cmd, query)
       report = parse_result(@output)
 
       return report
     end
 
+    def exec_genomenet_tab(query)
+      @format = 8
+      exec_genomenet(query)
+    end
 
     def exec_genomenet(query)
       host = "blast.genome.jp"
@@ -236,7 +270,7 @@ module Bio
         'prog'           => @program,
         'dbname'         => @db,
         'sequence'       => CGI.escape(query),
-        'other_param'    => CGI.escape(make_command_line_unix(opt)),
+        'other_param'    => CGI.escape(Bio::Command.make_command_line_unix(opt)),
         'matrix'         => matrix,
         'filter'         => filter,
         'V_value'        => 500, # default value for GenomeNet
@@ -253,7 +287,7 @@ module Bio
       report = nil
 
       begin
-        http = Net::HTTP.new(host)
+        http = Bio::Command.new_http(host)
         http.open_timeout = 300
         http.read_timeout = 600
         result, = http.post(path, data.join('&'))
@@ -284,20 +318,3 @@ module Bio
 
 end # module Bio
 
-
-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
-
-

data/lib/bio/appl/blast/format0.rb

@@ -1,11 +1,12 @@
 #
 # = bio/appl/blast/format0.rb - BLAST default output (-m 0) parser
 # 
-# Author:: Naohisa GOTO
-# Copyright:: Copyright (C) 2003-2006 GOTO Naohisa <ng@bioruby.org>
-# License:: Ruby's
+# Copyright::  Copyright (C) 2003-2006 GOTO Naohisa <ng@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: format0.rb,v 1.17 2006/02/22 08:46:15 ngoto Exp $
+# $Id: format0.rb,v 1.22 2007/04/21 08:58:17 ngoto Exp $
+#
+# == Description
 #
 # NCBI BLAST default (-m 0 option) output parser.
 #
@@ -326,7 +327,9 @@ module Bio
               sc.skip(/\s*/)
               while sc.rest?
                 if sc.match?(/Number of sequences better than +([e\-\.\d]+) *\: *(.+)/) then
-                  @expect = sc[1]
+                  ev = sc[1]
+                  ev = '1' + ev if ev[0] == ?e
+                  @expect = ev.to_f
                   @num_hits = sc[2].tr(',', '').to_i
                 end
                 if sc.skip(/([\-\,\.\'\(\)\#\w ]+)\: *(.*)/) then
@@ -656,8 +659,11 @@ module Bio
                     z.each { |y| y.reverse! }
                     h = Hit.new([ z.pop.to_s.sub(/\.+\z/, '') ])
                     bs = z.pop.to_s
+                    bs = '1' + bs if bs[0] == ?e
+                    bs = (bs.empty? ? nil : bs.to_f)
                     ev = z.pop.to_s
-                    #ev = '1' + ev if ev[0] == ?e
+                    ev = '1' + ev if ev[0] == ?e
+                    ev = (ev.empty? ? (1.0/0.0) : ev.to_f)
                     h.instance_eval { @bit_score = bs; @evalue = ev }
                     @hits << h
                   end
@@ -780,7 +786,7 @@ module Bio
           def initialize(data)
             @f0hitname = data.shift
             @hsps = []
-            while r = data[0] and /^\s+Score/ =~ r
+            while r = data[0] and /\A\s+Score/ =~ r
               @hsps << HSP.new(data)
             end
             @again = false
@@ -948,11 +954,14 @@ module Bio
               while sc.rest?
                 sc.skip(/\s*/)
                 if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then
-                  @evalue = sc[1]
-                  #@evalue = '1' + @evalue if @evalue[0] == ?e
+                  ev = sc[1].to_s
+                  ev = '1' + ev if ev[0] == ?e
+                  @evalue = ev.to_f
                 elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then
-                  @bit_score = sc[1]
-                  @score = sc[2]
+                  bs = sc[1]
+                  bs = '1' + bs if bs[0] == ?e
+                  @bit_score = bs.to_f
+                  @score = sc[2].to_i
                 elsif sc.skip(/(Identities|Positives|Gaps) *\= (\d+) *\/ *(\d+) *\(([\.\d]+) *\% *\)/) then
                   alen = sc[3].to_i
                   @align_len = alen unless defined?(@align_len)
@@ -960,13 +969,13 @@ module Bio
                   case sc[1]
                   when 'Identities'
                     @identity = sc[2].to_i
-                    @percent_identity = sc[4]
+                    @percent_identity = sc[4].to_i
                   when 'Positives'
                     @positive = sc[2].to_i
-                    @percent_positive = sc[4]
+                    @percent_positive = sc[4].to_i
                   when 'Gaps'
                     @gaps = sc[2].to_i
-                    @percent_gaps = sc[4]
+                    @percent_gaps = sc[4].to_i
                   else
                     raise ScanError
                   end
@@ -994,16 +1003,22 @@ module Bio
                   end
                 elsif sc.skip(/Score *\= *([e\-\.\d]+) +\(([e\-\.\d]+) *bits *\)/) then
                   #WU-BLAST
-                  @score = sc[1]
-                  @bit_score = sc[2]
+                  @score = sc[1].to_i
+                  bs = sc[2]
+                  bs = '1' + bs if bs[0] == ?e
+                  @bit_score = bs.to_f
                 elsif sc.skip(/P *\= * ([e\-\.\d]+)/) then
                   #WU-BLAST
                   @p_sum_n = nil
-                  @pvalue = sc[1]
+                  pv = sc[1]
+                  pv = '1' + pv if pv[0] == ?e
+                  @pvalue = pv.to_f
                 elsif sc.skip(/Sum +P *\( *(\d+) *\) *\= *([e\-\.\d]+)/) then
                   #WU-BLAST
                   @p_sum_n = sc[1].to_i
-                  @pvalue = sc[2]
+                  pv = sc[2]
+                  pv = '1' + pv if pv[0] == ?e
+                  @pvalue = pv.to_f
                 else
                   raise ScanError
                 end

data/lib/bio/appl/blast/format8.rb

@@ -1,23 +1,14 @@
 #
-# bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser
+# = bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser
 # 
-#   Copyright (C) 2002,2003 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2002, 2003 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.
+# $Id: format8.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $
 #
-#  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.
+# == Note
 #
-#  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: format8.rb,v 1.5 2005/09/08 01:22:08 k Exp $
+# This file is automatically loaded by bio/appl/blast/report.rb
 #
 
 module Bio
@@ -88,8 +79,3 @@ module Bio
 end
 
 
-=begin
-
-This file is automatically loaded by bio/appl/blast/report.rb
-
-=end