From k at dev.open-bio.org  Wed Jan  9 12:18:21 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Wed, 09 Jan 2008 17:18:21 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.88,1.89
Message-ID: <200801091718.m09HIKNg016110@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv16099/lib

Modified Files:
	bio.rb 
Log Message:
* Bio::Hinv module for the H-invitational DB (http://h-invitational.jp/)
  web service is added


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.88
retrieving revision 1.89
diff -C2 -d -r1.88 -r1.89
*** bio.rb	29 Dec 2007 19:19:07 -0000	1.88
--- bio.rb	9 Jan 2008 17:18:17 -0000	1.89
***************
*** 145,148 ****
--- 145,149 ----
  
    autoload :Ensembl,        'bio/io/ensembl'
+   autoload :Hinv,           'bio/io/hinv'
  
    ## below are described in bio/appl/blast.rb


From k at dev.open-bio.org  Wed Jan  9 12:18:21 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Wed, 09 Jan 2008 17:18:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io hinv.rb,NONE,1.1
Message-ID: <200801091718.m09HIK3X016111@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv16099/lib/bio/io

Added Files:
	hinv.rb 
Log Message:
* Bio::Hinv module for the H-invitational DB (http://h-invitational.jp/)
  web service is added


--- NEW FILE: hinv.rb ---
#
# = bio/io/hinv.rb - H-invDB web service (REST) client module
#
# Copyright::  Copyright (C) 2007 Toshiaki Katayama <k at bioruby.org>
# License::    The Ruby License
#
# $Id: hinv.rb,v 1.1 2008/01/09 17:18:18 k Exp $
#

require 'bio/command'
require 'rexml/document'

module Bio

  # = Bio::Hinv
  #
  # Accessing the H-invDB web services.
  #
  # * http://www.h-invitational.jp/
  # * http://www.jbirc.aist.go.jp/hinv/hws/doc/index.html
  #
  class Hinv

    BASE_URI = "http://www.jbirc.aist.go.jp/hinv/hws/"

    module Common
      def query(options = nil)
        response, = Bio::Command.post_form(@url, options)
        @result = response.body
        @xml = REXML::Document.new(@result)
      end
    end


    # Bio::Hinv.acc2hit("BC053657")  # => "HIT000053961"
    def self.acc2hit(acc)
      serv = Acc2hit.new
      serv.query("acc" => acc)
      serv.result
    end

    # Bio::Hinv.hit2acc("HIT000022181")  # => "AK097327"
    def self.hit2acc(hit)
      serv = Hit2acc.new
      serv.query("hit" => hit)
      serv.result
    end

    # Bio::Hinv.hit_cnt  # => 187156
    def self.hit_cnt
      serv = HitCnt.new
      serv.query
      serv.result
    end

    # Bio::Hinv.hit_definition("HIT000000001")  # => "Rho guanine ..."
    def self.hit_definition(hit)
      serv = HitDefinition.new
      serv.query("hit" => hit)
      serv.result
    end

    # Bio::Hinv.hit_pubmedid("HIT000053961")  # => [7624364, 11279095, ... ]
    def self.hit_pubmedid(hit)
      serv = HitPubmedId.new
      serv.query("hit" => hit)
      serv.result
    end

    # Bio::Hinv.hit_xml("HIT000000001")  # => "<?xml version="1.0" ..."
    def self.hit_xml(hit)
      serv = Bio::Hinv::HitXML.new
      serv.query("hit" => hit)
      puts serv.result
    end

    # Bio::Hinv.hix2hit("HIX0000004")  # => ["HIT000012846", ... ]
    def self.hix2hit(hix)
      serv = Bio::Hinv::Hix2hit.new
      serv.query("hix" => hix)
      serv.result
    end

    # Bio::Hinv.hix_cnt  # => 36073
    def self.hix_cnt
      serv = HixCnt.new
      serv.query
      serv.result
    end

    # Bio::Hinv.hix_represent("HIX0000001")  # => "HIT000022181"
    def self.hix_represent(hix)
      serv = HixRepresent.new
      serv.query("hix" => hix)
      serv.result
    end

    # Bio::Hinv.id_search("HIT00002218*")  # => ["HIT000022181", ... ]
    def self.id_search(query)
      serv = IdSearch.new
      serv.query("query" => query)
      serv.result
    end

    # Bio::Hinv.keyword_search("HIT00002218*")  # => ["HIT000022181", ... ]
    def self.keyword_search(query)
      serv = KeywordSearch.new
      serv.query("query" => query)
      serv.result
    end


    # serv = Bio::Hinv::Acc2hit.new
    # serv.query("acc" => "BC053657")
    # puts serv.result
    class Acc2hit
      include Common

      def initialize
        @url = BASE_URI + "acc2hit.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <H-INVITATIONAL-ID>HIT000053961</H-INVITATIONAL-ID>
      # </H-Inv>
      def result
        @xml.elements['//H-INVITATIONAL-ID'].text
      end
    end

    # serv = Bio::Hinv::Hit2acc.new
    # serv.query("hit" => "HIT000022181")
    # puts serv.result
    class Hit2acc
      include Common

      def initialize
        @url = BASE_URI + "hit2acc.php?hit="
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <ACCESSION-NO>AK097327</ACCESSION-NO>
      # </H-Inv>
      def result
        @xml.elements['//ACCESSION-NO'].text
      end
    end

    # serv = Bio::Hinv::HitCnt.new
    # serv.query
    # puts serv.result
    class HitCnt
      include Common

      def initialize
        @url = BASE_URI + "hit_cnt.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <TRANSCRIPT_CNT>187156</TRANSCRIPT_CNT>
      # </H-Inv>
      def result
        @xml.elements['//TRANSCRIPT_CNT'].text.to_i
      end
    end

    # serv = Bio::Hinv::HitDefinition.new
    # serv.query("hit" => "HIT000000001")
    # puts serv.result
    # puts serv.data_source_definition
    # puts serv.cdna_rep_h_invitational
    # puts serv.cdna_splicing_isoform_curation
    # puts serv.data_source_db_reference_protein_motif_id
    # puts serv.data_source_identity
    # puts serv.data_source_coverage
    # puts serv.data_source_homologous_species
    # puts serv.data_source_similarity_category
    class HitDefinition
      include Common

      def initialize
        @url = BASE_URI + "hit_definition.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <HIT_FUNCTION>
      #   <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
      #   <DATA-SOURCE_DEFINITION>Rho guanine nucleotide exchange factor 10.</DATA-SOURCE_DEFINITION>
      #   <CDNA_REP-H-INVITATIONAL>Representative transcript</CDNA_REP-H-INVITATIONAL>
      #   <CDNA_SPLICING-ISOFORM_CURATION></CDNA_SPLICING-ISOFORM_CURATION>
      #   <DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>NP_055444</DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>
      #   <DATA-SOURCE_IDENTITY>100.0</DATA-SOURCE_IDENTITY>
      #   <DATA-SOURCE_COVERAGE>100.0</DATA-SOURCE_COVERAGE>
      #   <DATA-SOURCE_HOMOLOGOUS_SPECIES>Homo sapiens</DATA-SOURCE_HOMOLOGOUS_SPECIES>
      #   <DATA-SOURCE_SIMILARITY-CATEGORY>Identical to known human protein(Category I).</DATA-SOURCE_SIMILARITY-CATEGORY>
      #  </HIT_FUNCTION>
      # </H-Inv>
      def result
        @xml.elements['//DATA-SOURCE_DEFINITION'].text
      end
      alias :data_source_definition :result

      def cdna_rep_h_invitational
        @xml.elements['//CDNA_REP-H-INVITATIONAL'].text
      end
      def cdna_splicing_isoform_curation
        @xml.elements['//CDNA_SPLICING-ISOFORM_CURATION'].text
      end
      def data_source_db_reference_protein_motif_id
        @xml.elements['//DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID'].text
      end
      def data_source_identity
        @xml.elements['//DATA-SOURCE_IDENTITY'].text.to_f
      end
      def data_source_coverage
        @xml.elements['//DATA-SOURCE_COVERAGE'].text.to_f
      end
      def data_source_homologous_species
        @xml.elements['//DATA-SOURCE_HOMOLOGOUS_SPECIES'].text
      end
      def data_source_similarity_category
        @xml.elements['//DATA-SOURCE_SIMILARITY-CATEGORY'].text
      end
    end

    # serv = Bio::Hinv::HitPubmedId.new
    # serv.query("hit" => "HIT000053961")
    # puts serv.result
    class HitPubmedId
      include Common

      def initialize
        @url = BASE_URI + "hit_pubmedid.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <CDNA_DB-REFERENCE_PUBMED>7624364</CDNA_DB-REFERENCE_PUBMED>
      #  <CDNA_DB-REFERENCE_PUBMED>11279095</CDNA_DB-REFERENCE_PUBMED>
      #  <CDNA_DB-REFERENCE_PUBMED>15489334</CDNA_DB-REFERENCE_PUBMED>
      # </H-Inv>
      def result
        list = []
        @xml.elements.each('//CDNA_DB-REFERENCE_PUBMED') do |e|
          list << e.text.to_i
        end
        return list
      end
    end

    # serv = Bio::Hinv::HitXML.new
    # serv.query("hit" => "HIT000000001")
    # puts serv.result
    class HitXML
      include Common

      def initialize
        @url = BASE_URI + "hit_xml.php"
      end

      # <?xml version="1.0" standalone="yes" ?>
      # <H-Inv>
      #  <cDNAXML>
      #  <CLUSTER-ID>HIX0021591</CLUSTER-ID>
      #  <CLUSTER-ID-VERSION>HIX0021591.11</CLUSTER-ID-VERSION>
      #  <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
      #    :
      #    </PROBE-MAPPING>
      #   </EXPRESSION>
      #  </cDNAXML>
      # </H-Inv>
      def result
        @result
      end
    end

    # serv = Bio::Hinv::Hix2hit.new
    # serv.query("hix" => "HIX0000004")
    # puts serv.result
    class Hix2hit
      include Common

      def initialize
        @url = BASE_URI + "hix2hit.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <H-INVITATIONAL-ID>HIT000012846</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022124</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000007722</H-INVITATIONAL-ID>
      #    :
      #  <H-INVITATIONAL-ID>HIT000262478</H-INVITATIONAL-ID>
      # </H-Inv>
      def result
        list = []
        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
          list << e.text
        end
        return list
      end
    end

    # serv = Bio::Hinv::HixCnt.new
    # serv.query
    # puts serv.result
    class HixCnt
      include Common

      def initialize
        @url = BASE_URI + "hix_cnt.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <LOCUS_CNT>36073</LOCUS_CNT>
      # </H-Inv>
      def result
        @xml.elements['//LOCUS_CNT'].text.to_i
      end
    end

    # serv = Bio::Hinv::HixRepresent.new
    # serv.query("hix" => "HIX0000001")
    # puts serv.result
    # puts serv.rep_h_invitational_id
    # puts serv.rep_accession_no
    class HixRepresent
      include Common

      def initialize
        @url = BASE_URI + "hix_represent.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <LOCUS>
      #   <CLUSTER-ID>HIX0000001</CLUSTER-ID>
      #   <REP-H-INVITATIONAL-ID>HIT000022181</REP-H-INVITATIONAL-ID>
      #   <REP-ACCESSION-NO>AK097327</REP-ACCESSION-NO>
      #  </LOCUS>
      # </H-Inv>
      def result
        @xml.elements['//REP-H-INVITATIONAL-ID'].text
      end
      alias :rep_h_invitational_id :result

      def rep_accession_no
        @xml.elements['//REP-ACCESSION-NO'].text
      end
    end

    # example at "http://www.jbirc.aist.go.jp/hinv/hws/doc/index_jp.html"
    # is for hit_xml.php (not for hix_xml.php)
    class HixXML
    end

    # serv = Bio::Hinv::KeywordSearch.new
    # serv.query("query" => "HIT00002218*", "start" => 1, "end" => 100)
    # puts serv.result
    # puts serv.size
    # puts serv.start
    # puts serv.end
    class KeywordSearch
      include Common

      def initialize
        @url = BASE_URI + "keyword_search.php"
      end

      def query(hash = {})
        default = {
          "start" => 1,
          "end" => 100
        }
        options = default.update(hash)
        super(options)
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <HINVDB_SEARCH>
      #  <QUERY>HIT00002218*</QUERY>
      #  <SIZE>8</SIZE>
      #  <START>1</START>
      #  <END>8</END>
      #  <H-INVITATIONAL-ID>HIT000022180</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022181</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022183</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022184</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022185</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022186</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022188</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022189</H-INVITATIONAL-ID>
      # </HINVDB_SEARCH>
      def result
        list = []
        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
          list << e.text
        end
        return list
      end

      def size
        @xml.elements['//SIZE'].text.to_i
      end
      def start
        @xml.elements['//START'].text.to_i
      end
      def end
        @xml.elements['//END'].text.to_i
      end
    end

    # serv = Bio::Hinv::IdSearch.new
    # serv.query("query" => "HIT00002218*", "id_type" => "H-INVITATIONAL-ID", "start" => 1, "end" => 100)
    # puts serv.result
    # puts serv.size
    # puts serv.start
    # puts serv.end
    class IdSearch < KeywordSearch
      def initialize
        @url = BASE_URI + "id_search.php"
      end

      def query(hash = {})
        default = {
          "id_type" => "H-INVITATIONAL-ID",
          "start" => 1,
          "end" => 100
        }
        options = default.update(hash)
        super(options)
      end
    end

  end
end



From k at dev.open-bio.org  Wed Jan  9 12:22:41 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Wed, 09 Jan 2008 17:22:41 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.79,1.80
Message-ID: <200801091722.m09HMfk7016152@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv16148

Modified Files:
	ChangeLog 
Log Message:
* Bio::Hinv is added


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.79
retrieving revision 1.80
diff -C2 -d -r1.79 -r1.80
*** ChangeLog	29 Dec 2007 19:19:06 -0000	1.79
--- ChangeLog	9 Jan 2008 17:22:39 -0000	1.80
***************
*** 1,2 ****
--- 1,9 ----
+ 2008-01-10  Toshiaki Katayama <k at bioruby.org>
+ 
+ 	* lib/bio/io/hinv.rb
+ 
+ 	  Bio::Hinv to access the H-invitational DB (http://h-invitational.jp/)
+ 	  web service in REST mode is added.
+ 
  2007-12-30  Toshiaki Katayama <k at bioruby.org>
  


From ngoto at dev.open-bio.org  Wed Jan  9 22:51:12 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 10 Jan 2008 03:51:12 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl emboss.rb,1.8,1.9
Message-ID: <200801100351.m0A3pCu9017201@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv17181/lib/bio/appl

Modified Files:
	emboss.rb 
Log Message:
Added a method Bio::EMBOSS.run(program, arguments...)
and Bio::EMBOSS.new is obsoleted.


Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** emboss.rb	5 Apr 2007 23:35:39 -0000	1.8
--- emboss.rb	10 Jan 2008 03:51:06 -0000	1.9
***************
*** 36,51 ****
  #  # 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+.
--- 36,52 ----
  #  # 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 String object
! #  # by using  Bio::EMBOSS.run method.
! #  xlrhodop = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
! #  puts xlrhodop
  #
  #  # Or all in one go:
! #  puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
  #
  #  # Similarly:
! #  puts Bio::EMBOSS.run('transeq', '-sbegin', '110','-send', '1171',
! #                       'embl:xlrhodop')
! #  puts Bio::EMBOSS.run('showfeat', 'embl:xlrhodop')
! #  puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop', '-osformat', 'acedb')
  #
  #  # A shortcut exists for this two-step process for +seqret+ and +entret+.
***************
*** 53,56 ****
--- 54,68 ----
  #  puts Bio::EMBOSS.entret('embl:xlrhodop')
  #
+ #  # You can use %w() syntax.
+ #  puts Bio::EMBOSS.run(*%w( transeq -sbegin 110 -send 1171 embl:xlrhodop ))
+ #
+ #  # You can also use Shellwords.shellwords.
+ #  require 'shellwords'
+ #  str = 'transeq -sbegin 110 -send 1171 embl:xlrhodop'
+ #  cmd = Shellwords.shellwords(str)
+ #  puts Bio::EMBOSS.run(*cmd)
+ #
+ 
+ #
  # == Pre-requisites
  #
***************
*** 77,82 ****
    # ---
    # *Arguments*:
!   # * (required) _command_: emboss command
!   # *Returns*:: Bio::EMBOSS object
    def self.seqret(arg)
      str = self.retrieve('seqret', arg)
--- 89,94 ----
    # ---
    # *Arguments*:
!   # * (required) _arg_: argument given to the emboss seqret command
!   # *Returns*:: String
    def self.seqret(arg)
      str = self.retrieve('seqret', arg)
***************
*** 93,102 ****
    # ---
    # *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_
--- 105,118 ----
    # ---
    # *Arguments*:
!   # * (required) _arg_: argument given to the emboss entret command
!   # *Returns*:: String
    def self.entret(arg)
      str = self.retrieve('entret', arg)
    end
  
+   # WARNING: Bio::EMBOSS.new will be changed in the future because
+   # Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole.
+   # Using Bio::EMBOSS.run(program, options...) is strongly recommended.
+   #
    # Initializes a new Bio::EMBOSS object. This provides a holder that can
    # subsequently be executed (see Bio::EMBOSS.exec). The object does _not_
***************
*** 115,118 ****
--- 131,135 ----
    # *Returns*:: Bio::EMBOSS object
    def initialize(cmd_line)
+     warn 'Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options...) is strongly recommended.'
      @cmd_line = cmd_line + ' -stdout -auto'
    end
***************
*** 143,146 ****
--- 160,195 ----
    attr_reader :result
  
+   # Runs an emboss program and get the result as string.
+   # Note that "-auto -stdout" are automatically added to the options.
+   #
+   # Example 1:
+   #
+   #   result = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
+   #
+   # Example 2:
+   #
+   #   result = Bio::EMBOSS.run('water',
+   #                             '-asequence', 'swissprot:slpi_human',
+   #                             '-bsequence', 'swissprot:slpi_mouse')
+   #
+   # Example 3:
+   #   options = %w( -asequence swissprot:slpi_human
+   #                 -bsequence swissprot:slpi_mouse )
+   #   result = Bio::EMBOSS.run('needle', *options)
+   #
+   # For an overview of commands that can be used with this method, see the
+   # emboss website.
+   # ---
+   # *Arguments*:
+   # * (required) _program_: command name, or filename of an emboss program
+   # * _options_: options given to the emboss program
+   # *Returns*:: String
+   def self.run(program, *options)
+     cmd = [ program, *options ]
+     cmd.push '-auto'
+     cmd.push '-stdout'
+     return Bio::Command.query_command(cmd)
+   end
+ 
    private
  


From nakao at dev.open-bio.org  Wed Jan 30 12:43:36 2008
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Wed, 30 Jan 2008 17:43:36 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl test_blast.rb,1.5,1.6
Message-ID: <200801301743.m0UHhal7013528@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv13486/test/unit/bio/appl

Modified Files:
	test_blast.rb 
Log Message:
* Fixed the bug at building the blastall command line options ('-m 0').


Index: test_blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_blast.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** test_blast.rb	5 Apr 2007 23:35:43 -0000	1.5
--- test_blast.rb	30 Jan 2008 17:43:33 -0000	1.6
***************
*** 82,85 ****
--- 82,91 ----
      end
  
+     def test_option_set_m0
+       @blast.option = '-m 0'
+       assert_equal('-m 0', @blast.option) 
+     end
+ 
+ 
      def test_server
        assert_equal(@server, @blast.server) 
***************
*** 127,130 ****
--- 133,147 ----
         end
       end
+      
+      def test_make_command_line
+        @blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
+        assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "7", "-F", "F"], 
+                     @blast.instance_eval { make_command_line })
+      end
+      def test_make_command_line_2
+        @blast = Bio::Blast.new(@program, @db, '-m 0 -F F')
+        assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "0", "-F",  "F"], 
+                     @blast.instance_eval { make_command_line })
+      end
  
       def test_parse_result


From nakao at dev.open-bio.org  Wed Jan 30 12:43:36 2008
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Wed, 30 Jan 2008 17:43:36 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl blast.rb,1.33,1.34
Message-ID: <200801301743.m0UHhafU013533@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv13486/lib/bio/appl

Modified Files:
	blast.rb 
Log Message:
* Fixed the bug at building the blastall command line options ('-m 0').


Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** blast.rb	5 Apr 2007 23:35:39 -0000	1.33
--- blast.rb	30 Jan 2008 17:43:34 -0000	1.34
***************
*** 2,6 ****
  # = bio/appl/blast.rb - BLAST wrapper
  # 
! # Copyright::  Copyright (C) 2001       Mitsuteru C. Nakao <n at bioruby.org>
  # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
--- 2,6 ----
  # = bio/appl/blast.rb - BLAST wrapper
  # 
! # Copyright::  Copyright (C) 2001,2008  Mitsuteru C. Nakao <n at bioruby.org>
  # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
***************
*** 182,201 ****
        @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
  
      # This method submits a sequence to a BLAST factory, which performs the
--- 182,190 ----
        @output   = ''
        @parser   = nil
+       @format   = 0
+ 
+       set_options(opt)
+     end      
  
  
      # This method submits a sequence to a BLAST factory, which performs the
***************
*** 225,231 ****
      end
  
- 
      private
  
  
      def parse_result(data)
--- 214,239 ----
      end
  
      private
  
+     def set_options(opt = nil)
+       opt = @options unless opt
+       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
+       else
+         @format = a[a.index('-m') + 1].to_i
+       end
+       @options = [ *a ]
+     end
+ 
  
      def parse_result(data)
***************
*** 234,244 ****
  
  
!     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
  
--- 242,272 ----
  
  
!     def make_command_line
!       set_options
        cmd = [ @blastall, '-p', @program, '-d', @db ]
!       if @matrix
!         cmd.concat([ '-M', @matrix ]) 
!         i = @options.index('-M')
!         @options.delete_at(i)
!         @options.delete_at(i)
!       end
!       if @filter
!         cmd.concat([ '-F', @filter ]) 
!         i = @options.index('-F')
!         @options.delete_at(i)
!         @options.delete_at(i)
!       end
!       if @format
!         cmd.concat([ '-m', @format.to_s ])
!         i = @options.index('-m')
!         @options.delete_at(i)
!         @options.delete_at(i)
!       end
        cmd.concat(@options) if @options
+     end
+ 
  
+     def exec_local(query)
+       cmd = make_command_line
        report = nil
  
***************
*** 249,252 ****
--- 277,281 ----
      end
  
+ 
      def exec_genomenet_tab(query)
        @format = 8
***************
*** 254,257 ****
--- 283,287 ----
      end
  
+ 
      def exec_genomenet(query)
        host = "blast.genome.jp"


From k at dev.open-bio.org  Wed Jan  9 17:18:21 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Wed, 09 Jan 2008 17:18:21 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.88,1.89
Message-ID: <200801091718.m09HIKNg016110@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv16099/lib

Modified Files:
	bio.rb 
Log Message:
* Bio::Hinv module for the H-invitational DB (http://h-invitational.jp/)
  web service is added


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.88
retrieving revision 1.89
diff -C2 -d -r1.88 -r1.89
*** bio.rb	29 Dec 2007 19:19:07 -0000	1.88
--- bio.rb	9 Jan 2008 17:18:17 -0000	1.89
***************
*** 145,148 ****
--- 145,149 ----
  
    autoload :Ensembl,        'bio/io/ensembl'
+   autoload :Hinv,           'bio/io/hinv'
  
    ## below are described in bio/appl/blast.rb



From k at dev.open-bio.org  Wed Jan  9 17:18:21 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Wed, 09 Jan 2008 17:18:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io hinv.rb,NONE,1.1
Message-ID: <200801091718.m09HIK3X016111@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv16099/lib/bio/io

Added Files:
	hinv.rb 
Log Message:
* Bio::Hinv module for the H-invitational DB (http://h-invitational.jp/)
  web service is added


--- NEW FILE: hinv.rb ---
#
# = bio/io/hinv.rb - H-invDB web service (REST) client module
#
# Copyright::  Copyright (C) 2007 Toshiaki Katayama <k at bioruby.org>
# License::    The Ruby License
#
# $Id: hinv.rb,v 1.1 2008/01/09 17:18:18 k Exp $
#

require 'bio/command'
require 'rexml/document'

module Bio

  # = Bio::Hinv
  #
  # Accessing the H-invDB web services.
  #
  # * http://www.h-invitational.jp/
  # * http://www.jbirc.aist.go.jp/hinv/hws/doc/index.html
  #
  class Hinv

    BASE_URI = "http://www.jbirc.aist.go.jp/hinv/hws/"

    module Common
      def query(options = nil)
        response, = Bio::Command.post_form(@url, options)
        @result = response.body
        @xml = REXML::Document.new(@result)
      end
    end


    # Bio::Hinv.acc2hit("BC053657")  # => "HIT000053961"
    def self.acc2hit(acc)
      serv = Acc2hit.new
      serv.query("acc" => acc)
      serv.result
    end

    # Bio::Hinv.hit2acc("HIT000022181")  # => "AK097327"
    def self.hit2acc(hit)
      serv = Hit2acc.new
      serv.query("hit" => hit)
      serv.result
    end

    # Bio::Hinv.hit_cnt  # => 187156
    def self.hit_cnt
      serv = HitCnt.new
      serv.query
      serv.result
    end

    # Bio::Hinv.hit_definition("HIT000000001")  # => "Rho guanine ..."
    def self.hit_definition(hit)
      serv = HitDefinition.new
      serv.query("hit" => hit)
      serv.result
    end

    # Bio::Hinv.hit_pubmedid("HIT000053961")  # => [7624364, 11279095, ... ]
    def self.hit_pubmedid(hit)
      serv = HitPubmedId.new
      serv.query("hit" => hit)
      serv.result
    end

    # Bio::Hinv.hit_xml("HIT000000001")  # => "<?xml version="1.0" ..."
    def self.hit_xml(hit)
      serv = Bio::Hinv::HitXML.new
      serv.query("hit" => hit)
      puts serv.result
    end

    # Bio::Hinv.hix2hit("HIX0000004")  # => ["HIT000012846", ... ]
    def self.hix2hit(hix)
      serv = Bio::Hinv::Hix2hit.new
      serv.query("hix" => hix)
      serv.result
    end

    # Bio::Hinv.hix_cnt  # => 36073
    def self.hix_cnt
      serv = HixCnt.new
      serv.query
      serv.result
    end

    # Bio::Hinv.hix_represent("HIX0000001")  # => "HIT000022181"
    def self.hix_represent(hix)
      serv = HixRepresent.new
      serv.query("hix" => hix)
      serv.result
    end

    # Bio::Hinv.id_search("HIT00002218*")  # => ["HIT000022181", ... ]
    def self.id_search(query)
      serv = IdSearch.new
      serv.query("query" => query)
      serv.result
    end

    # Bio::Hinv.keyword_search("HIT00002218*")  # => ["HIT000022181", ... ]
    def self.keyword_search(query)
      serv = KeywordSearch.new
      serv.query("query" => query)
      serv.result
    end


    # serv = Bio::Hinv::Acc2hit.new
    # serv.query("acc" => "BC053657")
    # puts serv.result
    class Acc2hit
      include Common

      def initialize
        @url = BASE_URI + "acc2hit.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <H-INVITATIONAL-ID>HIT000053961</H-INVITATIONAL-ID>
      # </H-Inv>
      def result
        @xml.elements['//H-INVITATIONAL-ID'].text
      end
    end

    # serv = Bio::Hinv::Hit2acc.new
    # serv.query("hit" => "HIT000022181")
    # puts serv.result
    class Hit2acc
      include Common

      def initialize
        @url = BASE_URI + "hit2acc.php?hit="
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <ACCESSION-NO>AK097327</ACCESSION-NO>
      # </H-Inv>
      def result
        @xml.elements['//ACCESSION-NO'].text
      end
    end

    # serv = Bio::Hinv::HitCnt.new
    # serv.query
    # puts serv.result
    class HitCnt
      include Common

      def initialize
        @url = BASE_URI + "hit_cnt.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <TRANSCRIPT_CNT>187156</TRANSCRIPT_CNT>
      # </H-Inv>
      def result
        @xml.elements['//TRANSCRIPT_CNT'].text.to_i
      end
    end

    # serv = Bio::Hinv::HitDefinition.new
    # serv.query("hit" => "HIT000000001")
    # puts serv.result
    # puts serv.data_source_definition
    # puts serv.cdna_rep_h_invitational
    # puts serv.cdna_splicing_isoform_curation
    # puts serv.data_source_db_reference_protein_motif_id
    # puts serv.data_source_identity
    # puts serv.data_source_coverage
    # puts serv.data_source_homologous_species
    # puts serv.data_source_similarity_category
    class HitDefinition
      include Common

      def initialize
        @url = BASE_URI + "hit_definition.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <HIT_FUNCTION>
      #   <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
      #   <DATA-SOURCE_DEFINITION>Rho guanine nucleotide exchange factor 10.</DATA-SOURCE_DEFINITION>
      #   <CDNA_REP-H-INVITATIONAL>Representative transcript</CDNA_REP-H-INVITATIONAL>
      #   <CDNA_SPLICING-ISOFORM_CURATION></CDNA_SPLICING-ISOFORM_CURATION>
      #   <DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>NP_055444</DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID>
      #   <DATA-SOURCE_IDENTITY>100.0</DATA-SOURCE_IDENTITY>
      #   <DATA-SOURCE_COVERAGE>100.0</DATA-SOURCE_COVERAGE>
      #   <DATA-SOURCE_HOMOLOGOUS_SPECIES>Homo sapiens</DATA-SOURCE_HOMOLOGOUS_SPECIES>
      #   <DATA-SOURCE_SIMILARITY-CATEGORY>Identical to known human protein(Category I).</DATA-SOURCE_SIMILARITY-CATEGORY>
      #  </HIT_FUNCTION>
      # </H-Inv>
      def result
        @xml.elements['//DATA-SOURCE_DEFINITION'].text
      end
      alias :data_source_definition :result

      def cdna_rep_h_invitational
        @xml.elements['//CDNA_REP-H-INVITATIONAL'].text
      end
      def cdna_splicing_isoform_curation
        @xml.elements['//CDNA_SPLICING-ISOFORM_CURATION'].text
      end
      def data_source_db_reference_protein_motif_id
        @xml.elements['//DATA-SOURCE_DB-REFERENCE_PROTEIN-MOTIF-ID'].text
      end
      def data_source_identity
        @xml.elements['//DATA-SOURCE_IDENTITY'].text.to_f
      end
      def data_source_coverage
        @xml.elements['//DATA-SOURCE_COVERAGE'].text.to_f
      end
      def data_source_homologous_species
        @xml.elements['//DATA-SOURCE_HOMOLOGOUS_SPECIES'].text
      end
      def data_source_similarity_category
        @xml.elements['//DATA-SOURCE_SIMILARITY-CATEGORY'].text
      end
    end

    # serv = Bio::Hinv::HitPubmedId.new
    # serv.query("hit" => "HIT000053961")
    # puts serv.result
    class HitPubmedId
      include Common

      def initialize
        @url = BASE_URI + "hit_pubmedid.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <CDNA_DB-REFERENCE_PUBMED>7624364</CDNA_DB-REFERENCE_PUBMED>
      #  <CDNA_DB-REFERENCE_PUBMED>11279095</CDNA_DB-REFERENCE_PUBMED>
      #  <CDNA_DB-REFERENCE_PUBMED>15489334</CDNA_DB-REFERENCE_PUBMED>
      # </H-Inv>
      def result
        list = []
        @xml.elements.each('//CDNA_DB-REFERENCE_PUBMED') do |e|
          list << e.text.to_i
        end
        return list
      end
    end

    # serv = Bio::Hinv::HitXML.new
    # serv.query("hit" => "HIT000000001")
    # puts serv.result
    class HitXML
      include Common

      def initialize
        @url = BASE_URI + "hit_xml.php"
      end

      # <?xml version="1.0" standalone="yes" ?>
      # <H-Inv>
      #  <cDNAXML>
      #  <CLUSTER-ID>HIX0021591</CLUSTER-ID>
      #  <CLUSTER-ID-VERSION>HIX0021591.11</CLUSTER-ID-VERSION>
      #  <H-INVITATIONAL-ID>HIT000000001</H-INVITATIONAL-ID>
      #    :
      #    </PROBE-MAPPING>
      #   </EXPRESSION>
      #  </cDNAXML>
      # </H-Inv>
      def result
        @result
      end
    end

    # serv = Bio::Hinv::Hix2hit.new
    # serv.query("hix" => "HIX0000004")
    # puts serv.result
    class Hix2hit
      include Common

      def initialize
        @url = BASE_URI + "hix2hit.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <H-INVITATIONAL-ID>HIT000012846</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022124</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000007722</H-INVITATIONAL-ID>
      #    :
      #  <H-INVITATIONAL-ID>HIT000262478</H-INVITATIONAL-ID>
      # </H-Inv>
      def result
        list = []
        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
          list << e.text
        end
        return list
      end
    end

    # serv = Bio::Hinv::HixCnt.new
    # serv.query
    # puts serv.result
    class HixCnt
      include Common

      def initialize
        @url = BASE_URI + "hix_cnt.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <LOCUS_CNT>36073</LOCUS_CNT>
      # </H-Inv>
      def result
        @xml.elements['//LOCUS_CNT'].text.to_i
      end
    end

    # serv = Bio::Hinv::HixRepresent.new
    # serv.query("hix" => "HIX0000001")
    # puts serv.result
    # puts serv.rep_h_invitational_id
    # puts serv.rep_accession_no
    class HixRepresent
      include Common

      def initialize
        @url = BASE_URI + "hix_represent.php"
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <H-Inv>
      #  <LOCUS>
      #   <CLUSTER-ID>HIX0000001</CLUSTER-ID>
      #   <REP-H-INVITATIONAL-ID>HIT000022181</REP-H-INVITATIONAL-ID>
      #   <REP-ACCESSION-NO>AK097327</REP-ACCESSION-NO>
      #  </LOCUS>
      # </H-Inv>
      def result
        @xml.elements['//REP-H-INVITATIONAL-ID'].text
      end
      alias :rep_h_invitational_id :result

      def rep_accession_no
        @xml.elements['//REP-ACCESSION-NO'].text
      end
    end

    # example at "http://www.jbirc.aist.go.jp/hinv/hws/doc/index_jp.html"
    # is for hit_xml.php (not for hix_xml.php)
    class HixXML
    end

    # serv = Bio::Hinv::KeywordSearch.new
    # serv.query("query" => "HIT00002218*", "start" => 1, "end" => 100)
    # puts serv.result
    # puts serv.size
    # puts serv.start
    # puts serv.end
    class KeywordSearch
      include Common

      def initialize
        @url = BASE_URI + "keyword_search.php"
      end

      def query(hash = {})
        default = {
          "start" => 1,
          "end" => 100
        }
        options = default.update(hash)
        super(options)
      end

      # <?xml version='1.0' encoding='UTF-8'?>
      # <HINVDB_SEARCH>
      #  <QUERY>HIT00002218*</QUERY>
      #  <SIZE>8</SIZE>
      #  <START>1</START>
      #  <END>8</END>
      #  <H-INVITATIONAL-ID>HIT000022180</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022181</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022183</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022184</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022185</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022186</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022188</H-INVITATIONAL-ID>
      #  <H-INVITATIONAL-ID>HIT000022189</H-INVITATIONAL-ID>
      # </HINVDB_SEARCH>
      def result
        list = []
        @xml.elements.each('//H-INVITATIONAL-ID') do |e|
          list << e.text
        end
        return list
      end

      def size
        @xml.elements['//SIZE'].text.to_i
      end
      def start
        @xml.elements['//START'].text.to_i
      end
      def end
        @xml.elements['//END'].text.to_i
      end
    end

    # serv = Bio::Hinv::IdSearch.new
    # serv.query("query" => "HIT00002218*", "id_type" => "H-INVITATIONAL-ID", "start" => 1, "end" => 100)
    # puts serv.result
    # puts serv.size
    # puts serv.start
    # puts serv.end
    class IdSearch < KeywordSearch
      def initialize
        @url = BASE_URI + "id_search.php"
      end

      def query(hash = {})
        default = {
          "id_type" => "H-INVITATIONAL-ID",
          "start" => 1,
          "end" => 100
        }
        options = default.update(hash)
        super(options)
      end
    end

  end
end




From k at dev.open-bio.org  Wed Jan  9 17:22:41 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Wed, 09 Jan 2008 17:22:41 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.79,1.80
Message-ID: <200801091722.m09HMfk7016152@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv16148

Modified Files:
	ChangeLog 
Log Message:
* Bio::Hinv is added


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.79
retrieving revision 1.80
diff -C2 -d -r1.79 -r1.80
*** ChangeLog	29 Dec 2007 19:19:06 -0000	1.79
--- ChangeLog	9 Jan 2008 17:22:39 -0000	1.80
***************
*** 1,2 ****
--- 1,9 ----
+ 2008-01-10  Toshiaki Katayama <k at bioruby.org>
+ 
+ 	* lib/bio/io/hinv.rb
+ 
+ 	  Bio::Hinv to access the H-invitational DB (http://h-invitational.jp/)
+ 	  web service in REST mode is added.
+ 
  2007-12-30  Toshiaki Katayama <k at bioruby.org>
  



From ngoto at dev.open-bio.org  Thu Jan 10 03:51:12 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 10 Jan 2008 03:51:12 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl emboss.rb,1.8,1.9
Message-ID: <200801100351.m0A3pCu9017201@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv17181/lib/bio/appl

Modified Files:
	emboss.rb 
Log Message:
Added a method Bio::EMBOSS.run(program, arguments...)
and Bio::EMBOSS.new is obsoleted.


Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** emboss.rb	5 Apr 2007 23:35:39 -0000	1.8
--- emboss.rb	10 Jan 2008 03:51:06 -0000	1.9
***************
*** 36,51 ****
  #  # 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+.
--- 36,52 ----
  #  # 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 String object
! #  # by using  Bio::EMBOSS.run method.
! #  xlrhodop = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
! #  puts xlrhodop
  #
  #  # Or all in one go:
! #  puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
  #
  #  # Similarly:
! #  puts Bio::EMBOSS.run('transeq', '-sbegin', '110','-send', '1171',
! #                       'embl:xlrhodop')
! #  puts Bio::EMBOSS.run('showfeat', 'embl:xlrhodop')
! #  puts Bio::EMBOSS.run('seqret', 'embl:xlrhodop', '-osformat', 'acedb')
  #
  #  # A shortcut exists for this two-step process for +seqret+ and +entret+.
***************
*** 53,56 ****
--- 54,68 ----
  #  puts Bio::EMBOSS.entret('embl:xlrhodop')
  #
+ #  # You can use %w() syntax.
+ #  puts Bio::EMBOSS.run(*%w( transeq -sbegin 110 -send 1171 embl:xlrhodop ))
+ #
+ #  # You can also use Shellwords.shellwords.
+ #  require 'shellwords'
+ #  str = 'transeq -sbegin 110 -send 1171 embl:xlrhodop'
+ #  cmd = Shellwords.shellwords(str)
+ #  puts Bio::EMBOSS.run(*cmd)
+ #
+ 
+ #
  # == Pre-requisites
  #
***************
*** 77,82 ****
    # ---
    # *Arguments*:
!   # * (required) _command_: emboss command
!   # *Returns*:: Bio::EMBOSS object
    def self.seqret(arg)
      str = self.retrieve('seqret', arg)
--- 89,94 ----
    # ---
    # *Arguments*:
!   # * (required) _arg_: argument given to the emboss seqret command
!   # *Returns*:: String
    def self.seqret(arg)
      str = self.retrieve('seqret', arg)
***************
*** 93,102 ****
    # ---
    # *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_
--- 105,118 ----
    # ---
    # *Arguments*:
!   # * (required) _arg_: argument given to the emboss entret command
!   # *Returns*:: String
    def self.entret(arg)
      str = self.retrieve('entret', arg)
    end
  
+   # WARNING: Bio::EMBOSS.new will be changed in the future because
+   # Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole.
+   # Using Bio::EMBOSS.run(program, options...) is strongly recommended.
+   #
    # Initializes a new Bio::EMBOSS object. This provides a holder that can
    # subsequently be executed (see Bio::EMBOSS.exec). The object does _not_
***************
*** 115,118 ****
--- 131,135 ----
    # *Returns*:: Bio::EMBOSS object
    def initialize(cmd_line)
+     warn 'Bio::EMBOSS.new(cmd_line) is inconvenient and potential security hole. Using Bio::EMBOSS.run(program, options...) is strongly recommended.'
      @cmd_line = cmd_line + ' -stdout -auto'
    end
***************
*** 143,146 ****
--- 160,195 ----
    attr_reader :result
  
+   # Runs an emboss program and get the result as string.
+   # Note that "-auto -stdout" are automatically added to the options.
+   #
+   # Example 1:
+   #
+   #   result = Bio::EMBOSS.run('seqret', 'embl:xlrhodop')
+   #
+   # Example 2:
+   #
+   #   result = Bio::EMBOSS.run('water',
+   #                             '-asequence', 'swissprot:slpi_human',
+   #                             '-bsequence', 'swissprot:slpi_mouse')
+   #
+   # Example 3:
+   #   options = %w( -asequence swissprot:slpi_human
+   #                 -bsequence swissprot:slpi_mouse )
+   #   result = Bio::EMBOSS.run('needle', *options)
+   #
+   # For an overview of commands that can be used with this method, see the
+   # emboss website.
+   # ---
+   # *Arguments*:
+   # * (required) _program_: command name, or filename of an emboss program
+   # * _options_: options given to the emboss program
+   # *Returns*:: String
+   def self.run(program, *options)
+     cmd = [ program, *options ]
+     cmd.push '-auto'
+     cmd.push '-stdout'
+     return Bio::Command.query_command(cmd)
+   end
+ 
    private
  



From nakao at dev.open-bio.org  Wed Jan 30 17:43:36 2008
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Wed, 30 Jan 2008 17:43:36 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl test_blast.rb,1.5,1.6
Message-ID: <200801301743.m0UHhal7013528@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv13486/test/unit/bio/appl

Modified Files:
	test_blast.rb 
Log Message:
* Fixed the bug at building the blastall command line options ('-m 0').


Index: test_blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_blast.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** test_blast.rb	5 Apr 2007 23:35:43 -0000	1.5
--- test_blast.rb	30 Jan 2008 17:43:33 -0000	1.6
***************
*** 82,85 ****
--- 82,91 ----
      end
  
+     def test_option_set_m0
+       @blast.option = '-m 0'
+       assert_equal('-m 0', @blast.option) 
+     end
+ 
+ 
      def test_server
        assert_equal(@server, @blast.server) 
***************
*** 127,130 ****
--- 133,147 ----
         end
       end
+      
+      def test_make_command_line
+        @blast = Bio::Blast.new(@program, @db, '-m 7 -F F')
+        assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "7", "-F", "F"], 
+                     @blast.instance_eval { make_command_line })
+      end
+      def test_make_command_line_2
+        @blast = Bio::Blast.new(@program, @db, '-m 0 -F F')
+        assert_equal(["blastall", "-p", "blastp", "-d", "test", "-m", "0", "-F",  "F"], 
+                     @blast.instance_eval { make_command_line })
+      end
  
       def test_parse_result



From nakao at dev.open-bio.org  Wed Jan 30 17:43:36 2008
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Wed, 30 Jan 2008 17:43:36 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl blast.rb,1.33,1.34
Message-ID: <200801301743.m0UHhafU013533@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv13486/lib/bio/appl

Modified Files:
	blast.rb 
Log Message:
* Fixed the bug at building the blastall command line options ('-m 0').


Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** blast.rb	5 Apr 2007 23:35:39 -0000	1.33
--- blast.rb	30 Jan 2008 17:43:34 -0000	1.34
***************
*** 2,6 ****
  # = bio/appl/blast.rb - BLAST wrapper
  # 
! # Copyright::  Copyright (C) 2001       Mitsuteru C. Nakao <n at bioruby.org>
  # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
--- 2,6 ----
  # = bio/appl/blast.rb - BLAST wrapper
  # 
! # Copyright::  Copyright (C) 2001,2008  Mitsuteru C. Nakao <n at bioruby.org>
  # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
***************
*** 182,201 ****
        @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
  
      # This method submits a sequence to a BLAST factory, which performs the
--- 182,190 ----
        @output   = ''
        @parser   = nil
+       @format   = 0
+ 
+       set_options(opt)
+     end      
  
  
      # This method submits a sequence to a BLAST factory, which performs the
***************
*** 225,231 ****
      end
  
- 
      private
  
  
      def parse_result(data)
--- 214,239 ----
      end
  
      private
  
+     def set_options(opt = nil)
+       opt = @options unless opt
+       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
+       else
+         @format = a[a.index('-m') + 1].to_i
+       end
+       @options = [ *a ]
+     end
+ 
  
      def parse_result(data)
***************
*** 234,244 ****
  
  
!     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
  
--- 242,272 ----
  
  
!     def make_command_line
!       set_options
        cmd = [ @blastall, '-p', @program, '-d', @db ]
!       if @matrix
!         cmd.concat([ '-M', @matrix ]) 
!         i = @options.index('-M')
!         @options.delete_at(i)
!         @options.delete_at(i)
!       end
!       if @filter
!         cmd.concat([ '-F', @filter ]) 
!         i = @options.index('-F')
!         @options.delete_at(i)
!         @options.delete_at(i)
!       end
!       if @format
!         cmd.concat([ '-m', @format.to_s ])
!         i = @options.index('-m')
!         @options.delete_at(i)
!         @options.delete_at(i)
!       end
        cmd.concat(@options) if @options
+     end
+ 
  
+     def exec_local(query)
+       cmd = make_command_line
        report = nil
  
***************
*** 249,252 ****
--- 277,281 ----
      end
  
+ 
      def exec_genomenet_tab(query)
        @format = 8
***************
*** 254,257 ****
--- 283,287 ----
      end
  
+ 
      def exec_genomenet(query)
        host = "blast.genome.jp"