bio 0.7.1 → 1.0.0

data/test/unit/bio/shell/plugin/test_seq.rb

@@ -1,23 +1,11 @@
 #
 # test/unit/bio/shell/plugin/test_seq.rb - Unit test for Bio::Shell plugin for biological sequence manipulations
 #
-#   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
+# Copyright::   Copyright (C) 2005 
+#               Mitsuteru Nakao <n@bioruby.org>
+# License::     Ruby's
 #
-#  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: test_seq.rb,v 1.5 2005/12/19 02:44:03 k Exp $
+# $Id: test_seq.rb,v 1.7 2006/02/27 09:40:13 nakao Exp $
 #
 
 require 'pathname'
@@ -25,13 +13,30 @@ libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cle
 $:.unshift(libpath) unless $:.include?(libpath)
 
 require 'test/unit'
-require 'bioruby'
+require 'bio/shell'
+require 'bio/shell/plugin/seq'
 
 module Bio
+
   class TestShellPluginSeq < Test::Unit::TestCase
+    include Bio::Shell
+
+    Bio::Shell.config = {:color => false}
+
+    def test_htmlseq
+      str = 'ATGC'
+      html =<<END
+<div style="font-family:monospace;">
+<span style="background:#64F73F;">a</span>
+<span style="background:#3C88EE;">t</span>
+<span style="background:#EB413C;">g</span>
+<span style="background:#FFB340;">c</span>
+<br>
+</div>
+END
+      assert_equal(html, htmlseq(str))
+    end
 
-#    include Bio::Shell
-#    Bio::Shell.instance_variable_set :@config, {}
 
     def test_naseq
       str = 'ACGT'
@@ -40,6 +45,7 @@ module Bio
       assert_equal('acgt', seq(str))
     end
 
+
     def test_aaseq
       str = 'WD'
       assert_equal(Bio::Sequence::AA, seq(str).class)
@@ -47,6 +53,7 @@ module Bio
       assert_equal('WD', seq(str))
     end
 
+
     def test_na_seqstat
       naseq = 'atgcatgcatgc'
       output =<<END
@@ -112,6 +119,7 @@ END
       assert_equal(output, $str)
     end
 
+
     def test_aa_seqstat
       aaseq = 'WD'
       output =<<END
@@ -138,6 +146,7 @@ END
       assert_equal(output, $str)
     end
 
+
     def test_doublehelix
       seq = 'ACGTACGTACGTACGT'
       output = <<END
@@ -172,4 +181,5 @@ END
     end
 
   end
+
 end

data/test/unit/bio/test_alignment.rb

@@ -18,7 +18,7 @@
 #  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: test_alignment.rb,v 1.6 2005/12/02 13:01:49 ngoto Exp $
+#  $Id: test_alignment.rb,v 1.7 2006/01/24 14:11:34 ngoto Exp $
 #
 
 require 'pathname'
@@ -519,12 +519,20 @@ module Bio
     end
 
     def test_alignment_subseq
-      a = A[ Sequence.new('a'), Sequence.new('at'), Sequence.new('atgca'),
-        Sequence.new('atg'), Sequence.new('') ]
-      assert_equal(Alignment::SequenceArray[ Sequence.new(''),
-                     Sequence.new('t'), Sequence.new('tgc'),
-                     Sequence.new('tg'), nil ],
-                   a.alignment_subseq(2,4))
+      a = A[
+        Sequence::NA.new('a'),
+        Sequence::NA.new('at'),
+        Sequence::NA.new('atgca'),
+        Sequence::NA.new('atg'),
+        Sequence::NA.new('')
+      ]
+      assert_equal(Alignment::SequenceArray[
+                     Sequence::NA.new(''),
+                     Sequence::NA.new('t'),
+                     Sequence::NA.new('tgc'),
+                     Sequence::NA.new('tg'),
+                     nil
+                   ], a.alignment_subseq(2,4))
     end
 
     def test_alignment_concat

data/test/unit/bio/test_reference.rb

@@ -0,0 +1,198 @@
+#
+# = test/bio/tc_pathway.rb - Unit test for Bio::Pathway
+#
+# Copyright::  Copyright (C) 2006 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# Lisence::    Ruby's
+#
+# $Id: test_reference.rb,v 1.1 2006/02/08 15:06:26 nakao Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "lib")).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/reference'
+
+
+module Bio
+  class TestReference < Test::Unit::TestCase
+    
+    def setup
+      hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ], 'title' => "Title of the study.",
+              'journal' => "Theor. J. Hoge", 'volume' => 12, 'issue' => 3, 'pages' => "123-145",
+              'year' => 2001, 'pubmed' => 12345678, 'medline' => 98765432, 'abstract' => "Hoge fuga. hoge fuga.",
+              'url' => "http://example.com", 'mesh' => ['Hoge'], 'affiliations' => ['Tokyo']}
+      @obj = Bio::Reference.new(hash)
+    end
+
+    def test_authors
+      ary = [ "Hoge, J.P.", "Fuga, F.B." ]
+      assert_equal(ary, @obj.authors)
+    end
+
+    def test_journal
+      str = 'Theor. J. Hoge'
+      assert_equal(str, @obj.journal)      
+    end
+    
+    def test_volume
+      str = 12
+      assert_equal(str, @obj.volume)      
+    end
+
+    def test_issue
+      str = 3
+      assert_equal(str, @obj.issue)      
+    end
+
+    def test_pages
+      str = '123-145'
+      assert_equal(str, @obj.pages)
+    end
+
+    def test_year
+      str = 2001
+      assert_equal(str, @obj.year)
+    end
+    
+    def test_pubmed
+      str = 12345678
+      assert_equal(str, @obj.pubmed)
+    end
+
+    def test_abstract
+      str = 'Hoge fuga. hoge fuga.'
+      assert_equal(str, @obj.abstract)
+    end
+
+    def test_url
+      str = 'http://example.com'
+      assert_equal(str, @obj.url)
+    end
+
+    def test_mesh
+      str = ['Hoge']
+      assert_equal(str, @obj.mesh)
+    end
+
+    def test_affiliations
+      str = ['Tokyo']
+      assert_equal(str, @obj.affiliations)
+    end
+
+    def test_format_general
+      str = 'Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.'
+      assert_equal(str, @obj.format)
+      assert_equal(str, @obj.format('general'))
+      assert_equal(str, @obj.general)
+    end
+
+    def test_format_endnote
+      str = "%0 Journal Article\n%A Hoge, J.P.\n%A Fuga, F.B.\n%D 2001\n%T Title of the study.\n%J Theor. J. Hoge\n%V 12\n%N 3\n%P 123-145\n%M 12345678\n%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12345678\n%X Hoge fuga. hoge fuga.\n%K Hoge\n%+ Tokyo"
+      assert_equal(str, @obj.format('endnote'))
+      assert_equal(str, @obj.endnote)
+    end
+
+    def test_format_bibitem
+      str = "\\bibitem{PMID:12345678}\nHoge, J.P., Fuga, F.B.\nTitle of the study.,\n{\\em Theor. J. Hoge}, 12(3):123--145, 2001."
+      assert_equal(str, @obj.format('bibitem'))
+      assert_equal(str, @obj.bibitem)
+    end
+
+    def test_format_bibtex
+      str =<<END
+        @article{PMID:12345678,
+          author  = {Hoge, J.P. and Fuga, F.B.},
+          title   = {Title of the study.},
+          journal = {Theor. J. Hoge},
+          year    = {2001},
+          volume  = {12},
+          number  = {3},
+          pages   = {123--145},
+        }
+END
+      assert_equal(str, @obj.format('bibtex'))
+      assert_equal(str, @obj.bibtex)
+    end
+
+    def test_format_rd
+      str = "== Title of the study.\n\n* Hoge, J.P. and Fuga, F.B.\n\n* Theor. J. Hoge 2001 12:123-145 [PMID:12345678]\n\nHoge fuga. hoge fuga."
+      assert_equal(str, @obj.format('rd'))
+      assert_equal(str, @obj.rd)
+    end
+
+    def test_format_nature
+      str = 'Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).'
+      assert_equal(str, @obj.format('Nature'))
+      assert_equal(str, @obj.format('nature'))
+      assert_equal(str, @obj.nature)
+    end
+
+    def test_format_science
+      str = 'J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).'
+      assert_equal(str, @obj.format('Science'))
+      assert_equal(str, @obj.format('science'))
+      assert_equal(str, @obj.science)
+    end
+
+    def test_format_genome_biol
+      str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
+      assert_equal(str, @obj.format('genome biol'))
+      assert_equal(str, @obj.genome_biol)
+    end
+
+    def test_format_genome_res
+      str = "Hoge, J.P. and Fuga, F.B. 2001.\n  Title of the study. Theor. J. Hoge 12: 123-145."
+      assert_equal(str, @obj.format('genome res'))
+      assert_equal(str, @obj.genome_res)
+    end
+
+    def test_format_nar
+      str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.'
+      assert_equal(str, @obj.format('nar'))
+      assert_equal(str, @obj.nar)
+    end
+
+    def test_format_current
+      str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
+      assert_equal(str, @obj.format('current biology'))
+    end
+
+    def test_format_trends
+      str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145'
+      assert_equal(str, @obj.trends)
+    end
+
+    def test_format_cell
+      str = 'Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.'
+      assert_equal(str, @obj.format('cell'))
+    end
+
+  end
+
+  class TestReferences < Test::Unit::TestCase
+
+    def setup
+      hash = {}
+      ary = [Bio::Reference.new(hash),
+             Bio::Reference.new(hash)]
+      @obj = Bio::References.new(ary)
+    end
+
+    def test_append
+      hash = {}
+      ref = Bio::Reference.new(hash)
+      assert(@obj.append(ref))
+    end
+
+    def test_each
+      @obj.each do |ref|
+        assert(ref)
+      end
+    end
+
+  end
+
+end

data/test/unit/bio/test_sequence.rb

@@ -1,7 +1,8 @@
 #
-# test/unit/bio/tc_sequence.rb - Unit test for Bio::Sequencce
+# test/unit/bio/test_sequence.rb - Unit test for Bio::Sequencce
 #
 #   Copyright (C) 2004 Moses Hohman <mmhohman@northwestern.edu>
+#   Copyright (C) 2006 Mitsuteru C. Nakao <n@bioruby.org>
 #
 #  This library is free software; you can redistribute it and/or
 #  modify it under the terms of the GNU Lesser General Public
@@ -17,7 +18,7 @@
 #  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: test_sequence.rb,v 1.5 2005/11/26 06:51:45 nakao Exp $
+#  $Id: test_sequence.rb,v 1.6 2006/02/05 17:39:27 nakao Exp $
 #
 
 require 'pathname'
@@ -29,34 +30,14 @@ require 'bio/sequence'
 
 module Bio
   class TestSequence < Test::Unit::TestCase
+
     def setup
       @na  = Sequence::NA.new('atgcatgcatgcatgcaaaa')
       @rna = Sequence::NA.new('augcaugcaugcaugcaaaa')
       @aa  = Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
     end
 
-    def test_to_s_returns_self_as_string
-      s = "abcefghijklmnop"
-      sequence = Sequence.new(s)
-      assert_equal(s, sequence.to_s, "wrong value")
-      assert_instance_of(String, sequence.to_s, "not a String")
-    end
-
-    def test_subseq_returns_nil_blank_sequence_default_end
-      sequence = Sequence.new("")
-      assert_nil(sequence.subseq(5))
-    end
 
-    def test_subseq_returns_nil_start_less_than_one
-      sequence = Sequence.new("blahblah")
-      assert_nil(sequence.subseq(0))
-    end
-    
-    def test_subseq_returns_subsequence
-      sequence = Sequence.new("hahasubhehe")
-      assert_equal("sub", sequence.subseq(5,7))
-    end
-    
     # "main" method tests translated into unit tests
     
     # Test Sequence::NA.new
@@ -124,32 +105,6 @@ module Bio
       assert_equal(?t, sequence[1])
     end
     
-    # Test Sequence#to_fasta
-    
-    def test_to_fasta
-      sequence = Sequence.new("agtc"*10)
-      header = "the header"
-      assert_equal(">the header\n" + ("agtc"*5) + "\n" + ("agtc"*5) + "\n", sequence.to_fasta(header, 20))
-    end
-    
-    # Test Sequence#window_wearch
-    
-    def test_window_search_with_width_3_default_step_no_residual
-      sequence = Sequence.new("agtca")
-      windows = []
-      returned_value = sequence.window_search(3) { |window| windows << window }
-      assert_equal(["agt", "gtc", "tca"], windows, "windows wrong")
-      assert_equal("", returned_value, "returned value wrong")
-    end
-    
-    # added
-    def test_window_search_with_width_3_step_two_with_residual
-      sequence = Sequence::NA.new("agtcat")
-      windows = []
-      returned_value = sequence.window_search(3, 2) { |window| windows << window }
-      assert_equal(["agt", "tca"], windows, "windows wrong")
-      assert_equal("t", returned_value, "returned value wrong")
-    end
     
     # Test Sequence#total
     

data/test/unit/bio/test_shell.rb

@@ -17,7 +17,7 @@
 #  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: test_shell.rb,v 1.4 2005/12/18 17:00:10 k Exp $
+#  $Id: test_shell.rb,v 1.5 2006/02/21 17:40:37 nakao Exp $
 #
 
 require 'pathname'
@@ -25,7 +25,7 @@ libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cle
 $:.unshift(libpath) unless $:.include?(libpath)
 
 require 'test/unit'
-require 'bioruby'
+require 'bio/shell'
 
 module Bio
 end

metadata

@@ -3,17 +3,17 @@ rubygems_version: 0.8.11
 specification_version: 1
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 0.7.1
-date: 2006-01-20 00:00:00 +09:00
-summary: BioRuby is a library for bioinformatics (biology + information science).
+  version: 1.0.0
+date: 2006-02-27 00:00:00 +09:00
+summary: Bioinformatics library
 require_paths: 
 - lib
 email: staff@bioruby.org
 homepage: http://bioruby.org/
-rubyforge_project: 
-description: 
+rubyforge_project: bioruby
+description: BioRuby is a library for bioinformatics (biology + information science).
 autorequire: bio
-default_executable: 
+default_executable: bioruby
 bindir: bin
 has_rdoc: false
 required_ruby_version: !ruby/object:Gem::Version::Requirement 
@@ -45,7 +45,6 @@ files:
 - etc/bioinformatics/seqdatabase.ini
 - lib/bio
 - lib/bio.rb
-- lib/bioruby.rb
 - lib/bio/alignment.rb
 - lib/bio/appl
 - lib/bio/command.rb
@@ -57,6 +56,7 @@ files:
 - lib/bio/location.rb
 - lib/bio/pathway.rb
 - lib/bio/reference.rb
+- lib/bio/sequence
 - lib/bio/sequence.rb
 - lib/bio/shell
 - lib/bio/shell.rb
@@ -147,11 +147,11 @@ files:
 - lib/bio/db/kegg/reaction.rb
 - lib/bio/db/pdb/atom.rb
 - lib/bio/db/pdb/chain.rb
+- lib/bio/db/pdb/chemicalcomponent.rb
 - lib/bio/db/pdb/model.rb
 - lib/bio/db/pdb/pdb.rb
 - lib/bio/db/pdb/residue.rb
 - lib/bio/db/pdb/utils.rb
-- lib/bio/io/brdb.rb
 - lib/bio/io/das.rb
 - lib/bio/io/dbget.rb
 - lib/bio/io/ddbjxml.rb
@@ -168,16 +168,91 @@ files:
 - lib/bio/io/flatfile/bdb.rb
 - lib/bio/io/flatfile/index.rb
 - lib/bio/io/flatfile/indexer.rb
+- lib/bio/sequence/aa.rb
+- lib/bio/sequence/common.rb
+- lib/bio/sequence/compat.rb
+- lib/bio/sequence/format.rb
+- lib/bio/sequence/generic.rb
+- lib/bio/sequence/na.rb
 - lib/bio/shell/core.rb
+- lib/bio/shell/demo.rb
+- lib/bio/shell/interface.rb
+- lib/bio/shell/object.rb
 - lib/bio/shell/plugin
-- lib/bio/shell/session.rb
+- lib/bio/shell/rails
+- lib/bio/shell/web.rb
 - lib/bio/shell/plugin/codon.rb
+- lib/bio/shell/plugin/emboss.rb
 - lib/bio/shell/plugin/entry.rb
 - lib/bio/shell/plugin/flatfile.rb
 - lib/bio/shell/plugin/keggapi.rb
 - lib/bio/shell/plugin/midi.rb
 - lib/bio/shell/plugin/obda.rb
 - lib/bio/shell/plugin/seq.rb
+- lib/bio/shell/rails/app
+- lib/bio/shell/rails/config
+- lib/bio/shell/rails/doc
+- lib/bio/shell/rails/public
+- lib/bio/shell/rails/Rakefile
+- lib/bio/shell/rails/script
+- lib/bio/shell/rails/test
+- lib/bio/shell/rails/app/controllers
+- lib/bio/shell/rails/app/helpers
+- lib/bio/shell/rails/app/models
+- lib/bio/shell/rails/app/views
+- lib/bio/shell/rails/app/controllers/application.rb
+- lib/bio/shell/rails/app/controllers/shell_controller.rb
+- lib/bio/shell/rails/app/helpers/application_helper.rb
+- lib/bio/shell/rails/app/models/shell_connection.rb
+- lib/bio/shell/rails/app/views/layouts
+- lib/bio/shell/rails/app/views/shell
+- lib/bio/shell/rails/app/views/layouts/shell.rhtml
+- lib/bio/shell/rails/app/views/shell/history.rhtml
+- lib/bio/shell/rails/app/views/shell/index.rhtml
+- lib/bio/shell/rails/app/views/shell/show.rhtml
+- lib/bio/shell/rails/config/boot.rb
+- lib/bio/shell/rails/config/database.yml
+- lib/bio/shell/rails/config/environment.rb
+- lib/bio/shell/rails/config/environments
+- lib/bio/shell/rails/config/routes.rb
+- lib/bio/shell/rails/config/environments/development.rb
+- lib/bio/shell/rails/config/environments/production.rb
+- lib/bio/shell/rails/config/environments/test.rb
+- lib/bio/shell/rails/doc/README_FOR_APP
+- lib/bio/shell/rails/public/404.html
+- lib/bio/shell/rails/public/500.html
+- lib/bio/shell/rails/public/dispatch.cgi
+- lib/bio/shell/rails/public/dispatch.fcgi
+- lib/bio/shell/rails/public/dispatch.rb
+- lib/bio/shell/rails/public/favicon.ico
+- lib/bio/shell/rails/public/images
+- lib/bio/shell/rails/public/index.html
+- lib/bio/shell/rails/public/javascripts
+- lib/bio/shell/rails/public/robots.txt
+- lib/bio/shell/rails/public/stylesheets
+- lib/bio/shell/rails/public/images/icon.png
+- lib/bio/shell/rails/public/images/rails.png
+- lib/bio/shell/rails/public/javascripts/controls.js
+- lib/bio/shell/rails/public/javascripts/dragdrop.js
+- lib/bio/shell/rails/public/javascripts/effects.js
+- lib/bio/shell/rails/public/javascripts/prototype.js
+- lib/bio/shell/rails/public/stylesheets/main.css
+- lib/bio/shell/rails/script/about
+- lib/bio/shell/rails/script/breakpointer
+- lib/bio/shell/rails/script/console
+- lib/bio/shell/rails/script/destroy
+- lib/bio/shell/rails/script/generate
+- lib/bio/shell/rails/script/performance
+- lib/bio/shell/rails/script/plugin
+- lib/bio/shell/rails/script/process
+- lib/bio/shell/rails/script/runner
+- lib/bio/shell/rails/script/server
+- lib/bio/shell/rails/script/performance/benchmarker
+- lib/bio/shell/rails/script/performance/profiler
+- lib/bio/shell/rails/script/process/reaper
+- lib/bio/shell/rails/script/process/spawner
+- lib/bio/shell/rails/script/process/spinner
+- lib/bio/shell/rails/test/test_helper.rb
 - lib/bio/util/color_scheme
 - lib/bio/util/color_scheme.rb
 - lib/bio/util/contingency_table.rb
@@ -190,6 +265,7 @@ files:
 - lib/bio/util/color_scheme/taylor.rb
 - lib/bio/util/color_scheme/turn.rb
 - lib/bio/util/color_scheme/zappo.rb
+- sample/any2fasta.rb
 - sample/biofetch.rb
 - sample/color_scheme_na.rb
 - sample/dbget
@@ -216,20 +292,29 @@ files:
 - test/functional
 - test/runner.rb
 - test/unit
+- test/data/aaindex
+- test/data/bl2seq
 - test/data/blast
 - test/data/embl
 - test/data/genscan
+- test/data/HMMER
 - test/data/prosite
 - test/data/refseq
 - test/data/SOSUI
 - test/data/TMHMM
 - test/data/uniprot
-- test/data/blast/eco:b0002.faa
-- test/data/blast/eco:b0002.faa.m0
-- test/data/blast/eco:b0002.faa.m7
-- test/data/blast/eco:b0002.faa.m8
+- test/data/aaindex/DAYM780301
+- test/data/aaindex/PRAM900102
+- test/data/bl2seq/cd8a_cd8b_blastp.bl2seq
+- test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq
+- test/data/blast/b0002.faa
+- test/data/blast/b0002.faa.m0
+- test/data/blast/b0002.faa.m7
+- test/data/blast/b0002.faa.m8
 - test/data/embl/AB090716.embl
 - test/data/genscan/sample.report
+- test/data/HMMER/hmmpfam.out
+- test/data/HMMER/hmmsearch.out
 - test/data/prosite/prosite.dat
 - test/data/refseq/nm_126355.entret
 - test/data/SOSUI/sample.report
@@ -243,6 +328,7 @@ files:
 - test/unit/bio/data
 - test/unit/bio/db
 - test/unit/bio/io
+- test/unit/bio/sequence
 - test/unit/bio/shell
 - test/unit/bio/test_alignment.rb
 - test/unit/bio/test_command.rb
@@ -250,19 +336,24 @@ files:
 - test/unit/bio/test_feature.rb
 - test/unit/bio/test_location.rb
 - test/unit/bio/test_pathway.rb
+- test/unit/bio/test_reference.rb
 - test/unit/bio/test_sequence.rb
 - test/unit/bio/test_shell.rb
 - test/unit/bio/util
+- test/unit/bio/appl/bl2seq
 - test/unit/bio/appl/blast
 - test/unit/bio/appl/genscan
+- test/unit/bio/appl/hmmer
 - test/unit/bio/appl/sosui
 - test/unit/bio/appl/targetp
 - test/unit/bio/appl/test_blast.rb
 - test/unit/bio/appl/test_fasta.rb
 - test/unit/bio/appl/tmhmm
+- test/unit/bio/appl/bl2seq/test_report.rb
 - test/unit/bio/appl/blast/test_report.rb
 - test/unit/bio/appl/blast/test_xmlparser.rb
 - test/unit/bio/appl/genscan/test_report.rb
+- test/unit/bio/appl/hmmer/test_report.rb
 - test/unit/bio/appl/sosui/test_report.rb
 - test/unit/bio/appl/targetp/test_report.rb
 - test/unit/bio/appl/tmhmm/test_report.rb
@@ -271,6 +362,8 @@ files:
 - test/unit/bio/data/test_na.rb
 - test/unit/bio/db/embl
 - test/unit/bio/db/kegg
+- test/unit/bio/db/pdb
+- test/unit/bio/db/test_aaindex.rb
 - test/unit/bio/db/test_fasta.rb
 - test/unit/bio/db/test_gff.rb
 - test/unit/bio/db/test_prosite.rb
@@ -280,8 +373,14 @@ files:
 - test/unit/bio/db/embl/test_sptr.rb
 - test/unit/bio/db/embl/test_uniprot.rb
 - test/unit/bio/db/kegg/test_genes.rb
+- test/unit/bio/db/pdb/test_pdb.rb
 - test/unit/bio/io/test_ddbjxml.rb
+- test/unit/bio/io/test_fastacmd.rb
 - test/unit/bio/io/test_soapwsdl.rb
+- test/unit/bio/sequence/test_aa.rb
+- test/unit/bio/sequence/test_common.rb
+- test/unit/bio/sequence/test_compat.rb
+- test/unit/bio/sequence/test_na.rb
 - test/unit/bio/shell/plugin
 - test/unit/bio/shell/plugin/test_seq.rb
 - test/unit/bio/util/test_color_scheme.rb
@@ -293,8 +392,12 @@ rdoc_options: []
 
 extra_rdoc_files: []
 
-executables: []
-
+executables: 
+- bioruby
+- br_biofetch.rb
+- br_biogetseq.rb
+- br_bioflat.rb
+- br_pmfetch.rb
 extensions: []
 
 requirements: []