bio 1.2.1 → 1.3.0

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_aligned_strands.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -13,10 +13,11 @@ libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cle
 $:.unshift(libpath) unless $:.include?(libpath)
 
 require 'test/unit'
+require 'bio/sequence'
 require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'
 require 'bio/util/restriction_enzyme/double_stranded'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestDoubleStrandedAlignedStrands < Test::Unit::TestCase #:nodoc:
 
@@ -97,4 +98,4 @@ class TestDoubleStrandedAlignedStrands < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_cut_location_pair.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestDoubleStrandedCutLocationPair < Test::Unit::TestCase #:nodoc:
 
@@ -72,4 +72,4 @@ class TestDoubleStrandedCutLocationPair < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_cut_location_pair_in_enzyme_notation.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestDoubleStrandedCutLocationPairInEnzymeNotation < Test::Unit::TestCase #:nodoc:
 
@@ -70,4 +70,4 @@ class TestDoubleStrandedCutLocationPairInEnzymeNotation < Test::Unit::TestCase #
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_cut_locations.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestDoubleStrandedCutLocations < Test::Unit::TestCase #:nodoc:
 
@@ -50,4 +50,4 @@ class TestDoubleStrandedCutLocations < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_cut_locations_in_enzyme_notation.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestDoubleStrandedCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodoc:
 
@@ -101,4 +101,4 @@ class TestDoubleStrandedCutLocationsInEnzymeNotation < Test::Unit::TestCase #:no
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_cut_locations_in_enzyme_notation.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestSingleStrandCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodoc:
 
@@ -80,4 +80,4 @@ class TestSingleStrandCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodo
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/test_analysis.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_analysis.rb,v 1.13 2007/07/16 19:29:32 k Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -16,7 +16,7 @@ require 'test/unit'
 require 'bio/util/restriction_enzyme/analysis'
 require 'bio/sequence'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestAnalysis < Test::Unit::TestCase #:nodoc:
 
@@ -243,4 +243,4 @@ class TestAnalysis < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_cut_symbol.rb,v 1.2 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,9 +15,9 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/cut_symbol'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
-class TestStringFormatting < Test::Unit::TestCase #:nodoc:
+class TestCutSymbol < Test::Unit::TestCase #:nodoc:
 
   include Bio::RestrictionEnzyme::CutSymbol
 
@@ -41,4 +41,4 @@ class TestStringFormatting < Test::Unit::TestCase #:nodoc:
   
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_double_stranded.rb,v 1.6 2007/07/16 19:29:32 k Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -16,7 +16,7 @@ require 'test/unit'
 require 'bio/util/restriction_enzyme/double_stranded'
 require 'bio/sequence'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestDoubleStranded < Test::Unit::TestCase #:nodoc:
 
@@ -112,4 +112,4 @@ class TestDoubleStranded < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_single_strand.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/single_strand'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestSingleStrand < Test::Unit::TestCase #:nodoc:
 
@@ -144,4 +144,4 @@ class TestSingleStrand < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_single_strand_complement.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/single_strand_complement'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestSingleStrandComplement < Test::Unit::TestCase #:nodoc:
 
@@ -144,4 +144,4 @@ class TestSingleStrandComplement < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_string_formatting.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme/string_formatting'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestStringFormatting < Test::Unit::TestCase #:nodoc:
 
@@ -57,4 +57,4 @@ class TestStringFormatting < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

data/test/unit/bio/util/test_restriction_enzyme.rb

@@ -5,7 +5,7 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: test_restriction_enzyme.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -15,7 +15,7 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/restriction_enzyme.rb'
 
-module Bio #:nodoc:
+module Bio; module TestRestrictionEnzyme #:nodoc:
 
 class TestRestrictionEnzyme < Test::Unit::TestCase #:nodoc:
 
@@ -39,4 +39,4 @@ class TestRestrictionEnzyme < Test::Unit::TestCase #:nodoc:
 
 end
 
-end
+end; end

metadata

@@ -1,127 +1,142 @@
 --- !ruby/object:Gem::Specification 
-rubygems_version: 0.9.4
-specification_version: 1
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.2.1
-date: 2007-12-30 00:00:00 +09:00
-summary: Bioinformatics library
-require_paths: 
-- lib
-email: staff@bioruby.org
-homepage: http://bioruby.org/
-rubyforge_project: bioruby
-description: BioRuby is a library for bioinformatics (biology + information science).
-autorequire: bio
-default_executable: bioruby
-bindir: bin
-has_rdoc: false
-required_ruby_version: !ruby/object:Gem::Version::Requirement 
-  requirements: 
-  - - ">"
-    - !ruby/object:Gem::Version 
-      version: 0.0.0
-  version: 
+  version: 1.3.0
 platform: ruby
-signing_key: 
-cert_chain: 
-post_install_message: 
 authors: 
 - BioRuby project
+autorequire: bio
+bindir: bin
+cert_chain: []
+
+date: 2009-02-20 00:00:00 +09:00
+default_executable: bioruby
+dependencies: []
+
+description: BioRuby is a library for bioinformatics (biology + information science).
+email: staff@bioruby.org
+executables: 
+- bioruby
+- br_biofetch.rb
+- br_bioflat.rb
+- br_biogetseq.rb
+- br_pmfetch.rb
+extensions: []
+
+extra_rdoc_files: 
+- ChangeLog
+- KNOWN_ISSUES.rdoc
+- README.rdoc
+- README_DEV.rdoc
+- doc/Changes-1.3.rdoc
 files: 
+- ChangeLog
+- KNOWN_ISSUES.rdoc
+- README.rdoc
+- README_DEV.rdoc
+- Rakefile
 - bin/bioruby
 - bin/br_biofetch.rb
 - bin/br_bioflat.rb
 - bin/br_biogetseq.rb
 - bin/br_pmfetch.rb
+- bioruby.gemspec
+- bioruby.gemspec.erb
 - doc/Changes-0.7.rd
+- doc/Changes-1.3.rdoc
 - doc/KEGG_API.rd
 - doc/KEGG_API.rd.ja
 - doc/Tutorial.rd
+- doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
-- etc/bioinformatics
+- doc/Tutorial.rd.ja.html
+- doc/bioruby.css
 - etc/bioinformatics/seqdatabase.ini
-- lib/bio
+- extconf.rb
+- lib/bio.rb
 - lib/bio/alignment.rb
-- lib/bio/appl
-- lib/bio/appl/bl2seq
 - lib/bio/appl/bl2seq/report.rb
-- lib/bio/appl/blast
+- lib/bio/appl/blast.rb
+- lib/bio/appl/blast/ddbj.rb
 - lib/bio/appl/blast/format0.rb
 - lib/bio/appl/blast/format8.rb
+- lib/bio/appl/blast/genomenet.rb
+- lib/bio/appl/blast/ncbioptions.rb
+- lib/bio/appl/blast/remote.rb
 - lib/bio/appl/blast/report.rb
 - lib/bio/appl/blast/rexml.rb
+- lib/bio/appl/blast/rpsblast.rb
 - lib/bio/appl/blast/wublast.rb
 - lib/bio/appl/blast/xmlparser.rb
-- lib/bio/appl/blast.rb
-- lib/bio/appl/blat
 - lib/bio/appl/blat/report.rb
-- lib/bio/appl/clustalw
-- lib/bio/appl/clustalw/report.rb
 - lib/bio/appl/clustalw.rb
+- lib/bio/appl/clustalw/report.rb
 - lib/bio/appl/emboss.rb
-- lib/bio/appl/fasta
-- lib/bio/appl/fasta/format10.rb
 - lib/bio/appl/fasta.rb
-- lib/bio/appl/gcg
+- lib/bio/appl/fasta/format10.rb
 - lib/bio/appl/gcg/msf.rb
 - lib/bio/appl/gcg/seq.rb
-- lib/bio/appl/genscan
 - lib/bio/appl/genscan/report.rb
-- lib/bio/appl/hmmer
-- lib/bio/appl/hmmer/report.rb
 - lib/bio/appl/hmmer.rb
-- lib/bio/appl/iprscan
+- lib/bio/appl/hmmer/report.rb
 - lib/bio/appl/iprscan/report.rb
-- lib/bio/appl/mafft
-- lib/bio/appl/mafft/report.rb
 - lib/bio/appl/mafft.rb
+- lib/bio/appl/mafft/report.rb
 - lib/bio/appl/muscle.rb
-- lib/bio/appl/phylip
+- lib/bio/appl/paml/baseml.rb
+- lib/bio/appl/paml/baseml/report.rb
+- lib/bio/appl/paml/codeml.rb
+- lib/bio/appl/paml/codeml/rates.rb
+- lib/bio/appl/paml/codeml/report.rb
+- lib/bio/appl/paml/common.rb
+- lib/bio/appl/paml/common_report.rb
+- lib/bio/appl/paml/yn00.rb
+- lib/bio/appl/paml/yn00/report.rb
 - lib/bio/appl/phylip/alignment.rb
 - lib/bio/appl/phylip/distance_matrix.rb
 - lib/bio/appl/probcons.rb
-- lib/bio/appl/psort
-- lib/bio/appl/psort/report.rb
 - lib/bio/appl/psort.rb
+- lib/bio/appl/psort/report.rb
 - lib/bio/appl/pts1.rb
-- lib/bio/appl/sim4
-- lib/bio/appl/sim4/report.rb
 - lib/bio/appl/sim4.rb
-- lib/bio/appl/sosui
+- lib/bio/appl/sim4/report.rb
 - lib/bio/appl/sosui/report.rb
-- lib/bio/appl/spidey
 - lib/bio/appl/spidey/report.rb
-- lib/bio/appl/targetp
 - lib/bio/appl/targetp/report.rb
 - lib/bio/appl/tcoffee.rb
-- lib/bio/appl/tmhmm
 - lib/bio/appl/tmhmm/report.rb
 - lib/bio/command.rb
-- lib/bio/data
+- lib/bio/compat/features.rb
+- lib/bio/compat/references.rb
 - lib/bio/data/aa.rb
 - lib/bio/data/codontable.rb
 - lib/bio/data/na.rb
-- lib/bio/db
+- lib/bio/db.rb
 - lib/bio/db/aaindex.rb
-- lib/bio/db/embl
+- lib/bio/db/biosql/biosql_to_biosequence.rb
+- lib/bio/db/biosql/sequence.rb
 - lib/bio/db/embl/common.rb
 - lib/bio/db/embl/embl.rb
+- lib/bio/db/embl/embl_to_biosequence.rb
+- lib/bio/db/embl/format_embl.rb
 - lib/bio/db/embl/sptr.rb
 - lib/bio/db/embl/swissprot.rb
 - lib/bio/db/embl/trembl.rb
 - lib/bio/db/embl/uniprot.rb
 - lib/bio/db/fantom.rb
 - lib/bio/db/fasta.rb
-- lib/bio/db/genbank
+- lib/bio/db/fasta/defline.rb
+- lib/bio/db/fasta/fasta_to_biosequence.rb
+- lib/bio/db/fasta/format_fasta.rb
 - lib/bio/db/genbank/common.rb
 - lib/bio/db/genbank/ddbj.rb
+- lib/bio/db/genbank/format_genbank.rb
 - lib/bio/db/genbank/genbank.rb
+- lib/bio/db/genbank/genbank_to_biosequence.rb
 - lib/bio/db/genbank/genpept.rb
 - lib/bio/db/genbank/refseq.rb
 - lib/bio/db/gff.rb
 - lib/bio/db/go.rb
-- lib/bio/db/kegg
 - lib/bio/db/kegg/brite.rb
 - lib/bio/db/kegg/compound.rb
 - lib/bio/db/kegg/drug.rb
@@ -141,7 +156,7 @@ files:
 - lib/bio/db/nbrf.rb
 - lib/bio/db/newick.rb
 - lib/bio/db/nexus.rb
-- lib/bio/db/pdb
+- lib/bio/db/pdb.rb
 - lib/bio/db/pdb/atom.rb
 - lib/bio/db/pdb/chain.rb
 - lib/bio/db/pdb/chemicalcomponent.rb
@@ -149,14 +164,40 @@ files:
 - lib/bio/db/pdb/pdb.rb
 - lib/bio/db/pdb/residue.rb
 - lib/bio/db/pdb/utils.rb
-- lib/bio/db/pdb.rb
 - lib/bio/db/prosite.rb
 - lib/bio/db/rebase.rb
 - lib/bio/db/soft.rb
 - lib/bio/db/transfac.rb
-- lib/bio/db.rb
 - lib/bio/feature.rb
-- lib/bio/io
+- lib/bio/io/biosql/biodatabase.rb
+- lib/bio/io/biosql/bioentry.rb
+- lib/bio/io/biosql/bioentry_dbxref.rb
+- lib/bio/io/biosql/bioentry_path.rb
+- lib/bio/io/biosql/bioentry_qualifier_value.rb
+- lib/bio/io/biosql/bioentry_reference.rb
+- lib/bio/io/biosql/bioentry_relationship.rb
+- lib/bio/io/biosql/biosequence.rb
+- lib/bio/io/biosql/comment.rb
+- lib/bio/io/biosql/config/database.yml
+- lib/bio/io/biosql/dbxref.rb
+- lib/bio/io/biosql/dbxref_qualifier_value.rb
+- lib/bio/io/biosql/location.rb
+- lib/bio/io/biosql/location_qualifier_value.rb
+- lib/bio/io/biosql/ontology.rb
+- lib/bio/io/biosql/reference.rb
+- lib/bio/io/biosql/seqfeature.rb
+- lib/bio/io/biosql/seqfeature_dbxref.rb
+- lib/bio/io/biosql/seqfeature_path.rb
+- lib/bio/io/biosql/seqfeature_qualifier_value.rb
+- lib/bio/io/biosql/seqfeature_relationship.rb
+- lib/bio/io/biosql/taxon.rb
+- lib/bio/io/biosql/taxon_name.rb
+- lib/bio/io/biosql/term.rb
+- lib/bio/io/biosql/term_dbxref.rb
+- lib/bio/io/biosql/term_path.rb
+- lib/bio/io/biosql/term_relationship.rb
+- lib/bio/io/biosql/term_relationship_term.rb
+- lib/bio/io/biosql/term_synonym.rb
 - lib/bio/io/das.rb
 - lib/bio/io/dbget.rb
 - lib/bio/io/ddbjxml.rb
@@ -164,37 +205,43 @@ files:
 - lib/bio/io/ensembl.rb
 - lib/bio/io/fastacmd.rb
 - lib/bio/io/fetch.rb
-- lib/bio/io/flatfile
+- lib/bio/io/flatfile.rb
+- lib/bio/io/flatfile/autodetection.rb
 - lib/bio/io/flatfile/bdb.rb
+- lib/bio/io/flatfile/buffer.rb
 - lib/bio/io/flatfile/index.rb
 - lib/bio/io/flatfile/indexer.rb
-- lib/bio/io/flatfile.rb
+- lib/bio/io/flatfile/splitter.rb
 - lib/bio/io/higet.rb
+- lib/bio/io/hinv.rb
 - lib/bio/io/keggapi.rb
+- lib/bio/io/ncbirest.rb
 - lib/bio/io/ncbisoap.rb
 - lib/bio/io/pubmed.rb
 - lib/bio/io/registry.rb
 - lib/bio/io/soapwsdl.rb
 - lib/bio/io/sql.rb
+- lib/bio/io/togows.rb
 - lib/bio/location.rb
 - lib/bio/map.rb
 - lib/bio/pathway.rb
 - lib/bio/reference.rb
-- lib/bio/sequence
+- lib/bio/sequence.rb
 - lib/bio/sequence/aa.rb
+- lib/bio/sequence/adapter.rb
 - lib/bio/sequence/common.rb
 - lib/bio/sequence/compat.rb
+- lib/bio/sequence/dblink.rb
 - lib/bio/sequence/format.rb
+- lib/bio/sequence/format_raw.rb
 - lib/bio/sequence/generic.rb
 - lib/bio/sequence/na.rb
-- lib/bio/sequence.rb
-- lib/bio/shell
+- lib/bio/shell.rb
 - lib/bio/shell/core.rb
 - lib/bio/shell/demo.rb
 - lib/bio/shell/interface.rb
 - lib/bio/shell/irb.rb
 - lib/bio/shell/object.rb
-- lib/bio/shell/plugin
 - lib/bio/shell/plugin/blast.rb
 - lib/bio/shell/plugin/codon.rb
 - lib/bio/shell/plugin/das.rb
@@ -203,40 +250,34 @@ files:
 - lib/bio/shell/plugin/flatfile.rb
 - lib/bio/shell/plugin/keggapi.rb
 - lib/bio/shell/plugin/midi.rb
+- lib/bio/shell/plugin/ncbirest.rb
 - lib/bio/shell/plugin/obda.rb
 - lib/bio/shell/plugin/psort.rb
 - lib/bio/shell/plugin/seq.rb
 - lib/bio/shell/plugin/soap.rb
-- lib/bio/shell/rails
-- lib/bio/shell/rails/vendor
-- lib/bio/shell/rails/vendor/plugins
-- lib/bio/shell/rails/vendor/plugins/generators
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-gem.png
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml
-- lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/spinner.gif
+- lib/bio/shell/plugin/togows.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
 - lib/bio/shell/script.rb
 - lib/bio/shell/setup.rb
 - lib/bio/shell/web.rb
-- lib/bio/shell.rb
 - lib/bio/tree.rb
-- lib/bio/util
-- lib/bio/util/color_scheme
+- lib/bio/util/color_scheme.rb
 - lib/bio/util/color_scheme/buried.rb
 - lib/bio/util/color_scheme/helix.rb
 - lib/bio/util/color_scheme/hydropathy.rb
@@ -245,44 +286,42 @@ files:
 - lib/bio/util/color_scheme/taylor.rb
 - lib/bio/util/color_scheme/turn.rb
 - lib/bio/util/color_scheme/zappo.rb
-- lib/bio/util/color_scheme.rb
 - lib/bio/util/contingency_table.rb
-- lib/bio/util/restriction_enzyme
+- lib/bio/util/restriction_enzyme.rb
 - lib/bio/util/restriction_enzyme/analysis.rb
 - lib/bio/util/restriction_enzyme/analysis_basic.rb
 - lib/bio/util/restriction_enzyme/cut_symbol.rb
-- lib/bio/util/restriction_enzyme/double_stranded
+- lib/bio/util/restriction_enzyme/double_stranded.rb
 - lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
 - lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
 - lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
 - lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
 - lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
-- lib/bio/util/restriction_enzyme/double_stranded.rb
 - lib/bio/util/restriction_enzyme/enzymes.yaml
-- lib/bio/util/restriction_enzyme/range
 - lib/bio/util/restriction_enzyme/range/cut_range.rb
 - lib/bio/util/restriction_enzyme/range/cut_ranges.rb
 - lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
-- lib/bio/util/restriction_enzyme/range/sequence_range
+- lib/bio/util/restriction_enzyme/range/sequence_range.rb
 - lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
 - lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
 - lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
-- lib/bio/util/restriction_enzyme/range/sequence_range.rb
 - lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
-- lib/bio/util/restriction_enzyme/single_strand
-- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
 - lib/bio/util/restriction_enzyme/single_strand.rb
+- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
 - lib/bio/util/restriction_enzyme/single_strand_complement.rb
 - lib/bio/util/restriction_enzyme/string_formatting.rb
-- lib/bio/util/restriction_enzyme.rb
 - lib/bio/util/sirna.rb
-- lib/bio.rb
+- lib/bio/version.rb
+- rdoc.zsh
 - sample/any2fasta.rb
 - sample/biofetch.rb
 - sample/color_scheme_na.rb
 - sample/dbget
+- sample/demo_sequence.rb
 - sample/enzymes.rb
 - sample/fasta2tab.rb
+- sample/fastagrep.rb
+- sample/fastasort.rb
 - sample/fsplit.rb
 - sample/gb2fasta.rb
 - sample/gb2tab.rb
@@ -294,6 +333,7 @@ files:
 - sample/genome2tab.rb
 - sample/goslim.rb
 - sample/gt2fasta.rb
+- sample/na2aa.rb
 - sample/pmfetch.rb
 - sample/pmsearch.rb
 - sample/psortplot_html.rb
@@ -301,114 +341,97 @@ files:
 - sample/tdiary.rb
 - sample/tfastx2tab.rb
 - sample/vs-genes.rb
-- test/data
-- test/data/aaindex
+- setup.rb
+- test/data/HMMER/hmmpfam.out
+- test/data/HMMER/hmmsearch.out
+- test/data/SOSUI/sample.report
+- test/data/TMHMM/sample.report
 - test/data/aaindex/DAYM780301
 - test/data/aaindex/PRAM900102
-- test/data/bl2seq
 - test/data/bl2seq/cd8a_cd8b_blastp.bl2seq
 - test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq
-- test/data/blast
 - test/data/blast/2.2.15.blastp.m7
 - 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
+- test/data/blast/blastp-multi.m7
+- test/data/command/echoarg2.bat
 - test/data/embl/AB090716.embl
 - test/data/embl/AB090716.embl.rel89
-- test/data/fasta
 - test/data/fasta/example1.txt
 - test/data/fasta/example2.txt
-- test/data/genscan
 - test/data/genscan/sample.report
-- test/data/HMMER
-- test/data/HMMER/hmmpfam.out
-- test/data/HMMER/hmmsearch.out
-- test/data/iprscan
 - test/data/iprscan/merged.raw
 - test/data/iprscan/merged.txt
-- test/data/prosite
+- test/data/paml/codeml/control_file.txt
+- test/data/paml/codeml/output.txt
+- test/data/paml/codeml/rates
 - test/data/prosite/prosite.dat
-- test/data/refseq
 - test/data/refseq/nm_126355.entret
-- test/data/soft
+- test/data/rpsblast/misc.rpsblast
 - test/data/soft/GDS100_partial.soft
 - test/data/soft/GSE3457_family_partial.soft
-- test/data/SOSUI
-- test/data/SOSUI/sample.report
-- test/data/TMHMM
-- test/data/TMHMM/sample.report
-- test/data/uniprot
 - test/data/uniprot/p53_human.uniprot
-- test/functional
-- test/functional/bio
-- test/functional/bio/io
+- test/functional/bio/appl/test_pts1.rb
 - test/functional/bio/io/test_ensembl.rb
 - test/functional/bio/io/test_soapwsdl.rb
+- test/functional/bio/io/test_togows.rb
+- test/functional/bio/sequence/test_output_embl.rb
+- test/functional/bio/test_command.rb
 - test/runner.rb
-- test/unit
-- test/unit/bio
-- test/unit/bio/appl
-- test/unit/bio/appl/bl2seq
 - test/unit/bio/appl/bl2seq/test_report.rb
-- test/unit/bio/appl/blast
+- test/unit/bio/appl/blast/test_ncbioptions.rb
 - test/unit/bio/appl/blast/test_report.rb
-- test/unit/bio/appl/blast/test_xmlparser.rb
-- test/unit/bio/appl/genscan
+- test/unit/bio/appl/blast/test_rpsblast.rb
 - test/unit/bio/appl/genscan/test_report.rb
-- test/unit/bio/appl/hmmer
 - test/unit/bio/appl/hmmer/test_report.rb
-- test/unit/bio/appl/iprscan
 - test/unit/bio/appl/iprscan/test_report.rb
-- test/unit/bio/appl/mafft
 - test/unit/bio/appl/mafft/test_report.rb
-- test/unit/bio/appl/sosui
+- test/unit/bio/appl/paml/codeml/test_rates.rb
+- test/unit/bio/appl/paml/codeml/test_report.rb
+- test/unit/bio/appl/paml/test_codeml.rb
 - test/unit/bio/appl/sosui/test_report.rb
-- test/unit/bio/appl/targetp
 - test/unit/bio/appl/targetp/test_report.rb
 - test/unit/bio/appl/test_blast.rb
 - test/unit/bio/appl/test_fasta.rb
 - test/unit/bio/appl/test_pts1.rb
-- test/unit/bio/appl/tmhmm
 - test/unit/bio/appl/tmhmm/test_report.rb
-- test/unit/bio/data
 - test/unit/bio/data/test_aa.rb
 - test/unit/bio/data/test_codontable.rb
 - test/unit/bio/data/test_na.rb
-- test/unit/bio/db
-- test/unit/bio/db/embl
 - test/unit/bio/db/embl/test_common.rb
 - test/unit/bio/db/embl/test_embl.rb
 - test/unit/bio/db/embl/test_embl_rel89.rb
+- test/unit/bio/db/embl/test_embl_to_bioseq.rb
 - test/unit/bio/db/embl/test_sptr.rb
 - test/unit/bio/db/embl/test_uniprot.rb
-- test/unit/bio/db/kegg
 - test/unit/bio/db/kegg/test_genes.rb
-- test/unit/bio/db/pdb
 - test/unit/bio/db/pdb/test_pdb.rb
 - 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_lasergene.rb
+- test/unit/bio/db/test_medline.rb
 - test/unit/bio/db/test_newick.rb
 - test/unit/bio/db/test_nexus.rb
 - test/unit/bio/db/test_prosite.rb
 - test/unit/bio/db/test_rebase.rb
 - test/unit/bio/db/test_soft.rb
-- test/unit/bio/io
+- test/unit/bio/io/flatfile/test_autodetection.rb
+- test/unit/bio/io/flatfile/test_buffer.rb
+- test/unit/bio/io/flatfile/test_splitter.rb
 - test/unit/bio/io/test_ddbjxml.rb
 - test/unit/bio/io/test_ensembl.rb
 - test/unit/bio/io/test_fastacmd.rb
 - test/unit/bio/io/test_flatfile.rb
 - test/unit/bio/io/test_soapwsdl.rb
-- test/unit/bio/sequence
+- test/unit/bio/io/test_togows.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_dblink.rb
 - test/unit/bio/sequence/test_na.rb
-- test/unit/bio/shell
-- test/unit/bio/shell/plugin
 - test/unit/bio/shell/plugin/test_seq.rb
 - test/unit/bio/test_alignment.rb
 - test/unit/bio/test_command.rb
@@ -421,19 +444,14 @@ files:
 - test/unit/bio/test_sequence.rb
 - test/unit/bio/test_shell.rb
 - test/unit/bio/test_tree.rb
-- test/unit/bio/util
-- test/unit/bio/util/restriction_enzyme
-- test/unit/bio/util/restriction_enzyme/analysis
 - test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb
 - test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb
 - test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb
-- test/unit/bio/util/restriction_enzyme/double_stranded
 - test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb
 - test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb
 - test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb
 - test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb
 - test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
-- test/unit/bio/util/restriction_enzyme/single_strand
 - test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
 - test/unit/bio/util/restriction_enzyme/test_analysis.rb
 - test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb
@@ -445,21 +463,38 @@ files:
 - test/unit/bio/util/test_contingency_table.rb
 - test/unit/bio/util/test_restriction_enzyme.rb
 - test/unit/bio/util/test_sirna.rb
-test_files: []
-
-rdoc_options: []
-
-extra_rdoc_files: []
-
-executables: 
-- bioruby
-- br_biofetch.rb
-- br_biogetseq.rb
-- br_bioflat.rb
-- br_pmfetch.rb
-extensions: []
-
+has_rdoc: true
+homepage: http://bioruby.org/
+post_install_message: 
+rdoc_options: 
+- --main
+- README.rdoc
+- --title
+- BioRuby API documentation
+- --exclude
+- \.yaml\z
+- --line-numbers
+- --inline-source
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
 requirements: []
 
-dependencies: []
+rubyforge_project: bioruby
+rubygems_version: 1.3.1
+signing_key: 
+specification_version: 2
+summary: Bioinformatics library
+test_files: []