bio 1.0.0 → 1.1.0

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

@@ -0,0 +1,147 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb - Unit test for Bio::RestrictionEnzyme::SingleStrandComplement
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# 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 $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/single_strand_complement'
+
+module Bio #:nodoc:
+
+class TestSingleStrandComplement < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::SingleStrandComplement
+    @cl = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
+    @s = Bio::Sequence::NA
+
+    @obj_1 = @t.new(@s.new('gata'), @cl.new(-2,1,3))
+    @obj_2 = @t.new('gata', -2, 1, 3)
+    @obj_3 = @t.new('garraxt', [-2, 1, 7])
+    @obj_4 = @t.new('nnnnnnngarraxtnn', [-2, 1, 7])
+
+    @obj_5 = @t.new('ga^rr^axt')
+    @obj_6 = @t.new('^ga^rr^axt')
+    @obj_7 = @t.new('n^ngar^raxtnn^n')
+  end
+
+  def test_pattern_palindromic?
+    assert_equal(true, @t.new('atgcat', 1).palindromic?)
+    assert_equal(false, @t.new('atgcgta', 1).palindromic?)
+
+    assert_equal(false, @obj_1.palindromic?)
+    assert_equal(false, @obj_2.palindromic?)
+    assert_equal(false, @obj_3.palindromic?)
+    assert_equal(false, @obj_4.palindromic?)
+  end
+
+  def test_stripped
+    assert_equal('gata', @obj_1.stripped)
+    assert_equal('gata', @obj_2.stripped)
+    assert_equal('garraxt', @obj_3.stripped)
+    assert_equal('garraxt', @obj_4.stripped)
+  end
+
+  def test_pattern
+    assert_equal('nngata', @obj_1.pattern)
+    assert_equal('nngata', @obj_2.pattern)
+    assert_equal('nngarraxtn', @obj_3.pattern)
+    assert_equal('nngarraxtn', @obj_4.pattern)
+
+    assert_equal('nngata', @obj_1)
+    assert_equal('nngata', @obj_2)
+    assert_equal('nngarraxtn', @obj_3)
+    assert_equal('nngarraxtn', @obj_4)
+  end
+
+  def test_with_cut_symbols
+    assert_equal('n^ng^at^a', @obj_1.with_cut_symbols)
+    assert_equal('n^ng^at^a', @obj_2.with_cut_symbols)
+    assert_equal('n^ng^arraxt^n', @obj_3.with_cut_symbols)
+    assert_equal('n^ng^arraxt^n', @obj_4.with_cut_symbols)
+  end
+
+  def test_with_spaces
+    assert_equal('n^n g^a t^a', @obj_1.with_spaces)
+    assert_equal('n^n g^a t^a', @obj_2.with_spaces)
+    assert_equal('n^n g^a r r a x t^n', @obj_3.with_spaces)
+    assert_equal('n^n g^a r r a x t^n', @obj_4.with_spaces)
+  end
+
+  def test_cut_locations_in_enzyme_notation
+    assert_equal([-2,1,3], @obj_1.cut_locations_in_enzyme_notation)
+    assert_equal([-2,1,3], @obj_2.cut_locations_in_enzyme_notation)
+    assert_equal([-2,1,7], @obj_3.cut_locations_in_enzyme_notation)
+    assert_equal([-2,1,7], @obj_4.cut_locations_in_enzyme_notation)
+
+    assert_equal([2,4], @obj_5.cut_locations_in_enzyme_notation)
+    assert_equal([-1,2,4], @obj_6.cut_locations_in_enzyme_notation)
+    assert_equal([-2,3,9], @obj_7.cut_locations_in_enzyme_notation)
+  end
+
+  def test_cut_locations
+    assert_equal([0,2,4], @obj_1.cut_locations)
+    assert_equal([0,2,4], @obj_2.cut_locations)
+    assert_equal([0,2,8], @obj_3.cut_locations)
+    assert_equal([0,2,8], @obj_4.cut_locations)
+
+    assert_equal([1,3], @obj_5.cut_locations)
+    assert_equal([0,2,4], @obj_6.cut_locations)
+    assert_equal([0,4,10], @obj_7.cut_locations)
+  end
+
+  def test_orientation
+    assert_equal([3,5], @obj_1.orientation)
+    assert_equal([3,5], @obj_2.orientation)
+    assert_equal([3,5], @obj_3.orientation)
+    assert_equal([3,5], @obj_4.orientation)
+  end
+
+  def test_creation_with_no_cuts
+    @obj_8 = @t.new('garraxt')
+    assert_equal([3,5], @obj_8.orientation)
+    assert_equal([], @obj_8.cut_locations)
+    assert_equal([], @obj_8.cut_locations_in_enzyme_notation)
+    assert_equal('garraxt', @obj_8.pattern)
+  end
+
+  # NOTE
+  def test_to_re
+  end
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new('a', [0,1,2]) }
+    assert_raise(ArgumentError) { @t.new('a', 0,1,2,0) }
+
+    assert_raise(ArgumentError) { @t.new('a', [nil,1,2]) }
+    assert_raise(ArgumentError) { @t.new('a', nil,1,2,nil) }
+
+    assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
+    assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
+
+    assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
+    assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
+    assert_raise(ArgumentError) { @t.new('gaat^^aca') }
+    assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
+
+    assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
+    assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
+    assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
+    assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
+    assert_raise(ArgumentError) { @t.new(1,2,3) }
+    assert_raise(ArgumentError) { @t.new(1,2,'g') }
+  end
+
+
+end
+
+end

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

@@ -0,0 +1,60 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_string_formatting.rb - Unit test for Bio::RestrictionEnzyme::StringFormatting
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# 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 $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/string_formatting'
+
+module Bio #:nodoc:
+
+class TestStringFormatting < Test::Unit::TestCase #:nodoc:
+
+  include Bio::RestrictionEnzyme::StringFormatting
+
+  def setup
+    @t = String
+    @obj_1 = @t.new('gata')
+    @obj_2 = @t.new('garraxt')
+    @obj_3 = @t.new('gArraXT')
+    @obj_4 = @t.new('nnnnnnngarraxtnn')
+  end
+
+  def test_strip_padding
+    assert_equal('gata', strip_padding(@obj_1))
+    assert_equal('garraxt', strip_padding(@obj_2))
+    assert_equal('gArraXT', strip_padding(@obj_3))
+    assert_equal('garraxt', strip_padding(@obj_4))
+  end
+
+  def test_left_padding
+    assert_equal('', left_padding(@obj_1))
+    assert_equal('', left_padding(@obj_2))
+    assert_equal('', left_padding(@obj_3))
+    assert_equal('nnnnnnn', left_padding(@obj_4))
+  end
+
+  def test_right_padding
+    assert_equal('', right_padding(@obj_1))
+    assert_equal('', right_padding(@obj_2))
+    assert_equal('', right_padding(@obj_3))
+    assert_equal('nn', right_padding(@obj_4))
+  end
+
+  def test_add_spacing
+    assert_equal('n^n g^a t^a', add_spacing('n^ng^at^a') )
+    assert_equal('n^n g^a r r a x t^n', add_spacing('n^ng^arraxt^n') )
+  end
+
+end
+
+end

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

@@ -1,23 +1,11 @@
 #
 # test/unit/bio/util/test_color_scheme.rb - Unit test for Bio::ColorScheme
 #
-#   Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_color_scheme.rb,v 1.1 2005/10/23 08:40:41 k Exp $
+#  $Id: test_color_scheme.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'
@@ -27,8 +15,8 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/color_scheme'
 
-module Bio
-  class TestColorScheme < Test::Unit::TestCase
+module Bio #:nodoc:
+  class TestColorScheme < Test::Unit::TestCase #:nodoc:
 
     def test_buried
       s = Bio::ColorScheme::Buried

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

@@ -1,23 +1,11 @@
 #
 # test/unit/bio/util/test_contingency_table.rb - Unit test for Bio::ContingencyTable
 #
-#   Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: test_contingency_table.rb,v 1.2 2005/11/23 11:55:17 nakao Exp $
+#  $Id: test_contingency_table.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'
@@ -27,8 +15,8 @@ $:.unshift(libpath) unless $:.include?(libpath)
 require 'test/unit'
 require 'bio/util/contingency_table'
 
-module Bio
-  class TestContingencyTable < Test::Unit::TestCase
+module Bio #:nodoc:
+  class TestContingencyTable < Test::Unit::TestCase #:nodoc:
  
     def lite_example(sequences, max_length, characters)
 

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

@@ -0,0 +1,42 @@
+#
+# test/unit/bio/util/restriction_enzyme.rb - Unit test for Bio::RestrictionEnzyme
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# 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 $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme.rb'
+
+module Bio #:nodoc:
+
+class TestRestrictionEnzyme < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme
+  end
+  
+  def test_rebase
+    assert_equal(@t.rebase.respond_to?(:enzymes), true)
+    assert_not_nil @t.rebase['AarI']
+    assert_nil @t.rebase['blah']
+  end
+  
+  def test_enzyme_name
+    assert_equal(@t.enzyme_name?('AarI'), true)
+    assert_equal(@t.enzyme_name?('atgc'), false)
+    assert_equal(@t.enzyme_name?('aari'), true)
+    assert_equal(@t.enzyme_name?('EcoRI'), true)
+    assert_equal(@t.enzyme_name?('EcoooRI'), false)
+  end
+
+end
+
+end

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

@@ -1,23 +1,10 @@
 #
 # test/unit/bio/util/test_sirna.rb - Unit test for Bio::SiRNA.
 #
-#   Copyright (C) 2005 Mitsuteru C. Nakap <n@bioruby.org>
+# Copyright::  Copyright (C) 2005 Mitsuteru C. Nakap <n@bioruby.org>
+# License::    The Ruby License
 #
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  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_sirna.rb,v 1.2 2005/12/27 17:27:38 k Exp $
+#  $Id: test_sirna.rb,v 1.4 2007/04/05 23:35:44 trevor Exp $
 #
 
 require 'pathname'

metadata

@@ -1,10 +1,10 @@
 --- !ruby/object:Gem::Specification 
-rubygems_version: 0.8.11
+rubygems_version: 0.9.2
 specification_version: 1
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.0.0
-date: 2006-02-27 00:00:00 +09:00
+  version: 1.1.0
+date: 2007-07-19 00:00:00 +09:00
 summary: Bioinformatics library
 require_paths: 
 - lib
@@ -25,6 +25,7 @@ required_ruby_version: !ruby/object:Gem::Version::Requirement
 platform: ruby
 signing_key: 
 cert_chain: 
+post_install_message: 
 authors: 
 - BioRuby project
 files: 
@@ -33,109 +34,97 @@ files:
 - bin/br_bioflat.rb
 - bin/br_biogetseq.rb
 - bin/br_pmfetch.rb
-- doc/BioRuby.rd.ja
 - doc/Changes-0.7.rd
-- doc/Design.rd.ja
 - doc/KEGG_API.rd
 - doc/KEGG_API.rd.ja
-- doc/TODO.rd.ja
 - doc/Tutorial.rd
 - doc/Tutorial.rd.ja
 - etc/bioinformatics
 - etc/bioinformatics/seqdatabase.ini
 - lib/bio
-- lib/bio.rb
 - lib/bio/alignment.rb
 - lib/bio/appl
-- lib/bio/command.rb
-- lib/bio/data
-- lib/bio/db
-- lib/bio/db.rb
-- lib/bio/feature.rb
-- lib/bio/io
-- 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
-- lib/bio/util
 - lib/bio/appl/bl2seq
+- lib/bio/appl/bl2seq/report.rb
 - lib/bio/appl/blast
+- lib/bio/appl/blast/format0.rb
+- lib/bio/appl/blast/format8.rb
+- lib/bio/appl/blast/report.rb
+- lib/bio/appl/blast/rexml.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/emboss.rb
 - lib/bio/appl/fasta
+- lib/bio/appl/fasta/format10.rb
 - lib/bio/appl/fasta.rb
+- lib/bio/appl/gcg
+- 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/iprscan/report.rb
 - lib/bio/appl/mafft
+- lib/bio/appl/mafft/report.rb
 - lib/bio/appl/mafft.rb
+- lib/bio/appl/muscle.rb
+- lib/bio/appl/phylip
+- 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/pts1.rb
 - lib/bio/appl/sim4
+- lib/bio/appl/sim4/report.rb
 - lib/bio/appl/sim4.rb
 - lib/bio/appl/sosui
-- lib/bio/appl/spidey
-- lib/bio/appl/targetp
-- lib/bio/appl/tmhmm
-- lib/bio/appl/bl2seq/report.rb
-- lib/bio/appl/blast/format0.rb
-- lib/bio/appl/blast/format8.rb
-- lib/bio/appl/blast/report.rb
-- lib/bio/appl/blast/rexml.rb
-- lib/bio/appl/blast/wublast.rb
-- lib/bio/appl/blast/xmlparser.rb
-- lib/bio/appl/blat/report.rb
-- lib/bio/appl/clustalw/report.rb
-- lib/bio/appl/fasta/format10.rb
-- lib/bio/appl/fasta/format6.rb
-- lib/bio/appl/genscan/report.rb
-- lib/bio/appl/hmmer/report.rb
-- lib/bio/appl/mafft/report.rb
-- lib/bio/appl/psort/report.rb
-- 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/data/aa.rb
 - lib/bio/data/codontable.rb
 - lib/bio/data/na.rb
+- lib/bio/db
 - lib/bio/db/aaindex.rb
 - lib/bio/db/embl
-- lib/bio/db/fantom.rb
-- lib/bio/db/fasta.rb
-- lib/bio/db/genbank
-- lib/bio/db/gff.rb
-- lib/bio/db/go.rb
-- lib/bio/db/kegg
-- lib/bio/db/litdb.rb
-- lib/bio/db/medline.rb
-- lib/bio/db/nbrf.rb
-- lib/bio/db/pdb
-- lib/bio/db/pdb.rb
-- lib/bio/db/prosite.rb
-- lib/bio/db/rebase.rb
-- lib/bio/db/transfac.rb
 - lib/bio/db/embl/common.rb
 - lib/bio/db/embl/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/genbank/common.rb
 - lib/bio/db/genbank/ddbj.rb
 - lib/bio/db/genbank/genbank.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/cell.rb
 - lib/bio/db/kegg/compound.rb
+- lib/bio/db/kegg/drug.rb
 - lib/bio/db/kegg/enzyme.rb
 - lib/bio/db/kegg/expression.rb
 - lib/bio/db/kegg/genes.rb
@@ -143,8 +132,16 @@ files:
 - lib/bio/db/kegg/glycan.rb
 - lib/bio/db/kegg/keggtab.rb
 - lib/bio/db/kegg/kgml.rb
-- lib/bio/db/kegg/ko.rb
+- lib/bio/db/kegg/orthology.rb
 - lib/bio/db/kegg/reaction.rb
+- lib/bio/db/kegg/taxonomy.rb
+- lib/bio/db/lasergene.rb
+- lib/bio/db/litdb.rb
+- lib/bio/db/medline.rb
+- lib/bio/db/nbrf.rb
+- lib/bio/db/newick.rb
+- lib/bio/db/nexus.rb
+- lib/bio/db/pdb
 - lib/bio/db/pdb/atom.rb
 - lib/bio/db/pdb/chain.rb
 - lib/bio/db/pdb/chemicalcomponent.rb
@@ -152,111 +149,94 @@ 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/das.rb
 - lib/bio/io/dbget.rb
 - lib/bio/io/ddbjxml.rb
+- lib/bio/io/ebisoap.rb
+- lib/bio/io/ensembl.rb
 - lib/bio/io/fastacmd.rb
 - lib/bio/io/fetch.rb
 - lib/bio/io/flatfile
+- lib/bio/io/flatfile/bdb.rb
+- lib/bio/io/flatfile/index.rb
+- lib/bio/io/flatfile/indexer.rb
 - lib/bio/io/flatfile.rb
 - lib/bio/io/higet.rb
 - lib/bio/io/keggapi.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/flatfile/bdb.rb
-- lib/bio/io/flatfile/index.rb
-- lib/bio/io/flatfile/indexer.rb
+- lib/bio/location.rb
+- lib/bio/map.rb
+- lib/bio/pathway.rb
+- lib/bio/reference.rb
+- lib/bio/sequence
 - 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/sequence.rb
+- lib/bio/shell
 - 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/rails
-- lib/bio/shell/web.rb
+- lib/bio/shell/plugin/blast.rb
 - lib/bio/shell/plugin/codon.rb
+- lib/bio/shell/plugin/das.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/psort.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/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-console.png
+- 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/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/contingency_table.rb
-- lib/bio/util/sirna.rb
 - lib/bio/util/color_scheme/buried.rb
 - lib/bio/util/color_scheme/helix.rb
 - lib/bio/util/color_scheme/hydropathy.rb
@@ -265,10 +245,43 @@ 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/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/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/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_complement.rb
+- lib/bio/util/restriction_enzyme/string_formatting.rb
+- lib/bio/util/restriction_enzyme.rb
+- lib/bio/util/sirna.rb
+- lib/bio.rb
 - sample/any2fasta.rb
 - sample/biofetch.rb
 - sample/color_scheme_na.rb
 - sample/dbget
+- sample/enzymes.rb
 - sample/fasta2tab.rb
 - sample/fsplit.rb
 - sample/gb2fasta.rb
@@ -289,102 +302,148 @@ files:
 - sample/tfastx2tab.rb
 - sample/vs-genes.rb
 - test/data
-- 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/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/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/prosite/prosite.dat
+- test/data/refseq
 - test/data/refseq/nm_126355.entret
+- test/data/soft
+- 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/io/test_ensembl.rb
 - test/functional/bio/io/test_soapwsdl.rb
+- test/runner.rb
+- test/unit
 - test/unit/bio
 - test/unit/bio/appl
-- 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
-- test/unit/bio/test_db.rb
-- 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/bl2seq/test_report.rb
 - test/unit/bio/appl/blast
+- 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/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/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/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
+- 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_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_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/embl/test_common.rb
-- test/unit/bio/db/embl/test_embl.rb
-- 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/db/test_soft.rb
+- test/unit/bio/io
 - 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/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
 - 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
+- test/unit/bio/test_db.rb
+- test/unit/bio/test_feature.rb
+- test/unit/bio/test_location.rb
+- test/unit/bio/test_map.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/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
+- test/unit/bio/util/restriction_enzyme/test_double_stranded.rb
+- test/unit/bio/util/restriction_enzyme/test_single_strand.rb
+- test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb
+- test/unit/bio/util/restriction_enzyme/test_string_formatting.rb
 - test/unit/bio/util/test_color_scheme.rb
 - 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: []