bio 1.0.0 → 1.1.0

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

@@ -0,0 +1,246 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_analysis.rb - Unit test for Bio::RestrictionEnzyme::Analysis
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# 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 $
+#
+
+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/analysis'
+require 'bio/sequence'
+
+module Bio #:nodoc:
+
+class TestAnalysis < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @enz = Bio::RestrictionEnzyme
+    @t = Bio::RestrictionEnzyme::Analysis
+    
+    @obj_1 = @t.cut('cagagag', 'ag^ag')
+    @obj_2 = @t.cut('agagag', 'ag^ag')
+    @obj_3 = @t.cut('cagagagt', 'ag^ag')
+
+    e1 = @enz.new('atgcatgc', [3,3])
+    @obj_4 = @t.cut('atgcatgcatgc', e1)
+
+    @obj_4bd = @t.cut('atgcatgcatgccc', e1, 'cc^c') # mix of always cut and sometimes cut
+
+    e2 = @enz.new('atgcatgc', [3,5])
+    @obj_5 = @t.cut('atgcatgcatgc', e2)
+
+    e3 = @enz.new('anna', [1,1], [3,3])
+    e4 = @enz.new('gg', [1,1])
+    @obj_6 = @t.cut('agga', e3, e4)
+
+    @obj_7 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII')
+    @obj_7b = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaaccc', 'EcoRII', 'HincII', 'cc^c')
+    @obj_7bd = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaaccc', 'EcoRII', 'HincII', 'cc^c')
+    
+    @obj_8 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', 'HincII')
+
+    @obj_9 = @t.cut('aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa', 'EcoRII')
+    @obj_9 = @t.cut('aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa', 'EcoRII', 'HincII')
+
+    @obj_1d = @t.cut_without_permutations('cagagag', 'ag^ag')
+    @obj_2d = @t.cut_without_permutations('agagag', 'ag^ag')
+    @obj_3d = @t.cut_without_permutations('cagagagt', 'ag^ag')
+
+    e1 = @enz.new('atgcatgc', [3,3])
+    @obj_4d = @t.cut_without_permutations('atgcatgcatgc', e1)
+
+    e2 = @enz.new('atgcatgc', [3,5])
+    @obj_5d = @t.cut_without_permutations('atgcatgcatgc', e2)
+
+    e3 = @enz.new('anna', [1,1], [3,3])
+    e4 = @enz.new('gg', [1,1])
+    @obj_6d = @t.cut_without_permutations('agga', e3, e4)
+
+    @obj_7d = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII')
+    @obj_8d = @t.cut_without_permutations('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', 'HincII')
+
+    @obj_98 = @t.cut('', 'EcoRII', 'HincII')
+    @obj_99 = @t.cut_without_permutations('', 'EcoRII', 'HincII')
+
+    @obj_vr1 = @t.cut('gaccaggaaaaagaccaggaaagcctggaaaagttaac', 'EcoRII', {:view_ranges => true})
+    @obj_vr2 = @t.cut('cagagag', {:view_ranges => true}, 'ag^ag')
+  end
+
+  def test_cut
+    assert_equal(["ag", "cag"], @obj_1.primary)
+    assert_equal(["gtc", "tc"], @obj_1.complement)
+    assert_equal(2, @obj_1.size)
+    assert_equal(Bio::RestrictionEnzyme::Fragments, @obj_1.class)
+    assert_equal(Bio::RestrictionEnzyme::Fragment, @obj_1[0].class)
+
+    assert_equal(["ag"], @obj_2.primary)
+    assert_equal(["ag", "agt", "cag"], @obj_3.primary)
+    assert_equal(["atg", "atgcatg", "catg", "catgc"], @obj_4.primary)
+
+=begin
+    A T G^C A T G C
+    
+    A T G C A T G C A T G C
+    
+    A T G^C A T G^C A T G C
+    
+    A T G C A T G^C A T G C
+=end
+    
+    assert_equal(["atg", "atgcatg", "catgc", "catgcatgc"], @obj_5.primary)
+    assert_equal(["a", "ag", "g", "ga"], @obj_6.primary)
+    assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_7.primary)
+    assert_equal(["aac", "ccaggaaaaaga", "ccaggaaag", "cctggaaaagtt", "ga"], @obj_8.primary)
+    
+=begin
+    e1 = @enz.new('atgcatgc', [3,3])
+    @obj_4bd = @t.cut('atgcatgcatgccc', e1, 'cc^c') # mix of sometimes cut and always cut
+
+    [#<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
+      primary="atgcatg",
+      complement="tacgtac">,
+     #<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
+      primary="catgcc",
+      complement="gtacg ">,
+     #<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
+      primary=" c",
+      complement="gg">,
+     #<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
+      primary="atg",
+      complement="tac">,
+     #<struct Bio::RestrictionEnzyme::Analysis::UniqueFragment
+      primary="catg",
+      complement="gtac">]
+=end
+    assert_equal(["atg", "atgcatg", "c", "catg", "catgcc"], @obj_4bd.primary)    
+    assert_equal(["gg", "gtac", "gtacg", "tac", "tacgtac"], @obj_4bd.complement)
+  end
+
+  def test_cut_without_permutations
+    assert_equal(["ag", "cag"], @obj_1d.primary)
+    assert_equal(["ag"], @obj_2d.primary)
+    assert_equal(["ag", "agt", "cag"], @obj_3d.primary)
+    assert_equal(["atg", "catg", "catgc"], @obj_4d.primary)
+    assert_equal(["atg", "catg", "catgc"], @obj_5d.primary)
+    assert_equal(["a", "g"], @obj_6d.primary)
+    assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_7d.primary)
+    assert_equal(["aac", "ccaggaaaaaga", "ccaggaaag", "cctggaaaagtt", "ga"], @obj_8d.primary)
+  end
+
+  def test_cut_from_bio_sequence_na
+    assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzyme('ag^ag').primary )
+    assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzymes('ag^ag').primary )
+    assert_equal(["ag", "cag"], Bio::Sequence::NA.new('cagagag').cut_with_enzymes('ag^ag', 'EcoRII').primary )
+
+    # Note how EcoRII needs extra padding on the beginning and ending of the
+    # sequence 'ccagg' to make the match since the cut must occur between 
+    # two nucleotides and can not occur on the very end of the sequence.
+    #   
+    #   EcoRII:
+    #     :blunt: "0"
+    #     :c2: "5"
+    #     :c4: "0"
+    #     :c1: "-1"
+    #     :pattern: CCWGG
+    #     :len: "5"
+    #     :name: EcoRII
+    #     :c3: "0"
+    #     :ncuts: "2"
+    #   
+    #        -1 1 2 3 4 5
+    #   5' - n^c c w g g n - 3'
+    #   3' - n g g w c c^n - 5'
+    #   
+    #   (w == [at])
+
+    assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary )
+    assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary )
+    assert_equal(:no_cuts_found, Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII') )
+
+    assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary )
+    assert_equal(["ag", "agccaggt", "cag"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag').primary )
+    assert_equal(["cagagag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').primary )
+    assert_equal(["a", "gtctctcggtcc"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('EcoRII').complement )  
+  end
+  
+  def test_view_ranges
+    assert_equal(["ccaggaaaaaga", "ccaggaaag", "cctggaaaagttaac", "ga"], @obj_vr1.primary)
+    assert_equal(["ctggtcc", "tttcggacc", "ttttcaattg", "tttttctggtcc"], @obj_vr1.complement)
+
+    a0 = @obj_vr1[0]
+    assert_equal('ga     ', a0.primary)
+    assert_equal('ctggtcc', a0.complement)
+    assert_equal(0, a0.p_left)
+    assert_equal(1, a0.p_right)
+    assert_equal(0, a0.c_left)
+    assert_equal(6, a0.c_right)
+    
+    a1 = @obj_vr1[1]
+    assert_equal('ccaggaaaaaga     ', a1.primary)
+    assert_equal('     tttttctggtcc', a1.complement)
+    assert_equal(2,  a1.p_left)
+    assert_equal(13, a1.p_right)
+    assert_equal(7,  a1.c_left)
+    assert_equal(18, a1.c_right)     
+
+    a2 = @obj_vr1[2]
+    assert_equal('ccaggaaag     ', a2.primary)
+    assert_equal('     tttcggacc', a2.complement)
+    assert_equal(14, a2.p_left)
+    assert_equal(22, a2.p_right)
+    assert_equal(19, a2.c_left)
+    assert_equal(27, a2.c_right)
+
+    a3 = @obj_vr1[3]
+    assert_equal('cctggaaaagttaac', a3.primary)
+    assert_equal('     ttttcaattg', a3.complement)
+    assert_equal(23, a3.p_left)
+    assert_equal(37, a3.p_right)
+    assert_equal(28, a3.c_left)
+    assert_equal(37, a3.c_right)
+    
+    a4 = @obj_vr1[4]
+    assert_equal(nil, a4)
+    
+    assert_equal(["ag", "ag", "cag"], @obj_vr2.primary)
+    assert_equal(["gtc", "tc", "tc"], @obj_vr2.complement)
+
+    a0 = @obj_vr2[0]
+    assert_equal('cag', a0.primary)
+    assert_equal('gtc', a0.complement)
+    assert_equal(0, a0.p_left)
+    assert_equal(2, a0.p_right)
+    assert_equal(0, a0.c_left)
+    assert_equal(2, a0.c_right)
+    
+    a1 = @obj_vr2[1]
+    assert_equal('ag', a1.primary)
+    assert_equal('tc', a1.complement)
+    assert_equal(3, a1.p_left)
+    assert_equal(4, a1.p_right)
+    assert_equal(3, a1.c_left)
+    assert_equal(4, a1.c_right)
+    
+    a2 = @obj_vr2[2]
+    assert_equal('ag', a2.primary)
+    assert_equal('tc', a2.complement)
+    assert_equal(5, a2.p_left)
+    assert_equal(6, a2.p_right)
+    assert_equal(5, a2.c_left)
+    assert_equal(6, a2.c_right)
+    
+    a3 = @obj_vr2[3]
+    assert_equal(nil, a3)
+  end
+  
+
+end
+
+end

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

@@ -0,0 +1,44 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb - Unit test for Bio::RestrictionEnzyme::CutSymbol
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# 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 $
+#
+
+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/cut_symbol'
+
+module Bio #:nodoc:
+
+class TestStringFormatting < Test::Unit::TestCase #:nodoc:
+
+  include Bio::RestrictionEnzyme::CutSymbol
+
+  def setup
+  end
+  
+  def test_methods
+    assert_equal('^', cut_symbol)
+    assert_equal('|', set_cut_symbol('|'))
+    assert_equal('|', cut_symbol)
+    assert_equal('\\|', escaped_cut_symbol)
+    assert_equal(/\|/, re_cut_symbol)
+    assert_equal('^', set_cut_symbol('^'))
+    
+    assert_equal(3, "abc^de" =~ re_cut_symbol)
+    assert_equal(nil, "abc^de" =~ re_cut_symbol_adjacent)
+    assert_equal(3, "abc^^de" =~ re_cut_symbol_adjacent)
+    assert_equal(4, "a^bc^^de" =~ re_cut_symbol_adjacent)
+    assert_equal(nil, "a^bc^de" =~ re_cut_symbol_adjacent)
+  end
+  
+end
+
+end

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

@@ -0,0 +1,115 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_double_stranded.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# 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 $
+#
+
+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/double_stranded'
+require 'bio/sequence'
+
+module Bio #:nodoc:
+
+class TestDoubleStranded < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded
+    @cl = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
+    @s = String
+
+
+    @obj_1 = @t.new(@s.new('gata'), [1,2])
+    @obj_2 = @t.new('gata', [1,2])
+    @obj_3 = @t.new('garraxt', [1,2])
+    @obj_4 = @t.new('nnnnnnngarraxtnn', [1,2])
+
+    @obj_5 = @t.new('garraxt', @cl.new(3,2), @cl.new(-2,-1), @cl.new(9,11))
+    @obj_6 = @t.new('garraxt', @cl.new(3,2))
+    @obj_7 = @t.new('garraxt', @cl.new(3,2), @cl.new(9,11))
+
+#    @obj_8 = @t.new('garraxt', 3..2, 9..11)
+    @obj_9 = @t.new('garraxt', [3,2], [9,11])
+
+    @obj_10 = @t.new('garraxt', [3,2], [9,11])
+
+    @obj_11 = @t.new('n^ngar^raxtnn^n')
+    @obj_12 = @t.new('nnnn^ngar^raxtnn^nnnn')
+
+    @obj_13 = @t.new(Bio::RestrictionEnzyme.rebase['EcoRII'])
+    @obj_14 = @t.new('EcoRII')
+    @obj_15 = @t.new('ecorii')
+  end
+
+  def test_primary
+    assert_equal('nngarraxtnnn', @obj_5.primary)
+  end
+
+  def test_primary_with_cut_symbols
+    assert_equal('n^ngar^raxtnn^n', @obj_5.primary.with_cut_symbols)
+    assert_equal('gar^raxt', @obj_6.primary.with_cut_symbols)
+    assert_equal('gar^raxtnn^n', @obj_7.primary.with_cut_symbols)
+
+#    assert_equal('gar^raxtnn^n', @obj_8.primary.with_cut_symbols)
+    assert_equal('gar^raxtnn^n', @obj_9.primary.with_cut_symbols)
+
+    assert_equal('gar^raxtnn^n', @obj_10.primary.with_cut_symbols)
+    
+    assert_equal('n^ngar^raxtnn^n', @obj_11.primary.with_cut_symbols)
+    assert_equal('n^ngar^raxtnn^n', @obj_12.primary.with_cut_symbols)
+
+    assert_equal('n^ccwgg', @obj_13.primary.with_cut_symbols)
+    assert_equal('n^ccwgg', @obj_14.primary.with_cut_symbols)
+    assert_equal('n^ccwgg', @obj_15.primary.with_cut_symbols)
+  end
+
+  def test_complement_with_cut_symbols
+    assert_equal('n^ct^yytxannnn^n', @obj_5.complement.with_cut_symbols)
+    assert_equal('ct^yytxa', @obj_6.complement.with_cut_symbols)
+    assert_equal('ct^yytxannnn^n', @obj_7.complement.with_cut_symbols)
+
+#    assert_equal('ct^yytxannnn^n', @obj_8.complement.with_cut_symbols)
+    assert_equal('ct^yytxannnn^n', @obj_9.complement.with_cut_symbols)
+
+    assert_equal('ct^yytxannnn^n', @obj_10.complement.with_cut_symbols)
+
+    assert_equal('n^nnctyy^txan^n', @obj_11.complement.with_cut_symbols)
+    assert_equal('n^nnctyy^txan^n', @obj_12.complement.with_cut_symbols)
+
+    assert_equal('ggwcc^n', @obj_13.complement.with_cut_symbols)
+    assert_equal('ggwcc^n', @obj_14.complement.with_cut_symbols)
+    assert_equal('ggwcc^n', @obj_15.complement.with_cut_symbols)
+  end
+
+  def test_complement
+    assert_equal('nctyytxannnnn', @obj_5.complement)
+  end
+
+  def test_cut_locations
+    assert_equal([[4, 3], [0, 1], [10, 12]], @obj_5.cut_locations)
+  end
+
+  def test_cut_locations_in_enzyme_notation
+    assert_equal([[3, 2], [-2, -1], [9, 11]], @obj_5.cut_locations_in_enzyme_notation)
+  end
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new('garraxt', [3,2,9,11]) }
+    assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['ecorii'] )}
+    assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['EzzRII']) }
+  end
+
+  # NOTE
+  def test_to_re
+  end
+
+end
+
+end

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

@@ -0,0 +1,147 @@
+#
+# test/unit/bio/util/restriction_enzyme/test_single_strand.rb - Unit test for Bio::RestrictionEnzyme::SingleStrand
+#
+# 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.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'
+
+module Bio #:nodoc:
+
+class TestSingleStrand < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::SingleStrand
+    @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([5,3], @obj_1.orientation)
+    assert_equal([5,3], @obj_2.orientation)
+    assert_equal([5,3], @obj_3.orientation)
+    assert_equal([5,3], @obj_4.orientation)
+  end
+
+  def test_creation_with_no_cuts
+    @obj_8 = @t.new('garraxt')
+    assert_equal([5,3], @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