bio-restriction_enzyme 1.0.0

data/test/bio-restriction_enzyme/test_cut_symbol.rb

@@ -0,0 +1,27 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/cut_symbol'
+
+class TestBioRestrictionEnzymeCutSymbol < Test::Unit::TestCase
+
+  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

data/test/bio-restriction_enzyme/test_double_stranded.rb

@@ -0,0 +1,98 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/double_stranded'
+require 'bio/sequence'
+
+class TestBioRestrictionEnzymeDoubleStranded < Test::Unit::TestCase
+
+  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

data/test/bio-restriction_enzyme/test_single_strand.rb

@@ -0,0 +1,131 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/single_strand'
+
+class TestBioRestrictionEnzymeSingleStrand < Test::Unit::TestCase
+
+  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) }
+
+  # NOTE t| 2009-09-19 commented out for library efficiency
+  # re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
+    # 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

data/test/bio-restriction_enzyme/test_single_strand_complement.rb

@@ -0,0 +1,131 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/single_strand_complement'
+
+class TestBioRestrictionEnzymeSingleStrandComplement < Test::Unit::TestCase
+
+  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) }
+
+  # NOTE t| 2009-09-19 commented out for library efficiency
+  # re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
+    # 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

data/test/bio-restriction_enzyme/test_string_formatting.rb

@@ -0,0 +1,43 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/string_formatting'
+
+class TestBioRestrictionEnzymeStringFormatting < Test::Unit::TestCase
+
+  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

data/test/helper.rb

@@ -0,0 +1,17 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-restriction_enzyme'
+
+class Test::Unit::TestCase
+end