bio-restriction_enzyme 1.0.0

data/test/bio-restriction_enzyme/analysis/test_cut_ranges.rb

@@ -0,0 +1,87 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..']*2, 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/range/sequence_range'
+require 'bio/util/restriction_enzyme/range/sequence_range/fragments'
+require 'bio/util/restriction_enzyme/range/cut_range'
+require 'bio/util/restriction_enzyme/range/horizontal_cut_range'
+require 'bio/util/restriction_enzyme/range/vertical_cut_range'
+require 'bio/util/restriction_enzyme/range/cut_ranges'
+
+class TestBioRestrictionEnzymeAnalysisCutRanges < Test::Unit::TestCase
+
+  def setup
+    @t = Bio::RestrictionEnzyme::Range::SequenceRange
+    @fs = Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
+    #a.add_cut_range(p_cut_left, p_cut_right, c_cut_left, c_cut_right )
+
+    @vcr = Bio::RestrictionEnzyme::Range::VerticalCutRange
+    @crs = Bio::RestrictionEnzyme::Range::CutRanges
+    @hcr = Bio::RestrictionEnzyme::Range::HorizontalCutRange
+
+    @obj_2 = @crs.new( [@vcr.new(0,2,nil,nil), @vcr.new(3,nil,4,nil)] )
+    @obj_3 = @crs.new( [@vcr.new(0,2,nil,nil), @vcr.new(3,nil,4,nil), @hcr.new(0), @hcr.new(5)] )
+    @obj_7 = @crs.new( [@vcr.new(nil,2,nil,nil), @hcr.new(0,2)] )
+    @obj_z = @crs.new( [@vcr.new(nil,2,nil,5), @hcr.new(1,6)] )
+  end
+
+  def test_obj_z
+    assert_equal(6, @obj_z.max)
+    assert_equal(1, @obj_z.min)
+
+    assert_equal(2, @obj_z.min_vertical)
+    assert_equal(5, @obj_z.max_vertical)
+
+    assert_equal(true, @obj_z.include?(6))
+    assert_equal(true, @obj_z.include?(4))
+    assert_equal(true, @obj_z.include?(2))
+    assert_equal(false, @obj_z.include?(-1))
+    assert_equal(false, @obj_z.include?(0))
+    assert_equal(false, @obj_z.include?(7))
+  end
+
+  def test_obj_7
+    assert_equal(2, @obj_7.max)
+    assert_equal(0, @obj_7.min)
+
+    assert_equal(2, @obj_7.min_vertical)
+    assert_equal(2, @obj_7.max_vertical)
+
+    assert_equal(true, @obj_7.include?(0))
+    assert_equal(true, @obj_7.include?(1))
+    assert_equal(true, @obj_7.include?(2))
+    assert_equal(false, @obj_7.include?(-1))
+    assert_equal(false, @obj_7.include?(3))
+  end
+
+  def test_obj_2
+    assert_equal(4, @obj_2.max)
+    assert_equal(0, @obj_2.min)
+
+    assert_equal(0, @obj_2.min_vertical)
+    assert_equal(4, @obj_2.max_vertical)
+
+    assert_equal(true, @obj_2.include?(0))
+    assert_equal(true, @obj_2.include?(1))
+    assert_equal(true, @obj_2.include?(3))
+    assert_equal(true, @obj_2.include?(4))
+    assert_equal(false, @obj_2.include?(-1))
+    assert_equal(false, @obj_2.include?(5))
+  end
+
+  def test_obj_3
+    assert_equal(5, @obj_3.max)
+    assert_equal(0, @obj_3.min)
+
+    assert_equal(0, @obj_3.min_vertical)
+    assert_equal(4, @obj_3.max_vertical)
+
+    assert_equal(true, @obj_3.include?(0))
+    assert_equal(true, @obj_3.include?(1))
+    assert_equal(true, @obj_3.include?(3))
+    assert_equal(true, @obj_3.include?(4))
+    assert_equal(true, @obj_3.include?(5))
+    assert_equal(false, @obj_3.include?(-1))
+    assert_equal(false, @obj_3.include?(6))
+  end
+
+end

data/test/bio-restriction_enzyme/analysis/test_sequence_range.rb

@@ -0,0 +1,223 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..']*2, 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/range/sequence_range'
+require 'bio/util/restriction_enzyme/range/sequence_range/fragments'
+require 'bio/util/restriction_enzyme/range/cut_range'
+require 'bio/util/restriction_enzyme/range/horizontal_cut_range'
+require 'bio/util/restriction_enzyme/range/vertical_cut_range'
+require 'bio/util/restriction_enzyme/range/cut_ranges'
+
+class TestBioRestrictionEnzymeAnalysisSequenceRange < Test::Unit::TestCase
+
+  def setup
+    @t = Bio::RestrictionEnzyme::Range::SequenceRange
+    @fs = Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
+    #a.add_cut_range(p_cut_left, p_cut_right, c_cut_left, c_cut_right )
+
+    @vcr = Bio::RestrictionEnzyme::Range::VerticalCutRange
+    @crs = Bio::RestrictionEnzyme::Range::CutRanges
+    @hcr = Bio::RestrictionEnzyme::Range::HorizontalCutRange
+
+    @obj_1 = @t.new(0,5)
+    @obj_1.add_cut_range(0,nil,nil,3)
+    @obj_1.add_cut_range(nil,2,nil,nil)
+
+    @obj_2 = @t.new(0,5)
+    @obj_2.add_cut_ranges( @crs.new( [@vcr.new(0,2,nil,nil), @vcr.new(3,nil,4,nil)] ))
+
+    @obj_3 = @t.new(0,5)
+    @obj_3.add_cut_ranges( @crs.new( [@vcr.new(0,2,nil,nil), @vcr.new(3,nil,4,nil)] ))
+    @obj_3.add_cut_ranges( @crs.new( [@hcr.new(0), @hcr.new(5)] ))
+
+    @obj_4 = @t.new(0,5)
+    @obj_4.add_cut_ranges( @crs.new( [@vcr.new(0,2,1,3)] ))
+
+    @obj_5 = @t.new(0,5)
+    @obj_5.add_cut_ranges( @crs.new( [@vcr.new(0,nil,nil,nil), @vcr.new(nil,4,3,nil), @hcr.new(1,2)] ))
+
+    @obj_6 = @t.new(0,5)
+    @obj_6.add_cut_ranges( @crs.new( [@vcr.new(nil,nil,0,nil), @hcr.new(1,2), @vcr.new(nil,4,3,nil)] ))
+
+    @obj_7 = @t.new(0,5)
+    @obj_7.add_cut_ranges( @crs.new( [@vcr.new(nil,2,nil,nil), @hcr.new(0,2)] ))
+
+    @obj_8 = @t.new(0,11)
+    @obj_8.add_cut_ranges( @crs.new( [@hcr.new(0,1), @vcr.new(nil,nil,nil,5), @hcr.new(7,8), @hcr.new(10), @vcr.new(nil,10,nil,nil)] ))
+
+    @obj_9 = @t.new(0,5)
+    @obj_9.add_cut_ranges( @crs.new( [@vcr.new(nil,3,nil,3)] ))
+
+    @obj_10 = @t.new(0,5)
+    @obj_10.add_cut_ranges( @crs.new( [@vcr.new(0,nil,nil,3), @vcr.new(nil,2,nil,2)] ))
+  end
+
+  def test_fragments
+    assert_equal(@fs, @obj_1.fragments.class)
+  end
+
+  # '0|1 2|3 4 5'
+  # ' +---+-+   '
+  # '0 1 2 3|4 5'
+  def test_fragments_for_display_1
+    x = @obj_1
+    assert_equal(3, x.fragments.for_display.size)
+
+    assert_equal('0   ', x.fragments.for_display[0].primary)
+    assert_equal('0123', x.fragments.for_display[0].complement)
+
+    assert_equal('12', x.fragments.for_display[1].primary)
+    assert_equal('  ', x.fragments.for_display[1].complement)
+
+    assert_equal('345', x.fragments.for_display[2].primary)
+    assert_equal(' 45', x.fragments.for_display[2].complement)
+  end
+
+  # '0|1 2|3|4 5'
+  # ' +---+ +-+ '
+  # '0 1 2 3 4|5'
+  def test_fragments_for_display_2
+    x = @obj_2
+    assert_equal(3, x.fragments.for_display.size)
+
+    assert_equal('0  3 ', x.fragments.for_display[0].primary)
+    assert_equal('01234', x.fragments.for_display[0].complement)
+
+    assert_equal('12', x.fragments.for_display[1].primary)
+    assert_equal('  ', x.fragments.for_display[1].complement)
+
+    assert_equal('45', x.fragments.for_display[2].primary)
+    assert_equal(' 5', x.fragments.for_display[2].complement)
+  end
+
+  # '0|1 2|3|4 5'
+  # '-+---+ +-+-'
+  # '0 1 2 3 4|5'
+  def test_fragments_for_display_3
+    x = @obj_3
+    assert_equal(5, x.fragments.for_display.size)
+
+    assert_equal('0', x.fragments.for_display[0].primary)
+    assert_equal(' ', x.fragments.for_display[0].complement)
+
+    assert_equal('   3 ', x.fragments.for_display[1].primary)
+    assert_equal('01234', x.fragments.for_display[1].complement)
+
+    assert_equal('12', x.fragments.for_display[2].primary)
+    assert_equal('  ', x.fragments.for_display[2].complement)
+
+    assert_equal('45', x.fragments.for_display[3].primary)
+    assert_equal('  ', x.fragments.for_display[3].complement)
+
+    assert_equal(' ', x.fragments.for_display[4].primary)
+    assert_equal('5', x.fragments.for_display[4].complement)
+  end
+
+  # '0|1 2|3 4 5'
+  # ' +-+-+-+   '
+  # '0 1|2 3|4 5'
+  def test_fragments_for_display_4
+    x = @obj_4
+    assert_equal(4, x.fragments.for_display.size)
+
+    assert_equal('0 ', x.fragments.for_display[0].primary)
+    assert_equal('01', x.fragments.for_display[0].complement)
+
+    assert_equal('12', x.fragments.for_display[1].primary)
+    assert_equal('  ', x.fragments.for_display[1].complement)
+
+    assert_equal('  ', x.fragments.for_display[2].primary)
+    assert_equal('23', x.fragments.for_display[2].complement)
+
+    assert_equal('345', x.fragments.for_display[3].primary)
+    assert_equal(' 45', x.fragments.for_display[3].complement)
+  end
+
+  # '0 1 2 3 4|5'
+  # '       +-+ '
+  # '0 1 2 3|4 5'
+  def test_fragments_for_display_5
+    x = @obj_5
+    assert_equal(2, x.fragments.for_display.size)
+
+    assert_equal('01234', x.fragments.for_display[0].primary)
+    assert_equal('0123 ', x.fragments.for_display[0].complement)
+
+    assert_equal(' 5', x.fragments.for_display[1].primary)
+    assert_equal('45', x.fragments.for_display[1].complement)
+  end
+
+  # '0 1 2 3 4|5'
+  # '       +-+ '
+  # '0 1 2 3|4 5'
+  def test_fragments_for_display_6
+    x = @obj_6
+    assert_equal(2, x.fragments.for_display.size)
+
+    assert_equal('01234', x.fragments.for_display[0].primary)
+    assert_equal('0123 ', x.fragments.for_display[0].complement)
+
+    assert_equal(' 5', x.fragments.for_display[1].primary)
+    assert_equal('45', x.fragments.for_display[1].complement)
+  end
+
+  # '0 1 2|3 4 5'
+  # '-----+     '
+  # '0 1 2 3 4 5'
+  def test_fragments_for_display_7
+    x = @obj_7
+    assert_equal(2, x.fragments.for_display.size)
+
+    assert_equal('012', x.fragments.for_display[0].primary)
+    assert_equal('   ', x.fragments.for_display[0].complement)
+
+    assert_equal('   345', x.fragments.for_display[1].primary)
+    assert_equal('012345', x.fragments.for_display[1].complement)
+  end
+
+
+  # '0 1 2 3 4 5 6 7 8 9 0 1'
+  # '                       '
+  # '0 1 2 3 4 5 6 7 8 9 0 1'
+  def test_fragments_for_display_8
+    x = @obj_8
+    assert_equal(1, x.fragments.for_display.size)
+
+    assert_equal('012345678901', x.fragments.for_display[0].primary)
+    assert_equal('012345678901', x.fragments.for_display[0].complement)
+  end
+
+  # '0 1 2 3|4 5'
+  # '       +   '
+  # '0 1 2 3|4 5'
+  def test_fragments_for_display_9
+    x = @obj_9
+    assert_equal(2, x.fragments.for_display.size)
+
+    assert_equal('0123', x.fragments.for_display[0].primary)
+    assert_equal('0123', x.fragments.for_display[0].complement)
+
+    assert_equal('45', x.fragments.for_display[1].primary)
+    assert_equal('45', x.fragments.for_display[1].complement)
+  end
+
+  # '0|1 2|3 4 5'
+  # ' +---+-+   '
+  # '0 1 2|3|4 5'
+  def test_fragments_for_display_10
+    x = @obj_10
+    assert_equal(4, x.fragments.for_display.size)
+
+    assert_equal('0  ', x.fragments.for_display[0].primary)
+    assert_equal('012', x.fragments.for_display[0].complement)
+
+    assert_equal('12', x.fragments.for_display[1].primary)
+    assert_equal('  ', x.fragments.for_display[1].complement)
+
+    assert_equal('345', x.fragments.for_display[2].primary)
+    assert_equal(' 45', x.fragments.for_display[2].complement)
+
+    assert_equal(' ', x.fragments.for_display[3].primary)
+    assert_equal('3', x.fragments.for_display[3].complement)
+  end
+
+end

data/test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb

@@ -0,0 +1,84 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..']*2, 'helper.rb')).cleanpath.to_s
+
+require 'bio/sequence'
+require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'
+require 'bio/util/restriction_enzyme/double_stranded'
+
+class TestBioRestrictionEnzymeDoubleStrandedAlignedStrands < Test::Unit::TestCase
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
+    @s = Bio::Sequence::NA
+
+    @ds = Bio::RestrictionEnzyme::DoubleStranded
+
+    @s_1 = @s.new('gattaca')
+    @s_2 = @s_1.forward_complement
+
+    @s_3 = @s.new('tttttttnnn')
+    @s_4 = @s.new('nnnaaaaaaa')
+
+    @ds_1 = @ds.new('nnnn^ngattacann^nn^n')
+
+    @obj_1 = @t.align(@s_1, @s_2)
+    @obj_2 = @t.align(@s_1, @s_3)
+    @obj_3 = @t.align(@s_1, @s_4)
+    @obj_4 = @t.align(@s_3, @s_4)
+
+    @obj_5 = @t.align(@ds_1.primary, @ds_1.complement)
+
+    @obj_8 = @t.align_with_cuts(@ds_1.primary, @ds_1.complement, @ds_1.primary.cut_locations, @ds_1.complement.cut_locations)
+
+    @obj_6 = @t.align_with_cuts(@s_1, @s_2, [1,2], [3,4])
+    @obj_7 = @t.align_with_cuts(@s_3, @s_4, [1,2], [3,4])
+
+  end
+
+  def test_ds
+    assert_equal('nngattacannnnn', @ds_1.primary)
+    assert_equal('nnnnnctaatgtnn', @ds_1.complement)
+    assert_equal(    'n^ngattacann^nn^n', @ds_1.primary.with_cut_symbols)
+    assert_equal('n^nn^nnctaatgtn^n'    , @ds_1.complement.with_cut_symbols)
+
+    assert_equal([0, 10, 12], @ds_1.primary.cut_locations)
+    assert_equal([0, 2, 12], @ds_1.complement.cut_locations)
+  end
+
+  def test_align
+    assert_equal('gattaca', @obj_1.primary)
+    assert_equal('ctaatgt', @obj_1.complement)
+
+    assert_equal('gattacannn', @obj_2.primary)
+    assert_equal('tttttttnnn', @obj_2.complement)
+
+    assert_equal('nnngattaca', @obj_3.primary)
+    assert_equal('nnnaaaaaaa', @obj_3.complement)
+
+    assert_equal('nnntttttttnnn', @obj_4.primary)
+    assert_equal('nnnaaaaaaannn', @obj_4.complement)
+
+    assert_equal('nnnnngattacannnnn', @obj_5.primary)
+    assert_equal('nnnnnctaatgtnnnnn', @obj_5.complement)
+  end
+
+  def test_align_with_cuts
+    assert_equal('g a^t^t a c a', @obj_6.primary)
+    assert_equal('c t a a^t^g t', @obj_6.complement)
+
+    # Looks incorrect at first, but this is deliberate.
+    # The correct cuts need to be supplied by the user.
+    assert_equal('n n n t t^t^t t t t n n n', @obj_7.primary)
+    assert_equal('n n n a^a^a a a a a n n n', @obj_7.complement)
+
+    assert_equal('n n n n^n g a t t a c a n n^n n^n', @obj_8.primary)
+    assert_equal('n^n n^n n c t a a t g t n^n n n n', @obj_8.complement)
+  end
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new('arg', 'agg') }
+    assert_raise(ArgumentError) { @t.new(@s.new('arg'), 'agg') }
+    assert_raise(ArgumentError) { @t.new('arg', @s.new('agg')) }
+    assert_raise(ArgumentError) { @t.new(@s.new('argg'), @s.new('agg')) }
+  end
+
+end

data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb

@@ -0,0 +1,58 @@
+load Pathname.new(File.join(File.dirname(__FILE__), ['..']*2, 'helper.rb')).cleanpath.to_s
+
+require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
+
+class TestBioRestrictionEnzymeDoubleStrandedCutLocationPair < Test::Unit::TestCase
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
+
+    @obj_1 = @t.new([3,5])
+    @obj_2 = @t.new(3, 5)
+    @obj_3 = @t.new((3..5))
+    @obj_4 = @t.new(0..5)
+    @obj_5 = @t.new(3)
+    @obj_6 = @t.new(nil,3)
+    @obj_7 = @t.new(3,nil)
+  end
+
+  def test_contents
+    assert_equal([3,5], @obj_1)
+    assert_equal([3,5], @obj_2)
+    assert_equal([3,5], @obj_3)
+    assert_equal([0,5], @obj_4)
+    assert_equal([3,nil], @obj_5)
+    assert_equal([nil,3], @obj_6)
+    assert_equal([3,nil], @obj_7)
+  end
+
+  def test_primary
+    assert_equal(3, @obj_1.primary)
+    assert_equal(3, @obj_2.primary)
+    assert_equal(3, @obj_3.primary)
+    assert_equal(0, @obj_4.primary)
+    assert_equal(3, @obj_5.primary)
+    assert_equal(nil, @obj_6.primary)
+    assert_equal(3, @obj_7.primary)
+  end
+
+  def test_complement
+    assert_equal(5, @obj_1.complement)
+    assert_equal(5, @obj_2.complement)
+    assert_equal(5, @obj_3.complement)
+    assert_equal(5, @obj_4.complement)
+    assert_equal(nil, @obj_5.complement)
+    assert_equal(3, @obj_6.complement)
+    assert_equal(nil, @obj_7.complement)
+  end
+
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new([3,5,6]) }
+    assert_raise(ArgumentError) { @t.new(3,-1) }
+    assert_raise(ArgumentError) { @t.new(-3,1) }
+    assert_raise(ArgumentError) { @t.new(nil,nil) }
+    assert_raise(ArgumentError) { @t.new('3',5) }
+  end
+
+end