bio-restriction_enzyme 1.0.0
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- data/.document +5 -0
- data/COPYING.txt +121 -0
- data/Gemfile +10 -0
- data/LICENSE.txt +7 -0
- data/README.rdoc +22 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/bio-restriction_enzyme.gemspec +99 -0
- data/lib/bio-restriction_enzyme.rb +1 -0
- data/lib/bio/util/restriction_enzyme.rb +218 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +241 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +209 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +99 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +313 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +127 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +95 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +30 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +68 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +99 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +16 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +39 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +59 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +249 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +236 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +43 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +33 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +69 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +193 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +127 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +15 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +103 -0
- data/test/bio-restriction_enzyme/analysis/test_calculated_cuts.rb +281 -0
- data/test/bio-restriction_enzyme/analysis/test_cut_ranges.rb +87 -0
- data/test/bio-restriction_enzyme/analysis/test_sequence_range.rb +223 -0
- data/test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb +84 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb +58 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +56 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_locations.rb +35 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +87 -0
- data/test/bio-restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +66 -0
- data/test/bio-restriction_enzyme/test_analysis.rb +228 -0
- data/test/bio-restriction_enzyme/test_cut_symbol.rb +27 -0
- data/test/bio-restriction_enzyme/test_double_stranded.rb +98 -0
- data/test/bio-restriction_enzyme/test_single_strand.rb +131 -0
- data/test/bio-restriction_enzyme/test_single_strand_complement.rb +131 -0
- data/test/bio-restriction_enzyme/test_string_formatting.rb +43 -0
- data/test/helper.rb +17 -0
- data/test/test_bio-restriction_enzyme.rb +21 -0
- metadata +153 -0
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
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require 'bio/util/restriction_enzyme/cut_symbol'
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class TestBioRestrictionEnzymeCutSymbol < Test::Unit::TestCase
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include Bio::RestrictionEnzyme::CutSymbol
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def setup
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end
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def test_methods
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assert_equal('^', cut_symbol)
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assert_equal('|', set_cut_symbol('|'))
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assert_equal('|', cut_symbol)
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assert_equal('\\|', escaped_cut_symbol)
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assert_equal(/\|/, re_cut_symbol)
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assert_equal('^', set_cut_symbol('^'))
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assert_equal(3, "abc^de" =~ re_cut_symbol)
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assert_equal(nil, "abc^de" =~ re_cut_symbol_adjacent)
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assert_equal(3, "abc^^de" =~ re_cut_symbol_adjacent)
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assert_equal(4, "a^bc^^de" =~ re_cut_symbol_adjacent)
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assert_equal(nil, "a^bc^de" =~ re_cut_symbol_adjacent)
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end
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end
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
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require 'bio/util/restriction_enzyme/double_stranded'
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require 'bio/sequence'
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class TestBioRestrictionEnzymeDoubleStranded < Test::Unit::TestCase
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def setup
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@t = Bio::RestrictionEnzyme::DoubleStranded
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@cl = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
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@s = String
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@obj_1 = @t.new(@s.new('gata'), [1,2])
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@obj_2 = @t.new('gata', [1,2])
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@obj_3 = @t.new('garraxt', [1,2])
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@obj_4 = @t.new('nnnnnnngarraxtnn', [1,2])
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@obj_5 = @t.new('garraxt', @cl.new(3,2), @cl.new(-2,-1), @cl.new(9,11))
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@obj_6 = @t.new('garraxt', @cl.new(3,2))
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@obj_7 = @t.new('garraxt', @cl.new(3,2), @cl.new(9,11))
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# @obj_8 = @t.new('garraxt', 3..2, 9..11)
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@obj_9 = @t.new('garraxt', [3,2], [9,11])
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@obj_10 = @t.new('garraxt', [3,2], [9,11])
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@obj_11 = @t.new('n^ngar^raxtnn^n')
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@obj_12 = @t.new('nnnn^ngar^raxtnn^nnnn')
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@obj_13 = @t.new(Bio::RestrictionEnzyme.rebase['EcoRII'])
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@obj_14 = @t.new('EcoRII')
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@obj_15 = @t.new('ecorii')
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end
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def test_primary
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assert_equal('nngarraxtnnn', @obj_5.primary)
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end
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def test_primary_with_cut_symbols
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assert_equal('n^ngar^raxtnn^n', @obj_5.primary.with_cut_symbols)
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assert_equal('gar^raxt', @obj_6.primary.with_cut_symbols)
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assert_equal('gar^raxtnn^n', @obj_7.primary.with_cut_symbols)
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# assert_equal('gar^raxtnn^n', @obj_8.primary.with_cut_symbols)
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assert_equal('gar^raxtnn^n', @obj_9.primary.with_cut_symbols)
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assert_equal('gar^raxtnn^n', @obj_10.primary.with_cut_symbols)
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assert_equal('n^ngar^raxtnn^n', @obj_11.primary.with_cut_symbols)
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assert_equal('n^ngar^raxtnn^n', @obj_12.primary.with_cut_symbols)
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assert_equal('n^ccwgg', @obj_13.primary.with_cut_symbols)
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assert_equal('n^ccwgg', @obj_14.primary.with_cut_symbols)
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assert_equal('n^ccwgg', @obj_15.primary.with_cut_symbols)
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end
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def test_complement_with_cut_symbols
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assert_equal('n^ct^yytxannnn^n', @obj_5.complement.with_cut_symbols)
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assert_equal('ct^yytxa', @obj_6.complement.with_cut_symbols)
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assert_equal('ct^yytxannnn^n', @obj_7.complement.with_cut_symbols)
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# assert_equal('ct^yytxannnn^n', @obj_8.complement.with_cut_symbols)
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assert_equal('ct^yytxannnn^n', @obj_9.complement.with_cut_symbols)
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assert_equal('ct^yytxannnn^n', @obj_10.complement.with_cut_symbols)
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assert_equal('n^nnctyy^txan^n', @obj_11.complement.with_cut_symbols)
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assert_equal('n^nnctyy^txan^n', @obj_12.complement.with_cut_symbols)
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assert_equal('ggwcc^n', @obj_13.complement.with_cut_symbols)
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assert_equal('ggwcc^n', @obj_14.complement.with_cut_symbols)
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assert_equal('ggwcc^n', @obj_15.complement.with_cut_symbols)
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end
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def test_complement
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assert_equal('nctyytxannnnn', @obj_5.complement)
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end
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def test_cut_locations
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assert_equal([[4, 3], [0, 1], [10, 12]], @obj_5.cut_locations)
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end
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def test_cut_locations_in_enzyme_notation
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assert_equal([[3, 2], [-2, -1], [9, 11]], @obj_5.cut_locations_in_enzyme_notation)
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end
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def test_argument_error
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assert_raise(ArgumentError) { @t.new('garraxt', [3,2,9,11]) }
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assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['ecorii'] )}
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assert_raise(ArgumentError) { @t.new(Bio::RestrictionEnzyme.rebase['EzzRII']) }
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end
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# NOTE
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def test_to_re
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end
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end
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
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require 'bio/util/restriction_enzyme/single_strand'
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class TestBioRestrictionEnzymeSingleStrand < Test::Unit::TestCase
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def setup
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@t = Bio::RestrictionEnzyme::SingleStrand
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@cl = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
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@s = Bio::Sequence::NA
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@obj_1 = @t.new(@s.new('gata'), @cl.new(-2,1,3))
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@obj_2 = @t.new('gata', -2, 1, 3)
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@obj_3 = @t.new('garraxt', [-2, 1, 7])
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@obj_4 = @t.new('nnnnnnngarraxtnn', [-2, 1, 7])
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@obj_5 = @t.new('ga^rr^axt')
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@obj_6 = @t.new('^ga^rr^axt')
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@obj_7 = @t.new('n^ngar^raxtnn^n')
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end
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def test_pattern_palindromic?
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assert_equal(true, @t.new('atgcat', 1).palindromic?)
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assert_equal(false, @t.new('atgcgta', 1).palindromic?)
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assert_equal(false, @obj_1.palindromic?)
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assert_equal(false, @obj_2.palindromic?)
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assert_equal(false, @obj_3.palindromic?)
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assert_equal(false, @obj_4.palindromic?)
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end
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def test_stripped
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assert_equal('gata', @obj_1.stripped)
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assert_equal('gata', @obj_2.stripped)
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assert_equal('garraxt', @obj_3.stripped)
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assert_equal('garraxt', @obj_4.stripped)
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end
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def test_pattern
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assert_equal('nngata', @obj_1.pattern)
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assert_equal('nngata', @obj_2.pattern)
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assert_equal('nngarraxtn', @obj_3.pattern)
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assert_equal('nngarraxtn', @obj_4.pattern)
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assert_equal('nngata', @obj_1)
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assert_equal('nngata', @obj_2)
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assert_equal('nngarraxtn', @obj_3)
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assert_equal('nngarraxtn', @obj_4)
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end
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def test_with_cut_symbols
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assert_equal('n^ng^at^a', @obj_1.with_cut_symbols)
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assert_equal('n^ng^at^a', @obj_2.with_cut_symbols)
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assert_equal('n^ng^arraxt^n', @obj_3.with_cut_symbols)
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assert_equal('n^ng^arraxt^n', @obj_4.with_cut_symbols)
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end
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def test_with_spaces
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assert_equal('n^n g^a t^a', @obj_1.with_spaces)
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assert_equal('n^n g^a t^a', @obj_2.with_spaces)
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assert_equal('n^n g^a r r a x t^n', @obj_3.with_spaces)
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assert_equal('n^n g^a r r a x t^n', @obj_4.with_spaces)
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end
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def test_cut_locations_in_enzyme_notation
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assert_equal([-2,1,3], @obj_1.cut_locations_in_enzyme_notation)
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assert_equal([-2,1,3], @obj_2.cut_locations_in_enzyme_notation)
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assert_equal([-2,1,7], @obj_3.cut_locations_in_enzyme_notation)
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assert_equal([-2,1,7], @obj_4.cut_locations_in_enzyme_notation)
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assert_equal([2,4], @obj_5.cut_locations_in_enzyme_notation)
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assert_equal([-1,2,4], @obj_6.cut_locations_in_enzyme_notation)
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assert_equal([-2,3,9], @obj_7.cut_locations_in_enzyme_notation)
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end
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def test_cut_locations
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assert_equal([0,2,4], @obj_1.cut_locations)
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assert_equal([0,2,4], @obj_2.cut_locations)
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assert_equal([0,2,8], @obj_3.cut_locations)
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assert_equal([0,2,8], @obj_4.cut_locations)
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assert_equal([1,3], @obj_5.cut_locations)
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assert_equal([0,2,4], @obj_6.cut_locations)
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assert_equal([0,4,10], @obj_7.cut_locations)
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end
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def test_orientation
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assert_equal([5,3], @obj_1.orientation)
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assert_equal([5,3], @obj_2.orientation)
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assert_equal([5,3], @obj_3.orientation)
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assert_equal([5,3], @obj_4.orientation)
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end
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def test_creation_with_no_cuts
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@obj_8 = @t.new('garraxt')
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assert_equal([5,3], @obj_8.orientation)
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assert_equal([], @obj_8.cut_locations)
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assert_equal([], @obj_8.cut_locations_in_enzyme_notation)
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assert_equal('garraxt', @obj_8.pattern)
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end
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# NOTE
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def test_to_re
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end
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def test_argument_error
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assert_raise(ArgumentError) { @t.new('a', [0,1,2]) }
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assert_raise(ArgumentError) { @t.new('a', 0,1,2,0) }
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assert_raise(ArgumentError) { @t.new('a', [nil,1,2]) }
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assert_raise(ArgumentError) { @t.new('a', nil,1,2,nil) }
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assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
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assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
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# NOTE t| 2009-09-19 commented out for library efficiency
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# re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
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# assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
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# assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
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# assert_raise(ArgumentError) { @t.new('gaat^^aca') }
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# assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
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#
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# assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
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# assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
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# assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
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# assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
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# assert_raise(ArgumentError) { @t.new(1,2,3) }
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# assert_raise(ArgumentError) { @t.new(1,2,'g') }
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end
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end
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
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require 'bio/util/restriction_enzyme/single_strand_complement'
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4
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+
|
5
|
+
class TestBioRestrictionEnzymeSingleStrandComplement < Test::Unit::TestCase
|
6
|
+
|
7
|
+
def setup
|
8
|
+
@t = Bio::RestrictionEnzyme::SingleStrandComplement
|
9
|
+
@cl = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
|
10
|
+
@s = Bio::Sequence::NA
|
11
|
+
|
12
|
+
@obj_1 = @t.new(@s.new('gata'), @cl.new(-2,1,3))
|
13
|
+
@obj_2 = @t.new('gata', -2, 1, 3)
|
14
|
+
@obj_3 = @t.new('garraxt', [-2, 1, 7])
|
15
|
+
@obj_4 = @t.new('nnnnnnngarraxtnn', [-2, 1, 7])
|
16
|
+
|
17
|
+
@obj_5 = @t.new('ga^rr^axt')
|
18
|
+
@obj_6 = @t.new('^ga^rr^axt')
|
19
|
+
@obj_7 = @t.new('n^ngar^raxtnn^n')
|
20
|
+
end
|
21
|
+
|
22
|
+
def test_pattern_palindromic?
|
23
|
+
assert_equal(true, @t.new('atgcat', 1).palindromic?)
|
24
|
+
assert_equal(false, @t.new('atgcgta', 1).palindromic?)
|
25
|
+
|
26
|
+
assert_equal(false, @obj_1.palindromic?)
|
27
|
+
assert_equal(false, @obj_2.palindromic?)
|
28
|
+
assert_equal(false, @obj_3.palindromic?)
|
29
|
+
assert_equal(false, @obj_4.palindromic?)
|
30
|
+
end
|
31
|
+
|
32
|
+
def test_stripped
|
33
|
+
assert_equal('gata', @obj_1.stripped)
|
34
|
+
assert_equal('gata', @obj_2.stripped)
|
35
|
+
assert_equal('garraxt', @obj_3.stripped)
|
36
|
+
assert_equal('garraxt', @obj_4.stripped)
|
37
|
+
end
|
38
|
+
|
39
|
+
def test_pattern
|
40
|
+
assert_equal('nngata', @obj_1.pattern)
|
41
|
+
assert_equal('nngata', @obj_2.pattern)
|
42
|
+
assert_equal('nngarraxtn', @obj_3.pattern)
|
43
|
+
assert_equal('nngarraxtn', @obj_4.pattern)
|
44
|
+
|
45
|
+
assert_equal('nngata', @obj_1)
|
46
|
+
assert_equal('nngata', @obj_2)
|
47
|
+
assert_equal('nngarraxtn', @obj_3)
|
48
|
+
assert_equal('nngarraxtn', @obj_4)
|
49
|
+
end
|
50
|
+
|
51
|
+
def test_with_cut_symbols
|
52
|
+
assert_equal('n^ng^at^a', @obj_1.with_cut_symbols)
|
53
|
+
assert_equal('n^ng^at^a', @obj_2.with_cut_symbols)
|
54
|
+
assert_equal('n^ng^arraxt^n', @obj_3.with_cut_symbols)
|
55
|
+
assert_equal('n^ng^arraxt^n', @obj_4.with_cut_symbols)
|
56
|
+
end
|
57
|
+
|
58
|
+
def test_with_spaces
|
59
|
+
assert_equal('n^n g^a t^a', @obj_1.with_spaces)
|
60
|
+
assert_equal('n^n g^a t^a', @obj_2.with_spaces)
|
61
|
+
assert_equal('n^n g^a r r a x t^n', @obj_3.with_spaces)
|
62
|
+
assert_equal('n^n g^a r r a x t^n', @obj_4.with_spaces)
|
63
|
+
end
|
64
|
+
|
65
|
+
def test_cut_locations_in_enzyme_notation
|
66
|
+
assert_equal([-2,1,3], @obj_1.cut_locations_in_enzyme_notation)
|
67
|
+
assert_equal([-2,1,3], @obj_2.cut_locations_in_enzyme_notation)
|
68
|
+
assert_equal([-2,1,7], @obj_3.cut_locations_in_enzyme_notation)
|
69
|
+
assert_equal([-2,1,7], @obj_4.cut_locations_in_enzyme_notation)
|
70
|
+
|
71
|
+
assert_equal([2,4], @obj_5.cut_locations_in_enzyme_notation)
|
72
|
+
assert_equal([-1,2,4], @obj_6.cut_locations_in_enzyme_notation)
|
73
|
+
assert_equal([-2,3,9], @obj_7.cut_locations_in_enzyme_notation)
|
74
|
+
end
|
75
|
+
|
76
|
+
def test_cut_locations
|
77
|
+
assert_equal([0,2,4], @obj_1.cut_locations)
|
78
|
+
assert_equal([0,2,4], @obj_2.cut_locations)
|
79
|
+
assert_equal([0,2,8], @obj_3.cut_locations)
|
80
|
+
assert_equal([0,2,8], @obj_4.cut_locations)
|
81
|
+
|
82
|
+
assert_equal([1,3], @obj_5.cut_locations)
|
83
|
+
assert_equal([0,2,4], @obj_6.cut_locations)
|
84
|
+
assert_equal([0,4,10], @obj_7.cut_locations)
|
85
|
+
end
|
86
|
+
|
87
|
+
def test_orientation
|
88
|
+
assert_equal([3,5], @obj_1.orientation)
|
89
|
+
assert_equal([3,5], @obj_2.orientation)
|
90
|
+
assert_equal([3,5], @obj_3.orientation)
|
91
|
+
assert_equal([3,5], @obj_4.orientation)
|
92
|
+
end
|
93
|
+
|
94
|
+
def test_creation_with_no_cuts
|
95
|
+
@obj_8 = @t.new('garraxt')
|
96
|
+
assert_equal([3,5], @obj_8.orientation)
|
97
|
+
assert_equal([], @obj_8.cut_locations)
|
98
|
+
assert_equal([], @obj_8.cut_locations_in_enzyme_notation)
|
99
|
+
assert_equal('garraxt', @obj_8.pattern)
|
100
|
+
end
|
101
|
+
|
102
|
+
# NOTE
|
103
|
+
def test_to_re
|
104
|
+
end
|
105
|
+
|
106
|
+
def test_argument_error
|
107
|
+
assert_raise(ArgumentError) { @t.new('a', [0,1,2]) }
|
108
|
+
assert_raise(ArgumentError) { @t.new('a', 0,1,2,0) }
|
109
|
+
|
110
|
+
assert_raise(ArgumentError) { @t.new('a', [nil,1,2]) }
|
111
|
+
assert_raise(ArgumentError) { @t.new('a', nil,1,2,nil) }
|
112
|
+
|
113
|
+
assert_raise(ArgumentError) { @t.new('a', [1,1,2]) }
|
114
|
+
assert_raise(ArgumentError) { @t.new('a', 1,1,2,2) }
|
115
|
+
|
116
|
+
# NOTE t| 2009-09-19 commented out for library efficiency
|
117
|
+
# re: validate_args(sequence, c) in util/restriction_enzyme/single_strand/single_strand.rb
|
118
|
+
# assert_raise(ArgumentError) { @t.new(1, [1,2,3]) }
|
119
|
+
# assert_raise(ArgumentError) { @t.new('gaat^aca', [1,2,3]) }
|
120
|
+
# assert_raise(ArgumentError) { @t.new('gaat^^aca') }
|
121
|
+
# assert_raise(ArgumentError) { @t.new('z', [1,2,3]) }
|
122
|
+
#
|
123
|
+
# assert_raise(ArgumentError) { @t.new('g', [0,1,2]) }
|
124
|
+
# assert_raise(ArgumentError) { @t.new('g', 0,1,2,0) }
|
125
|
+
# assert_raise(ArgumentError) { @t.new('g', [0,1,1,2]) }
|
126
|
+
# assert_raise(ArgumentError) { @t.new('g', 0,1,1,2,2) }
|
127
|
+
# assert_raise(ArgumentError) { @t.new(1,2,3) }
|
128
|
+
# assert_raise(ArgumentError) { @t.new(1,2,'g') }
|
129
|
+
end
|
130
|
+
|
131
|
+
end
|
@@ -0,0 +1,43 @@
|
|
1
|
+
load Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'helper.rb')).cleanpath.to_s
|
2
|
+
|
3
|
+
require 'bio/util/restriction_enzyme/string_formatting'
|
4
|
+
|
5
|
+
class TestBioRestrictionEnzymeStringFormatting < Test::Unit::TestCase
|
6
|
+
|
7
|
+
include Bio::RestrictionEnzyme::StringFormatting
|
8
|
+
|
9
|
+
def setup
|
10
|
+
@t = String
|
11
|
+
@obj_1 = @t.new('gata')
|
12
|
+
@obj_2 = @t.new('garraxt')
|
13
|
+
@obj_3 = @t.new('gArraXT')
|
14
|
+
@obj_4 = @t.new('nnnnnnngarraxtnn')
|
15
|
+
end
|
16
|
+
|
17
|
+
def test_strip_padding
|
18
|
+
assert_equal('gata', strip_padding(@obj_1))
|
19
|
+
assert_equal('garraxt', strip_padding(@obj_2))
|
20
|
+
assert_equal('gArraXT', strip_padding(@obj_3))
|
21
|
+
assert_equal('garraxt', strip_padding(@obj_4))
|
22
|
+
end
|
23
|
+
|
24
|
+
def test_left_padding
|
25
|
+
assert_equal('', left_padding(@obj_1))
|
26
|
+
assert_equal('', left_padding(@obj_2))
|
27
|
+
assert_equal('', left_padding(@obj_3))
|
28
|
+
assert_equal('nnnnnnn', left_padding(@obj_4))
|
29
|
+
end
|
30
|
+
|
31
|
+
def test_right_padding
|
32
|
+
assert_equal('', right_padding(@obj_1))
|
33
|
+
assert_equal('', right_padding(@obj_2))
|
34
|
+
assert_equal('', right_padding(@obj_3))
|
35
|
+
assert_equal('nn', right_padding(@obj_4))
|
36
|
+
end
|
37
|
+
|
38
|
+
def test_add_spacing
|
39
|
+
assert_equal('n^n g^a t^a', add_spacing('n^ng^at^a') )
|
40
|
+
assert_equal('n^n g^a r r a x t^n', add_spacing('n^ng^arraxt^n') )
|
41
|
+
end
|
42
|
+
|
43
|
+
end
|
data/test/helper.rb
ADDED
@@ -0,0 +1,17 @@
|
|
1
|
+
require 'rubygems'
|
2
|
+
require 'bundler'
|
3
|
+
begin
|
4
|
+
Bundler.setup(:default, :development)
|
5
|
+
rescue Bundler::BundlerError => e
|
6
|
+
$stderr.puts e.message
|
7
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
8
|
+
exit e.status_code
|
9
|
+
end
|
10
|
+
require 'test/unit'
|
11
|
+
|
12
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
13
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
14
|
+
require 'bio-restriction_enzyme'
|
15
|
+
|
16
|
+
class Test::Unit::TestCase
|
17
|
+
end
|