bio 1.4.1 → 1.4.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/ChangeLog +954 -0
- data/KNOWN_ISSUES.rdoc +40 -5
- data/README.rdoc +36 -35
- data/RELEASE_NOTES.rdoc +87 -59
- data/bioruby.gemspec +24 -2
- data/doc/RELEASE_NOTES-1.4.1.rdoc +104 -0
- data/doc/Tutorial.rd +162 -200
- data/doc/Tutorial.rd.html +149 -146
- data/lib/bio.rb +1 -0
- data/lib/bio/appl/blast.rb +1 -1
- data/lib/bio/appl/blast/ddbj.rb +26 -34
- data/lib/bio/appl/blast/genomenet.rb +21 -11
- data/lib/bio/db/embl/sptr.rb +193 -21
- data/lib/bio/db/fasta.rb +1 -1
- data/lib/bio/db/fastq.rb +14 -0
- data/lib/bio/db/fastq/format_fastq.rb +2 -2
- data/lib/bio/db/genbank/ddbj.rb +1 -2
- data/lib/bio/db/genbank/format_genbank.rb +1 -1
- data/lib/bio/db/medline.rb +1 -0
- data/lib/bio/db/newick.rb +3 -1
- data/lib/bio/db/pdb/pdb.rb +9 -9
- data/lib/bio/db/pdb/residue.rb +2 -2
- data/lib/bio/io/ddbjrest.rb +344 -0
- data/lib/bio/io/ncbirest.rb +121 -1
- data/lib/bio/location.rb +2 -2
- data/lib/bio/reference.rb +3 -4
- data/lib/bio/shell/plugin/entry.rb +7 -3
- data/lib/bio/shell/plugin/ncbirest.rb +5 -1
- data/lib/bio/util/restriction_enzyme.rb +3 -0
- data/lib/bio/util/restriction_enzyme/dense_int_array.rb +195 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +7 -7
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +57 -18
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +2 -2
- data/lib/bio/util/restriction_enzyme/sorted_num_array.rb +219 -0
- data/lib/bio/version.rb +1 -1
- data/sample/test_restriction_enzyme_long.rb +4403 -0
- data/test/data/fasta/EFTU_BACSU.fasta +8 -0
- data/test/data/genbank/CAA35997.gp +48 -0
- data/test/data/genbank/SCU49845.gb +167 -0
- data/test/data/litdb/1717226.litdb +13 -0
- data/test/data/pir/CRAB_ANAPL.pir +6 -0
- data/test/functional/bio/appl/blast/test_remote.rb +93 -0
- data/test/functional/bio/appl/test_blast.rb +61 -0
- data/test/functional/bio/io/test_ddbjrest.rb +47 -0
- data/test/functional/bio/test_command.rb +3 -3
- data/test/unit/bio/db/embl/test_sptr.rb +6 -6
- data/test/unit/bio/db/embl/test_uniprot_new_part.rb +208 -0
- data/test/unit/bio/db/genbank/test_common.rb +274 -0
- data/test/unit/bio/db/genbank/test_genbank.rb +401 -0
- data/test/unit/bio/db/genbank/test_genpept.rb +81 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +3287 -11
- data/test/unit/bio/db/test_fasta.rb +34 -12
- data/test/unit/bio/db/test_fastq.rb +26 -0
- data/test/unit/bio/db/test_litdb.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +1 -0
- data/test/unit/bio/db/test_nbrf.rb +82 -0
- data/test/unit/bio/db/test_newick.rb +22 -4
- data/test/unit/bio/test_reference.rb +35 -0
- data/test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb +201 -0
- data/test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb +281 -0
- metadata +44 -38
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#
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# test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb - Unit test for Bio::RestrictionEnzyme::SortedNumArray
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#
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# Copyright:: Copyright (C) 2011
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# loading helper routine for testing bioruby
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require 'pathname'
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
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'bioruby_test_helper.rb')).cleanpath.to_s
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# libraries needed for the tests
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require 'test/unit'
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require 'bio/util/restriction_enzyme'
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require 'bio/util/restriction_enzyme/sorted_num_array'
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module Bio
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module TestRestrictionEnzyme
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class TestSortedNumArray < Test::Unit::TestCase
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def setup
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@klass = Bio::RestrictionEnzyme::SortedNumArray
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@obj = @klass[14, 265, 4626, -1, 358, 159, 979, 3238, 3]
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end
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def test_self_bracket
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assert_equal([ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ],
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@obj.to_a)
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end
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def test_self_new
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a = @klass.new
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assert_instance_of(Bio::RestrictionEnzyme::SortedNumArray, a)
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end
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def test_dup
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assert_equal(@obj.to_a, @obj.dup.to_a)
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h_obj = @obj.instance_eval { internal_data_hash }
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h_dup = @obj.dup.instance_eval { internal_data_hash }
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assert(h_obj == h_dup)
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assert_not_equal(h_obj.__id__, h_dup.__id__)
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end
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def test_internal_data_hash
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h = @obj.instance_eval { internal_data_hash }
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expected = { -1 => true,
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3 => true, 14 => true, 159 => true, 265 => true,
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358 => true, 979 => true, 3238 => true, 4626 => true }
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assert_equal(expected, h)
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end
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def test_internal_data_hash_eq
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h = { 0 => true, 50 => true, 100 => true }
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@obj.last # creating cache (if exists)
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@obj.instance_eval { self.internal_data_hash = h }
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assert_equal(100, @obj.last)
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assert_equal([0, 50, 100], @obj.to_a)
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end
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#def test_private_clear_cache
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# assert_nothing_raised {
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# @obj.instance_eval { clear_cache }
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# }
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# @obj.last # creating cache
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# @obj.instance_eval { clear_cache }
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# assert_nil(@obj.instance_eval { @sorted_keys })
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#end
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def test_private_sorted_keys
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a = @obj.instance_eval { sorted_keys }
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assert_equal([ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ], a)
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end
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def test_private_push_element
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assert_equal(false, @obj.include?(50))
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@obj.instance_eval {
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push_element(50)
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}
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assert_equal(true, @obj.include?(50))
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end
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def test_private_push_element_noeffect
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assert_equal(true, @obj.include?(159))
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@obj.instance_eval {
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push_element(159)
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}
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assert_equal(true, @obj.include?(159))
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end
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def test_private_push_element_last
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@obj.last # creating cache (if exists)
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@obj.instance_eval {
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push_element(9999)
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}
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assert_equal(true, @obj.include?(9999))
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assert_equal(9999, @obj.last)
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end
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def test_private_push_element_intermediate
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@obj.last # creating cache (if exists)
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@obj.instance_eval {
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push_element(100)
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}
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assert_equal(true, @obj.include?(100))
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assert_equal(4626, @obj.last)
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end
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def test_private_unshift_element
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assert_equal(false, @obj.include?(50))
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@obj.instance_eval {
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unshift_element(50)
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}
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assert_equal(true, @obj.include?(50))
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end
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def test_private_unshift_element_noeffect
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assert_equal(true, @obj.include?(159))
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@obj.instance_eval {
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unshift_element(159)
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}
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assert_equal(true, @obj.include?(159))
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end
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def test_private_unshift_element_first
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@obj.last # creating cache (if exists)
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@obj.instance_eval {
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unshift_element(-999)
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}
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assert_equal(true, @obj.include?(-999))
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assert_equal(-999, @obj.first)
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end
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def test_private_unshift_element_intermediate
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@obj.last # creating cache (if exists)
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@obj.instance_eval {
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unshift_element(100)
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}
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assert_equal(true, @obj.include?(100))
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assert_equal(-1, @obj.first)
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end
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def test_bracket
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assert_equal(-1, @obj[0])
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assert_equal(159, @obj[3])
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assert_equal(4626, @obj[-1])
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assert_equal([14, 159, 265], @obj[2..4])
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assert_equal([14, 159, 265], @obj[2,3])
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end
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def test_bracket_eq
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assert_raise(NotImplementedError) {
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@obj[3] = 999
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}
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end
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def test_each
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expected_values = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
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@obj.each do |i|
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assert_equal(expected_values.shift, i)
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end
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end
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def test_reverse_each
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expected_values = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
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@obj.reverse_each do |i|
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assert_equal(expected_values.pop, i)
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end
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end
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def test_plus
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obj2 = @klass[ 2, 3, 14, 15 ]
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assert_equal([ -1, 2, 3, 14, 15, 159, 265, 358, 979, 3238, 4626 ],
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(@obj + obj2).to_a)
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end
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def test_plus_error
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assert_raise(TypeError) {
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@obj + 2
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}
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end
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def test_eqeq
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obj2 = @klass[ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
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assert_equal(true, @obj == obj2)
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end
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def test_eqeq_self
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assert_equal(true, @obj == @obj)
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end
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def test_eqeq_false
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obj2 = @klass[ 2, 3, 14, 15 ]
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assert_equal(false, @obj == obj2)
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end
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def test_eqeq_other
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obj2 = 'test'
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assert_equal(false, @obj == obj2)
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end
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def test_concat
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ary = [ 9999, -2, 14, 15 ]
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expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
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# checks if the method returns self
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assert_equal(@obj, @obj.concat(ary))
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# checks the value
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assert_equal(expected, @obj.to_a)
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end
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def test_push
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expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
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# checks if the method returns self
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assert_equal(@obj, @obj.push(15, 14, -2, 9999))
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# checks the value
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assert_equal(expected, @obj.to_a)
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end
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def test_unshift
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expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
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# checks if the method returns self
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assert_equal(@obj, @obj.unshift(15, 14, -2, 9999))
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# checks the value
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assert_equal(expected, @obj.to_a)
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end
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def test_ltlt
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expected = [ -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626 ]
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# checks if the method returns self
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assert_equal(@obj, @obj << 15)
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# checks the value
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assert_equal(expected, @obj.to_a)
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end
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def test_ltlt_noeffect
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expected = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
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# checks if the method returns self
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assert_equal(@obj, @obj << 159)
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# checks the value
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assert_equal(expected, @obj.to_a)
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end
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def test_include?
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assert_equal(true, @obj.include?(159))
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assert_equal(false, @obj.include?(999))
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end
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def test_size
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assert_equal(9, @obj.size)
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end
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def test_length
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assert_equal(9, @obj.length)
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end
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def test_delete
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assert_equal(nil, @obj.delete(100))
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assert_equal(159, @obj.delete(159))
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end
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def test_sort!
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assert_equal(@obj, @obj.sort!)
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end
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def test_uniq!
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assert_equal(@obj, @obj.uniq!)
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end
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def test_to_a
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expected = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
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assert_equal(expected, @obj.to_a)
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end
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end #class TestSortedNumArray
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end #module TestRestrictionEnzyme
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end #module Bio
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metadata
CHANGED
@@ -1,34 +1,26 @@
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--- !ruby/object:Gem::Specification
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--- !ruby/object:Gem::Specification
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name: bio
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version: !ruby/object:Gem::Version
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- 1
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version: 1.4.1
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version: !ruby/object:Gem::Version
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version: 1.4.2
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prerelease:
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platform: ruby
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authors:
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authors:
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- BioRuby project
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autorequire: bio
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bindir: bin
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cert_chain: []
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-
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date: 2010-10-22 00:00:00 +09:00
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default_executable: bioruby
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date: 2011-08-26 00:00:00.000000000 Z
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dependencies: []
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-
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description: BioRuby is a library for bioinformatics (biology + information science).
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email: staff@bioruby.org
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executables:
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executables:
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- bioruby
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- br_biofetch.rb
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- br_bioflat.rb
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- br_biogetseq.rb
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- br_pmfetch.rb
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extensions: []
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-
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extra_rdoc_files:
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