bio 1.4.1 → 1.4.2

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Files changed (61) hide show
  1. data/ChangeLog +954 -0
  2. data/KNOWN_ISSUES.rdoc +40 -5
  3. data/README.rdoc +36 -35
  4. data/RELEASE_NOTES.rdoc +87 -59
  5. data/bioruby.gemspec +24 -2
  6. data/doc/RELEASE_NOTES-1.4.1.rdoc +104 -0
  7. data/doc/Tutorial.rd +162 -200
  8. data/doc/Tutorial.rd.html +149 -146
  9. data/lib/bio.rb +1 -0
  10. data/lib/bio/appl/blast.rb +1 -1
  11. data/lib/bio/appl/blast/ddbj.rb +26 -34
  12. data/lib/bio/appl/blast/genomenet.rb +21 -11
  13. data/lib/bio/db/embl/sptr.rb +193 -21
  14. data/lib/bio/db/fasta.rb +1 -1
  15. data/lib/bio/db/fastq.rb +14 -0
  16. data/lib/bio/db/fastq/format_fastq.rb +2 -2
  17. data/lib/bio/db/genbank/ddbj.rb +1 -2
  18. data/lib/bio/db/genbank/format_genbank.rb +1 -1
  19. data/lib/bio/db/medline.rb +1 -0
  20. data/lib/bio/db/newick.rb +3 -1
  21. data/lib/bio/db/pdb/pdb.rb +9 -9
  22. data/lib/bio/db/pdb/residue.rb +2 -2
  23. data/lib/bio/io/ddbjrest.rb +344 -0
  24. data/lib/bio/io/ncbirest.rb +121 -1
  25. data/lib/bio/location.rb +2 -2
  26. data/lib/bio/reference.rb +3 -4
  27. data/lib/bio/shell/plugin/entry.rb +7 -3
  28. data/lib/bio/shell/plugin/ncbirest.rb +5 -1
  29. data/lib/bio/util/restriction_enzyme.rb +3 -0
  30. data/lib/bio/util/restriction_enzyme/dense_int_array.rb +195 -0
  31. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +7 -7
  32. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +57 -18
  33. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +2 -2
  34. data/lib/bio/util/restriction_enzyme/sorted_num_array.rb +219 -0
  35. data/lib/bio/version.rb +1 -1
  36. data/sample/test_restriction_enzyme_long.rb +4403 -0
  37. data/test/data/fasta/EFTU_BACSU.fasta +8 -0
  38. data/test/data/genbank/CAA35997.gp +48 -0
  39. data/test/data/genbank/SCU49845.gb +167 -0
  40. data/test/data/litdb/1717226.litdb +13 -0
  41. data/test/data/pir/CRAB_ANAPL.pir +6 -0
  42. data/test/functional/bio/appl/blast/test_remote.rb +93 -0
  43. data/test/functional/bio/appl/test_blast.rb +61 -0
  44. data/test/functional/bio/io/test_ddbjrest.rb +47 -0
  45. data/test/functional/bio/test_command.rb +3 -3
  46. data/test/unit/bio/db/embl/test_sptr.rb +6 -6
  47. data/test/unit/bio/db/embl/test_uniprot_new_part.rb +208 -0
  48. data/test/unit/bio/db/genbank/test_common.rb +274 -0
  49. data/test/unit/bio/db/genbank/test_genbank.rb +401 -0
  50. data/test/unit/bio/db/genbank/test_genpept.rb +81 -0
  51. data/test/unit/bio/db/pdb/test_pdb.rb +3287 -11
  52. data/test/unit/bio/db/test_fasta.rb +34 -12
  53. data/test/unit/bio/db/test_fastq.rb +26 -0
  54. data/test/unit/bio/db/test_litdb.rb +95 -0
  55. data/test/unit/bio/db/test_medline.rb +1 -0
  56. data/test/unit/bio/db/test_nbrf.rb +82 -0
  57. data/test/unit/bio/db/test_newick.rb +22 -4
  58. data/test/unit/bio/test_reference.rb +35 -0
  59. data/test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb +201 -0
  60. data/test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb +281 -0
  61. metadata +44 -38
@@ -0,0 +1,281 @@
1
+ #
2
+ # test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb - Unit test for Bio::RestrictionEnzyme::SortedNumArray
3
+ #
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+ # Copyright:: Copyright (C) 2011
5
+ # Naohisa Goto <ng@bioruby.org>
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+ # License:: The Ruby License
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+ #
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+
9
+ # loading helper routine for testing bioruby
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+ require 'pathname'
11
+ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
12
+ 'bioruby_test_helper.rb')).cleanpath.to_s
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+
14
+ # libraries needed for the tests
15
+ require 'test/unit'
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+ require 'bio/util/restriction_enzyme'
17
+ require 'bio/util/restriction_enzyme/sorted_num_array'
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+
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+ module Bio
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+ module TestRestrictionEnzyme
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+
22
+ class TestSortedNumArray < Test::Unit::TestCase
23
+
24
+ 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]
27
+ end
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+
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+ def test_self_bracket
30
+ assert_equal([ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ],
31
+ @obj.to_a)
32
+ end
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+
34
+ def test_self_new
35
+ a = @klass.new
36
+ assert_instance_of(Bio::RestrictionEnzyme::SortedNumArray, a)
37
+ end
38
+
39
+ def test_dup
40
+ assert_equal(@obj.to_a, @obj.dup.to_a)
41
+ h_obj = @obj.instance_eval { internal_data_hash }
42
+ 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__)
45
+ end
46
+
47
+ def test_internal_data_hash
48
+ h = @obj.instance_eval { internal_data_hash }
49
+ expected = { -1 => true,
50
+ 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)
53
+ end
54
+
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+ def test_internal_data_hash_eq
56
+ 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)
61
+ end
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+
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+ #def test_private_clear_cache
64
+ # assert_nothing_raised {
65
+ # @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 })
70
+ #end
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+
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+ def test_private_sorted_keys
73
+ a = @obj.instance_eval { sorted_keys }
74
+ assert_equal([ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ], a)
75
+ end
76
+
77
+ def test_private_push_element
78
+ assert_equal(false, @obj.include?(50))
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+ @obj.instance_eval {
80
+ push_element(50)
81
+ }
82
+ assert_equal(true, @obj.include?(50))
83
+ end
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+
85
+ def test_private_push_element_noeffect
86
+ assert_equal(true, @obj.include?(159))
87
+ @obj.instance_eval {
88
+ push_element(159)
89
+ }
90
+ assert_equal(true, @obj.include?(159))
91
+ end
92
+
93
+ def test_private_push_element_last
94
+ @obj.last # creating cache (if exists)
95
+ @obj.instance_eval {
96
+ push_element(9999)
97
+ }
98
+ assert_equal(true, @obj.include?(9999))
99
+ assert_equal(9999, @obj.last)
100
+ end
101
+
102
+ def test_private_push_element_intermediate
103
+ @obj.last # creating cache (if exists)
104
+ @obj.instance_eval {
105
+ push_element(100)
106
+ }
107
+ assert_equal(true, @obj.include?(100))
108
+ assert_equal(4626, @obj.last)
109
+ end
110
+
111
+ def test_private_unshift_element
112
+ assert_equal(false, @obj.include?(50))
113
+ @obj.instance_eval {
114
+ unshift_element(50)
115
+ }
116
+ assert_equal(true, @obj.include?(50))
117
+ end
118
+
119
+ def test_private_unshift_element_noeffect
120
+ assert_equal(true, @obj.include?(159))
121
+ @obj.instance_eval {
122
+ unshift_element(159)
123
+ }
124
+ assert_equal(true, @obj.include?(159))
125
+ end
126
+
127
+ def test_private_unshift_element_first
128
+ @obj.last # creating cache (if exists)
129
+ @obj.instance_eval {
130
+ unshift_element(-999)
131
+ }
132
+ assert_equal(true, @obj.include?(-999))
133
+ assert_equal(-999, @obj.first)
134
+ end
135
+
136
+ def test_private_unshift_element_intermediate
137
+ @obj.last # creating cache (if exists)
138
+ @obj.instance_eval {
139
+ unshift_element(100)
140
+ }
141
+ assert_equal(true, @obj.include?(100))
142
+ assert_equal(-1, @obj.first)
143
+ end
144
+
145
+ def test_bracket
146
+ assert_equal(-1, @obj[0])
147
+ assert_equal(159, @obj[3])
148
+ assert_equal(4626, @obj[-1])
149
+ assert_equal([14, 159, 265], @obj[2..4])
150
+ assert_equal([14, 159, 265], @obj[2,3])
151
+ end
152
+
153
+ def test_bracket_eq
154
+ assert_raise(NotImplementedError) {
155
+ @obj[3] = 999
156
+ }
157
+ end
158
+
159
+ def test_each
160
+ expected_values = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
161
+ @obj.each do |i|
162
+ assert_equal(expected_values.shift, i)
163
+ end
164
+ end
165
+
166
+ def test_reverse_each
167
+ expected_values = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
168
+ @obj.reverse_each do |i|
169
+ assert_equal(expected_values.pop, i)
170
+ end
171
+ end
172
+
173
+ def test_plus
174
+ obj2 = @klass[ 2, 3, 14, 15 ]
175
+ assert_equal([ -1, 2, 3, 14, 15, 159, 265, 358, 979, 3238, 4626 ],
176
+ (@obj + obj2).to_a)
177
+ end
178
+
179
+ def test_plus_error
180
+ assert_raise(TypeError) {
181
+ @obj + 2
182
+ }
183
+ end
184
+
185
+ def test_eqeq
186
+ obj2 = @klass[ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
187
+ assert_equal(true, @obj == obj2)
188
+ end
189
+
190
+ def test_eqeq_self
191
+ assert_equal(true, @obj == @obj)
192
+ end
193
+
194
+ def test_eqeq_false
195
+ obj2 = @klass[ 2, 3, 14, 15 ]
196
+ assert_equal(false, @obj == obj2)
197
+ end
198
+
199
+ def test_eqeq_other
200
+ obj2 = 'test'
201
+ assert_equal(false, @obj == obj2)
202
+ end
203
+
204
+ def test_concat
205
+ ary = [ 9999, -2, 14, 15 ]
206
+ expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
207
+ # checks if the method returns self
208
+ assert_equal(@obj, @obj.concat(ary))
209
+ # checks the value
210
+ assert_equal(expected, @obj.to_a)
211
+ end
212
+
213
+ def test_push
214
+ expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
215
+ # checks if the method returns self
216
+ assert_equal(@obj, @obj.push(15, 14, -2, 9999))
217
+ # checks the value
218
+ assert_equal(expected, @obj.to_a)
219
+ end
220
+
221
+ def test_unshift
222
+ expected = [ -2, -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626, 9999 ]
223
+ # checks if the method returns self
224
+ assert_equal(@obj, @obj.unshift(15, 14, -2, 9999))
225
+ # checks the value
226
+ assert_equal(expected, @obj.to_a)
227
+ end
228
+
229
+ def test_ltlt
230
+ expected = [ -1, 3, 14, 15, 159, 265, 358, 979, 3238, 4626 ]
231
+ # checks if the method returns self
232
+ assert_equal(@obj, @obj << 15)
233
+ # checks the value
234
+ assert_equal(expected, @obj.to_a)
235
+ end
236
+
237
+ def test_ltlt_noeffect
238
+ expected = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
239
+ # checks if the method returns self
240
+ assert_equal(@obj, @obj << 159)
241
+ # checks the value
242
+ assert_equal(expected, @obj.to_a)
243
+ end
244
+
245
+ def test_include?
246
+ assert_equal(true, @obj.include?(159))
247
+ assert_equal(false, @obj.include?(999))
248
+ end
249
+
250
+ def test_size
251
+ assert_equal(9, @obj.size)
252
+ end
253
+
254
+ def test_length
255
+ assert_equal(9, @obj.length)
256
+ end
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+
258
+ def test_delete
259
+ assert_equal(nil, @obj.delete(100))
260
+ assert_equal(159, @obj.delete(159))
261
+ end
262
+
263
+ def test_sort!
264
+ assert_equal(@obj, @obj.sort!)
265
+ end
266
+
267
+ def test_uniq!
268
+ assert_equal(@obj, @obj.uniq!)
269
+ end
270
+
271
+ def test_to_a
272
+ expected = [ -1, 3, 14, 159, 265, 358, 979, 3238, 4626 ]
273
+ assert_equal(expected, @obj.to_a)
274
+ end
275
+
276
+ end #class TestSortedNumArray
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+
278
+ end #module TestRestrictionEnzyme
279
+ end #module Bio
280
+
281
+
metadata CHANGED
@@ -1,34 +1,26 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: bio
3
- version: !ruby/object:Gem::Version
4
- prerelease: false
5
- segments:
6
- - 1
7
- - 4
8
- - 1
9
- version: 1.4.1
3
+ version: !ruby/object:Gem::Version
4
+ version: 1.4.2
5
+ prerelease:
10
6
  platform: ruby
11
- authors:
7
+ authors:
12
8
  - BioRuby project
13
9
  autorequire: bio
14
10
  bindir: bin
15
11
  cert_chain: []
16
-
17
- date: 2010-10-22 00:00:00 +09:00
18
- default_executable: bioruby
12
+ date: 2011-08-26 00:00:00.000000000 Z
19
13
  dependencies: []
20
-
21
14
  description: BioRuby is a library for bioinformatics (biology + information science).
22
15
  email: staff@bioruby.org
23
- executables:
16
+ executables:
24
17
  - bioruby
25
18
  - br_biofetch.rb
26
19
  - br_bioflat.rb
27
20
  - br_biogetseq.rb
28
21
  - br_pmfetch.rb
29
22
  extensions: []
30
-
31
- extra_rdoc_files:
23
+ extra_rdoc_files:
32
24
  - ChangeLog
33
25
  - KNOWN_ISSUES.rdoc
34
26
  - README.rdoc
@@ -36,7 +28,8 @@ extra_rdoc_files:
36
28
  - RELEASE_NOTES.rdoc
37
29
  - doc/Changes-1.3.rdoc
38
30
  - doc/RELEASE_NOTES-1.4.0.rdoc
39
- files:
31
+ - doc/RELEASE_NOTES-1.4.1.rdoc
32
+ files:
40
33
  - COPYING
41
34
  - COPYING.ja
42
35
  - ChangeLog
@@ -61,6 +54,7 @@ files:
61
54
  - doc/KEGG_API.rd
62
55
  - doc/KEGG_API.rd.ja
63
56
  - doc/RELEASE_NOTES-1.4.0.rdoc
57
+ - doc/RELEASE_NOTES-1.4.1.rdoc
64
58
  - doc/Tutorial.rd
65
59
  - doc/Tutorial.rd.html
66
60
  - doc/Tutorial.rd.ja
@@ -209,6 +203,7 @@ files:
209
203
  - lib/bio/io/biosql/config/database.yml
210
204
  - lib/bio/io/das.rb
211
205
  - lib/bio/io/dbget.rb
206
+ - lib/bio/io/ddbjrest.rb
212
207
  - lib/bio/io/ddbjxml.rb
213
208
  - lib/bio/io/ebisoap.rb
214
209
  - lib/bio/io/ensembl.rb
@@ -302,6 +297,7 @@ files:
302
297
  - lib/bio/util/restriction_enzyme/analysis.rb
303
298
  - lib/bio/util/restriction_enzyme/analysis_basic.rb
304
299
  - lib/bio/util/restriction_enzyme/cut_symbol.rb
300
+ - lib/bio/util/restriction_enzyme/dense_int_array.rb
305
301
  - lib/bio/util/restriction_enzyme/double_stranded.rb
306
302
  - lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
307
303
  - lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
@@ -320,6 +316,7 @@ files:
320
316
  - lib/bio/util/restriction_enzyme/single_strand.rb
321
317
  - lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
322
318
  - lib/bio/util/restriction_enzyme/single_strand_complement.rb
319
+ - lib/bio/util/restriction_enzyme/sorted_num_array.rb
323
320
  - lib/bio/util/restriction_enzyme/string_formatting.rb
324
321
  - lib/bio/util/sirna.rb
325
322
  - lib/bio/version.rb
@@ -386,6 +383,7 @@ files:
386
383
  - sample/ssearch2tab.rb
387
384
  - sample/tdiary.rb
388
385
  - sample/test_phyloxml_big.rb
386
+ - sample/test_restriction_enzyme_long.rb
389
387
  - sample/tfastx2tab.rb
390
388
  - sample/vs-genes.rb
391
389
  - setup.rb
@@ -425,6 +423,7 @@ files:
425
423
  - test/data/command/echoarg2.bat
426
424
  - test/data/embl/AB090716.embl
427
425
  - test/data/embl/AB090716.embl.rel89
426
+ - test/data/fasta/EFTU_BACSU.fasta
428
427
  - test/data/fasta/example1.txt
429
428
  - test/data/fasta/example2.txt
430
429
  - test/data/fastq/README.txt
@@ -479,12 +478,15 @@ files:
479
478
  - test/data/fastq/wrapping_as_solexa.fastq
480
479
  - test/data/fastq/wrapping_original_sanger.fastq
481
480
  - test/data/gcg/pileup-aa.msf
481
+ - test/data/genbank/CAA35997.gp
482
+ - test/data/genbank/SCU49845.gb
482
483
  - test/data/genscan/sample.report
483
484
  - test/data/go/selected_component.ontology
484
485
  - test/data/go/selected_gene_association.sgd
485
486
  - test/data/go/selected_wikipedia2go
486
487
  - test/data/iprscan/merged.raw
487
488
  - test/data/iprscan/merged.txt
489
+ - test/data/litdb/1717226.litdb
488
490
  - test/data/medline/20146148_modified.medline
489
491
  - test/data/meme/db
490
492
  - test/data/meme/mast
@@ -504,6 +506,7 @@ files:
504
506
  - test/data/phyloxml/made_up.xml
505
507
  - test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml
506
508
  - test/data/phyloxml/phyloxml_examples.xml
509
+ - test/data/pir/CRAB_ANAPL.pir
507
510
  - test/data/prosite/prosite.dat
508
511
  - test/data/refseq/nm_126355.entret
509
512
  - test/data/rpsblast/misc.rpsblast
@@ -516,7 +519,10 @@ files:
516
519
  - test/data/soft/GDS100_partial.soft
517
520
  - test/data/soft/GSE3457_family_partial.soft
518
521
  - test/data/uniprot/p53_human.uniprot
522
+ - test/functional/bio/appl/blast/test_remote.rb
523
+ - test/functional/bio/appl/test_blast.rb
519
524
  - test/functional/bio/appl/test_pts1.rb
525
+ - test/functional/bio/io/test_ddbjrest.rb
520
526
  - test/functional/bio/io/test_ensembl.rb
521
527
  - test/functional/bio/io/test_pubmed.rb
522
528
  - test/functional/bio/io/test_soapwsdl.rb
@@ -559,9 +565,13 @@ files:
559
565
  - test/unit/bio/db/embl/test_embl_to_bioseq.rb
560
566
  - test/unit/bio/db/embl/test_sptr.rb
561
567
  - test/unit/bio/db/embl/test_uniprot.rb
568
+ - test/unit/bio/db/embl/test_uniprot_new_part.rb
562
569
  - test/unit/bio/db/fasta/test_defline.rb
563
570
  - test/unit/bio/db/fasta/test_defline_misc.rb
564
571
  - test/unit/bio/db/fasta/test_format_qual.rb
572
+ - test/unit/bio/db/genbank/test_common.rb
573
+ - test/unit/bio/db/genbank/test_genbank.rb
574
+ - test/unit/bio/db/genbank/test_genpept.rb
565
575
  - test/unit/bio/db/kegg/test_compound.rb
566
576
  - test/unit/bio/db/kegg/test_drug.rb
567
577
  - test/unit/bio/db/kegg/test_enzyme.rb
@@ -581,7 +591,9 @@ files:
581
591
  - test/unit/bio/db/test_gff.rb
582
592
  - test/unit/bio/db/test_go.rb
583
593
  - test/unit/bio/db/test_lasergene.rb
594
+ - test/unit/bio/db/test_litdb.rb
584
595
  - test/unit/bio/db/test_medline.rb
596
+ - test/unit/bio/db/test_nbrf.rb
585
597
  - test/unit/bio/db/test_newick.rb
586
598
  - test/unit/bio/db/test_nexus.rb
587
599
  - test/unit/bio/db/test_phyloxml.rb
@@ -629,20 +641,20 @@ files:
629
641
  - test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
630
642
  - test/unit/bio/util/restriction_enzyme/test_analysis.rb
631
643
  - test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb
644
+ - test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb
632
645
  - test/unit/bio/util/restriction_enzyme/test_double_stranded.rb
633
646
  - test/unit/bio/util/restriction_enzyme/test_single_strand.rb
634
647
  - test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb
648
+ - test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb
635
649
  - test/unit/bio/util/restriction_enzyme/test_string_formatting.rb
636
650
  - test/unit/bio/util/test_color_scheme.rb
637
651
  - test/unit/bio/util/test_contingency_table.rb
638
652
  - test/unit/bio/util/test_restriction_enzyme.rb
639
653
  - test/unit/bio/util/test_sirna.rb
640
- has_rdoc: true
641
654
  homepage: http://bioruby.org/
642
655
  licenses: []
643
-
644
656
  post_install_message:
645
- rdoc_options:
657
+ rdoc_options:
646
658
  - --main
647
659
  - README.rdoc
648
660
  - --title
@@ -651,30 +663,24 @@ rdoc_options:
651
663
  - \.yaml\z
652
664
  - --line-numbers
653
665
  - --inline-source
654
- require_paths:
666
+ require_paths:
655
667
  - lib
656
- required_ruby_version: !ruby/object:Gem::Requirement
668
+ required_ruby_version: !ruby/object:Gem::Requirement
657
669
  none: false
658
- requirements:
659
- - - ">="
660
- - !ruby/object:Gem::Version
661
- segments:
662
- - 0
663
- version: "0"
664
- required_rubygems_version: !ruby/object:Gem::Requirement
670
+ requirements:
671
+ - - ! '>='
672
+ - !ruby/object:Gem::Version
673
+ version: '0'
674
+ required_rubygems_version: !ruby/object:Gem::Requirement
665
675
  none: false
666
- requirements:
667
- - - ">="
668
- - !ruby/object:Gem::Version
669
- segments:
670
- - 0
671
- version: "0"
676
+ requirements:
677
+ - - ! '>='
678
+ - !ruby/object:Gem::Version
679
+ version: '0'
672
680
  requirements: []
673
-
674
681
  rubyforge_project: bioruby
675
- rubygems_version: 1.3.7
682
+ rubygems_version: 1.8.10
676
683
  signing_key:
677
684
  specification_version: 3
678
685
  summary: Bioinformatics library
679
686
  test_files: []
680
-