bio-ngs 0.4.2.alpha.01 → 0.4.4.alpha.01

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.
Files changed (24) hide show
  1. data/Gemfile +5 -4
  2. data/Gemfile.lock +34 -32
  3. data/README.rdoc +3 -0
  4. data/VERSION +1 -1
  5. data/bin/biongs +0 -5
  6. data/bio-ngs.gemspec +17 -28
  7. data/ext/mkrf_conf.rb +5 -1
  8. data/lib/bio-ngs.rb +9 -2
  9. data/lib/bio/appl/ngs/bcftools.rb +100 -0
  10. data/lib/bio/appl/ngs/bwa.rb +210 -0
  11. data/lib/bio/appl/ngs/fastx.rb +22 -6
  12. data/lib/bio/appl/ngs/samtools.rb +85 -0
  13. data/lib/bio/appl/ngs/tophat.rb +1 -1
  14. data/lib/bio/ngs/ext/versions.yaml +16 -0
  15. data/lib/bio/ngs/record.rb +2 -2
  16. data/lib/bio/ngs/utils.rb +11 -8
  17. data/lib/enumerable.rb +13 -1
  18. data/lib/tasks/bwa.thor +32 -106
  19. data/lib/tasks/filter.thor +75 -0
  20. data/lib/tasks/pre.thor +17 -37
  21. data/lib/tasks/project.thor +2 -1
  22. data/lib/tasks/quality.thor +27 -5
  23. data/lib/wrapper.rb +32 -5
  24. metadata +100 -99
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-ngs
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.4.2.alpha.01
4
+ version: 0.4.4.alpha.01
5
5
  prerelease: 6
6
6
  platform: ruby
7
7
  authors:
@@ -10,11 +10,11 @@ authors:
10
10
  autorequire:
11
11
  bindir: bin
12
12
  cert_chain: []
13
- date: 2012-02-13 00:00:00.000000000 Z
13
+ date: 2012-03-21 00:00:00.000000000 Z
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
16
  name: bio
17
- requirement: &2157120300 !ruby/object:Gem::Requirement
17
+ requirement: &2154269220 !ruby/object:Gem::Requirement
18
18
  none: false
19
19
  requirements:
20
20
  - - ! '>='
@@ -22,21 +22,10 @@ dependencies:
22
22
  version: 1.4.2
23
23
  type: :runtime
24
24
  prerelease: false
25
- version_requirements: *2157120300
26
- - !ruby/object:Gem::Dependency
27
- name: bio-bwa
28
- requirement: &2157119680 !ruby/object:Gem::Requirement
29
- none: false
30
- requirements:
31
- - - ! '>='
32
- - !ruby/object:Gem::Version
33
- version: 0.2.2
34
- type: :runtime
35
- prerelease: false
36
- version_requirements: *2157119680
25
+ version_requirements: *2154269220
37
26
  - !ruby/object:Gem::Dependency
38
27
  name: bio-samtools
39
- requirement: &2157119100 !ruby/object:Gem::Requirement
28
+ requirement: &2154267300 !ruby/object:Gem::Requirement
40
29
  none: false
41
30
  requirements:
42
31
  - - ! '>='
@@ -44,10 +33,10 @@ dependencies:
44
33
  version: 0.3.2
45
34
  type: :runtime
46
35
  prerelease: false
47
- version_requirements: *2157119100
36
+ version_requirements: *2154267300
48
37
  - !ruby/object:Gem::Dependency
49
38
  name: thor
50
- requirement: &2157118540 !ruby/object:Gem::Requirement
39
+ requirement: &2154282240 !ruby/object:Gem::Requirement
51
40
  none: false
52
41
  requirements:
53
42
  - - ! '>='
@@ -55,10 +44,10 @@ dependencies:
55
44
  version: 0.14.6
56
45
  type: :runtime
57
46
  prerelease: false
58
- version_requirements: *2157118540
47
+ version_requirements: *2154282240
59
48
  - !ruby/object:Gem::Dependency
60
49
  name: rubyvis
61
- requirement: &2157117900 !ruby/object:Gem::Requirement
50
+ requirement: &2154281240 !ruby/object:Gem::Requirement
62
51
  none: false
63
52
  requirements:
64
53
  - - ! '>='
@@ -66,10 +55,10 @@ dependencies:
66
55
  version: 0.5.0
67
56
  type: :runtime
68
57
  prerelease: false
69
- version_requirements: *2157117900
58
+ version_requirements: *2154281240
70
59
  - !ruby/object:Gem::Dependency
71
60
  name: daemons
72
- requirement: &2157133620 !ruby/object:Gem::Requirement
61
+ requirement: &2154280320 !ruby/object:Gem::Requirement
73
62
  none: false
74
63
  requirements:
75
64
  - - ! '>='
@@ -77,10 +66,10 @@ dependencies:
77
66
  version: 1.1.0
78
67
  type: :runtime
79
68
  prerelease: false
80
- version_requirements: *2157133620
69
+ version_requirements: *2154280320
81
70
  - !ruby/object:Gem::Dependency
82
71
  name: ruby-ensembl-api
83
- requirement: &2157133000 !ruby/object:Gem::Requirement
72
+ requirement: &2154278980 !ruby/object:Gem::Requirement
84
73
  none: false
85
74
  requirements:
86
75
  - - ! '>='
@@ -88,10 +77,10 @@ dependencies:
88
77
  version: 1.0.1
89
78
  type: :runtime
90
79
  prerelease: false
91
- version_requirements: *2157133000
80
+ version_requirements: *2154278980
92
81
  - !ruby/object:Gem::Dependency
93
82
  name: activerecord
94
- requirement: &2157132300 !ruby/object:Gem::Requirement
83
+ requirement: &2154277960 !ruby/object:Gem::Requirement
95
84
  none: false
96
85
  requirements:
97
86
  - - ! '>='
@@ -99,10 +88,10 @@ dependencies:
99
88
  version: 3.0.5
100
89
  type: :runtime
101
90
  prerelease: false
102
- version_requirements: *2157132300
91
+ version_requirements: *2154277960
103
92
  - !ruby/object:Gem::Dependency
104
93
  name: sqlite3
105
- requirement: &2157131680 !ruby/object:Gem::Requirement
94
+ requirement: &2154277080 !ruby/object:Gem::Requirement
106
95
  none: false
107
96
  requirements:
108
97
  - - ! '>='
@@ -110,10 +99,10 @@ dependencies:
110
99
  version: 1.3.3
111
100
  type: :runtime
112
101
  prerelease: false
113
- version_requirements: *2157131680
102
+ version_requirements: *2154277080
114
103
  - !ruby/object:Gem::Dependency
115
104
  name: bio-blastxmlparser
116
- requirement: &2157131060 !ruby/object:Gem::Requirement
105
+ requirement: &2154276060 !ruby/object:Gem::Requirement
117
106
  none: false
118
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  requirements:
119
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  - - ! '>='
@@ -121,10 +110,10 @@ dependencies:
121
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  version: '0'
122
111
  type: :runtime
123
112
  prerelease: false
124
- version_requirements: *2157131060
113
+ version_requirements: *2154276060
125
114
  - !ruby/object:Gem::Dependency
126
115
  name: progressbar
127
- requirement: &2157130440 !ruby/object:Gem::Requirement
116
+ requirement: &2154275100 !ruby/object:Gem::Requirement
128
117
  none: false
129
118
  requirements:
130
119
  - - ! '>='
@@ -132,10 +121,10 @@ dependencies:
132
121
  version: 0.9.0
133
122
  type: :runtime
134
123
  prerelease: false
135
- version_requirements: *2157130440
124
+ version_requirements: *2154275100
136
125
  - !ruby/object:Gem::Dependency
137
126
  name: rake
138
- requirement: &2157129820 !ruby/object:Gem::Requirement
127
+ requirement: &2154290640 !ruby/object:Gem::Requirement
139
128
  none: false
140
129
  requirements:
141
130
  - - =
@@ -143,10 +132,32 @@ dependencies:
143
132
  version: 0.9.2.2
144
133
  type: :runtime
145
134
  prerelease: false
146
- version_requirements: *2157129820
135
+ version_requirements: *2154290640
136
+ - !ruby/object:Gem::Dependency
137
+ name: json
138
+ requirement: &2154288840 !ruby/object:Gem::Requirement
139
+ none: false
140
+ requirements:
141
+ - - ! '>='
142
+ - !ruby/object:Gem::Version
143
+ version: '0'
144
+ type: :runtime
145
+ prerelease: false
146
+ version_requirements: *2154288840
147
+ - !ruby/object:Gem::Dependency
148
+ name: parallel
149
+ requirement: &2154285720 !ruby/object:Gem::Requirement
150
+ none: false
151
+ requirements:
152
+ - - ! '>='
153
+ - !ruby/object:Gem::Version
154
+ version: '0'
155
+ type: :runtime
156
+ prerelease: false
157
+ version_requirements: *2154285720
147
158
  - !ruby/object:Gem::Dependency
148
159
  name: shoulda
149
- requirement: &2157129080 !ruby/object:Gem::Requirement
160
+ requirement: &2154299000 !ruby/object:Gem::Requirement
150
161
  none: false
151
162
  requirements:
152
163
  - - ! '>='
@@ -154,32 +165,32 @@ dependencies:
154
165
  version: '0'
155
166
  type: :development
156
167
  prerelease: false
157
- version_requirements: *2157129080
168
+ version_requirements: *2154299000
158
169
  - !ruby/object:Gem::Dependency
159
170
  name: bundler
160
- requirement: &2157128200 !ruby/object:Gem::Requirement
171
+ requirement: &2154297180 !ruby/object:Gem::Requirement
161
172
  none: false
162
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  requirements:
163
174
  - - ~>
164
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  - !ruby/object:Gem::Version
165
- version: 1.0.0
176
+ version: 1.1.0
166
177
  type: :development
167
178
  prerelease: false
168
- version_requirements: *2157128200
179
+ version_requirements: *2154297180
169
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  - !ruby/object:Gem::Dependency
170
181
  name: jeweler
171
- requirement: &2157127280 !ruby/object:Gem::Requirement
182
+ requirement: &2154296480 !ruby/object:Gem::Requirement
172
183
  none: false
173
184
  requirements:
174
185
  - - ~>
175
186
  - !ruby/object:Gem::Version
176
- version: 1.5.2
187
+ version: 1.8.3
177
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  type: :development
178
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  prerelease: false
179
- version_requirements: *2157127280
190
+ version_requirements: *2154296480
180
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  - !ruby/object:Gem::Dependency
181
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  name: rcov
182
- requirement: &2157126720 !ruby/object:Gem::Requirement
193
+ requirement: &2154295940 !ruby/object:Gem::Requirement
183
194
  none: false
184
195
  requirements:
185
196
  - - ~>
@@ -187,10 +198,10 @@ dependencies:
187
198
  version: 0.9.11
188
199
  type: :development
189
200
  prerelease: false
190
- version_requirements: *2157126720
201
+ version_requirements: *2154295940
191
202
  - !ruby/object:Gem::Dependency
192
203
  name: bio
193
- requirement: &2157473200 !ruby/object:Gem::Requirement
204
+ requirement: &2154302280 !ruby/object:Gem::Requirement
194
205
  none: false
195
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  requirements:
196
207
  - - ! '>='
@@ -198,10 +209,10 @@ dependencies:
198
209
  version: 1.4.2
199
210
  type: :development
200
211
  prerelease: false
201
- version_requirements: *2157473200
212
+ version_requirements: *2154302280
202
213
  - !ruby/object:Gem::Dependency
203
214
  name: thor
204
- requirement: &2157472260 !ruby/object:Gem::Requirement
215
+ requirement: &2154300720 !ruby/object:Gem::Requirement
205
216
  none: false
206
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  requirements:
207
218
  - - ! '>='
@@ -209,10 +220,10 @@ dependencies:
209
220
  version: 0.14.6
210
221
  type: :development
211
222
  prerelease: false
212
- version_requirements: *2157472260
223
+ version_requirements: *2154300720
213
224
  - !ruby/object:Gem::Dependency
214
225
  name: ffi
215
- requirement: &2157471560 !ruby/object:Gem::Requirement
226
+ requirement: &2154314940 !ruby/object:Gem::Requirement
216
227
  none: false
217
228
  requirements:
218
229
  - - ! '>='
@@ -220,10 +231,10 @@ dependencies:
220
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  version: 1.0.6
221
232
  type: :development
222
233
  prerelease: false
223
- version_requirements: *2157471560
234
+ version_requirements: *2154314940
224
235
  - !ruby/object:Gem::Dependency
225
236
  name: rubyvis
226
- requirement: &2157470260 !ruby/object:Gem::Requirement
237
+ requirement: &2154313100 !ruby/object:Gem::Requirement
227
238
  none: false
228
239
  requirements:
229
240
  - - ! '>='
@@ -231,10 +242,10 @@ dependencies:
231
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  version: 0.5.0
232
243
  type: :development
233
244
  prerelease: false
234
- version_requirements: *2157470260
245
+ version_requirements: *2154313100
235
246
  - !ruby/object:Gem::Dependency
236
247
  name: rspec
237
- requirement: &2157468020 !ruby/object:Gem::Requirement
248
+ requirement: &2154311240 !ruby/object:Gem::Requirement
238
249
  none: false
239
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  requirements:
240
251
  - - ! '>='
@@ -242,10 +253,10 @@ dependencies:
242
253
  version: 2.5.0
243
254
  type: :development
244
255
  prerelease: false
245
- version_requirements: *2157468020
256
+ version_requirements: *2154311240
246
257
  - !ruby/object:Gem::Dependency
247
258
  name: daemons
248
- requirement: &2157467300 !ruby/object:Gem::Requirement
259
+ requirement: &2154309900 !ruby/object:Gem::Requirement
249
260
  none: false
250
261
  requirements:
251
262
  - - ! '>='
@@ -253,10 +264,10 @@ dependencies:
253
264
  version: 1.1.0
254
265
  type: :development
255
266
  prerelease: false
256
- version_requirements: *2157467300
267
+ version_requirements: *2154309900
257
268
  - !ruby/object:Gem::Dependency
258
269
  name: bio-samtools
259
- requirement: &2157465240 !ruby/object:Gem::Requirement
270
+ requirement: &2154309200 !ruby/object:Gem::Requirement
260
271
  none: false
261
272
  requirements:
262
273
  - - ! '>='
@@ -264,10 +275,10 @@ dependencies:
264
275
  version: 0.3.2
265
276
  type: :development
266
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  prerelease: false
267
- version_requirements: *2157465240
278
+ version_requirements: *2154309200
268
279
  - !ruby/object:Gem::Dependency
269
280
  name: ruby-ensembl-api
270
- requirement: &2157480640 !ruby/object:Gem::Requirement
281
+ requirement: &2154308560 !ruby/object:Gem::Requirement
271
282
  none: false
272
283
  requirements:
273
284
  - - ! '>='
@@ -275,21 +286,10 @@ dependencies:
275
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  version: 1.0.1
276
287
  type: :development
277
288
  prerelease: false
278
- version_requirements: *2157480640
279
- - !ruby/object:Gem::Dependency
280
- name: bio-bwa
281
- requirement: &2157479520 !ruby/object:Gem::Requirement
282
- none: false
283
- requirements:
284
- - - ! '>='
285
- - !ruby/object:Gem::Version
286
- version: 0.2.2
287
- type: :development
288
- prerelease: false
289
- version_requirements: *2157479520
289
+ version_requirements: *2154308560
290
290
  - !ruby/object:Gem::Dependency
291
291
  name: activerecord
292
- requirement: &2157478880 !ruby/object:Gem::Requirement
292
+ requirement: &2154323680 !ruby/object:Gem::Requirement
293
293
  none: false
294
294
  requirements:
295
295
  - - ! '>='
@@ -297,10 +297,10 @@ dependencies:
297
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  version: 3.0.5
298
298
  type: :development
299
299
  prerelease: false
300
- version_requirements: *2157478880
300
+ version_requirements: *2154323680
301
301
  - !ruby/object:Gem::Dependency
302
302
  name: sqlite3
303
- requirement: &2157477800 !ruby/object:Gem::Requirement
303
+ requirement: &2154322400 !ruby/object:Gem::Requirement
304
304
  none: false
305
305
  requirements:
306
306
  - - ! '>='
@@ -308,10 +308,10 @@ dependencies:
308
308
  version: 1.3.3
309
309
  type: :development
310
310
  prerelease: false
311
- version_requirements: *2157477800
311
+ version_requirements: *2154322400
312
312
  - !ruby/object:Gem::Dependency
313
313
  name: bio-blastxmlparser
314
- requirement: &2157476620 !ruby/object:Gem::Requirement
314
+ requirement: &2154320940 !ruby/object:Gem::Requirement
315
315
  none: false
316
316
  requirements:
317
317
  - - ! '>='
@@ -319,10 +319,10 @@ dependencies:
319
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  version: '0'
320
320
  type: :development
321
321
  prerelease: false
322
- version_requirements: *2157476620
322
+ version_requirements: *2154320940
323
323
  - !ruby/object:Gem::Dependency
324
324
  name: progressbar
325
- requirement: &2157475400 !ruby/object:Gem::Requirement
325
+ requirement: &2154320180 !ruby/object:Gem::Requirement
326
326
  none: false
327
327
  requirements:
328
328
  - - ! '>='
@@ -330,10 +330,10 @@ dependencies:
330
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  version: 0.9.0
331
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  type: :development
332
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  prerelease: false
333
- version_requirements: *2157475400
333
+ version_requirements: *2154320180
334
334
  - !ruby/object:Gem::Dependency
335
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  name: json
336
- requirement: &2157473980 !ruby/object:Gem::Requirement
336
+ requirement: &2154319540 !ruby/object:Gem::Requirement
337
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  none: false
338
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  requirements:
339
339
  - - ! '>='
@@ -341,10 +341,10 @@ dependencies:
341
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  version: '0'
342
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  type: :development
343
343
  prerelease: false
344
- version_requirements: *2157473980
344
+ version_requirements: *2154319540
345
345
  - !ruby/object:Gem::Dependency
346
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  name: rake
347
- requirement: &2157626640 !ruby/object:Gem::Requirement
347
+ requirement: &2154318340 !ruby/object:Gem::Requirement
348
348
  none: false
349
349
  requirements:
350
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  - - =
@@ -352,7 +352,18 @@ dependencies:
352
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  version: 0.9.2.2
353
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  type: :development
354
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  prerelease: false
355
- version_requirements: *2157626640
355
+ version_requirements: *2154318340
356
+ - !ruby/object:Gem::Dependency
357
+ name: parallel
358
+ requirement: &2154317580 !ruby/object:Gem::Requirement
359
+ none: false
360
+ requirements:
361
+ - - ! '>='
362
+ - !ruby/object:Gem::Version
363
+ version: '0'
364
+ type: :development
365
+ prerelease: false
366
+ version_requirements: *2154317580
356
367
  description: bio-ngs provides a framework for handling NGS data with BioRuby
357
368
  email: francesco.strozzi@gmail.com
358
369
  executables:
@@ -374,9 +385,11 @@ files:
374
385
  - bio-ngs.gemspec
375
386
  - ext/mkrf_conf.rb
376
387
  - lib/bio-ngs.rb
388
+ - lib/bio/appl/ngs/bcftools.rb
377
389
  - lib/bio/appl/ngs/bcl2qseq.rb
378
390
  - lib/bio/appl/ngs/blast.rb
379
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  - lib/bio/appl/ngs/bowtie-inspect.rb
392
+ - lib/bio/appl/ngs/bwa.rb
380
393
  - lib/bio/appl/ngs/cufflinks.rb
381
394
  - lib/bio/appl/ngs/cufflinks/iterators.rb
382
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  - lib/bio/appl/ngs/fastx.rb
@@ -410,6 +423,7 @@ files:
410
423
  - lib/enumerable.rb
411
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  - lib/tasks/bwa.thor
412
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  - lib/tasks/convert.thor
426
+ - lib/tasks/filter.thor
413
427
  - lib/tasks/history.thor
414
428
  - lib/tasks/homology.thor
415
429
  - lib/tasks/ontology.thor
@@ -455,7 +469,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
455
469
  version: '0'
456
470
  segments:
457
471
  - 0
458
- hash: 4413176982890419271
472
+ hash: 1080687296344900764
459
473
  required_rubygems_version: !ruby/object:Gem::Requirement
460
474
  none: false
461
475
  requirements:
@@ -468,17 +482,4 @@ rubygems_version: 1.8.10
468
482
  signing_key:
469
483
  specification_version: 3
470
484
  summary: bio-ngs provides a framework for handling NGS data with BioRuby
471
- test_files:
472
- - spec/converter_qseq_spec.rb
473
- - spec/quality_spec.rb
474
- - spec/sff_extract_spec.rb
475
- - spec/spec_helper.rb
476
- - spec/tophat_spec.rb
477
- - spec/utils_spec.rb
478
- - test/helper.rb
479
- - test/test_bio-ngs.rb
480
- - test/test_db.rb
481
- - test/test_homology.rb
482
- - test/test_ngs.rb
483
- - test/test_ontology.rb
484
- - test/test_utils.rb
485
+ test_files: []