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

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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
107
  requirements:
119
108
  - - ! '>='
@@ -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
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  - - ! '>='
@@ -154,32 +165,32 @@ dependencies:
154
165
  version: '0'
155
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  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
173
  requirements:
163
174
  - - ~>
164
175
  - !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
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  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
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  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
217
  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
231
  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
277
  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
331
  type: :development
332
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  prerelease: false
333
- version_requirements: *2157475400
333
+ version_requirements: *2154320180
334
334
  - !ruby/object:Gem::Dependency
335
335
  name: json
336
- requirement: &2157473980 !ruby/object:Gem::Requirement
336
+ requirement: &2154319540 !ruby/object:Gem::Requirement
337
337
  none: false
338
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  requirements:
339
339
  - - ! '>='
@@ -341,10 +341,10 @@ dependencies:
341
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  version: '0'
342
342
  type: :development
343
343
  prerelease: false
344
- version_requirements: *2157473980
344
+ version_requirements: *2154319540
345
345
  - !ruby/object:Gem::Dependency
346
346
  name: rake
347
- requirement: &2157626640 !ruby/object:Gem::Requirement
347
+ requirement: &2154318340 !ruby/object:Gem::Requirement
348
348
  none: false
349
349
  requirements:
350
350
  - - =
@@ -352,7 +352,18 @@ dependencies:
352
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  version: 0.9.2.2
353
353
  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
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  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
391
  - 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
395
  - lib/bio/appl/ngs/fastx.rb
@@ -410,6 +423,7 @@ files:
410
423
  - lib/enumerable.rb
411
424
  - lib/tasks/bwa.thor
412
425
  - 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: []