bio-ngs 0.4.6.alpha.02 → 0.4.7.alpha.02

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 (7) hide show
  1. data/VERSION +1 -1
  2. data/bio-ngs.gemspec +3 -3
  3. data/lib/bio/ngs/illumina/fastq.rb +1 -1
  4. data/lib/bio/ngs/illumina/project.rb +1 -1
  5. data/lib/bio/ngs/illumina/sample.rb +25 -7
  6. data/lib/meta.rb +22 -3
  7. metadata +67 -67
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.4.6.alpha.02
1
+ 0.4.7.alpha.02
data/bio-ngs.gemspec CHANGED
@@ -5,11 +5,11 @@
5
5
 
6
6
  Gem::Specification.new do |s|
7
7
  s.name = "bio-ngs"
8
- s.version = "0.4.6.alpha.01"
8
+ s.version = "0.4.7.alpha.02"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
11
11
  s.authors = ["Francesco Strozzi", "Raoul J.P. Bonnal"]
12
- s.date = "2012-05-18"
12
+ s.date = "2012-05-25"
13
13
  s.description = "bio-ngs provides a framework for handling NGS data with BioRuby"
14
14
  s.email = "francesco.strozzi@gmail.com"
15
15
  s.executables = ["biongs"]
@@ -131,7 +131,7 @@ Gem::Specification.new do |s|
131
131
  s.homepage = "http://github.com/helios/bioruby-ngs"
132
132
  s.licenses = ["MIT"]
133
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  s.require_paths = ["lib"]
134
- s.rubygems_version = "1.8.15"
134
+ s.rubygems_version = "1.8.10"
135
135
  s.summary = "bio-ngs provides a framework for handling NGS data with BioRuby"
136
136
 
137
137
  if s.respond_to? :specification_version then
data/lib/bio/ngs/illumina/fastq.rb CHANGED
@@ -21,7 +21,7 @@ module Bio
21
21
  end
22
22
  end
23
23
 
24
- module FastqGz
24
+ module FastqGz #TODO this module can be move in another namespace more generic
25
25
  require 'zlib'
26
26
  class << self
27
27
 
data/lib/bio/ngs/illumina/project.rb CHANGED
@@ -31,7 +31,7 @@ module Bio
31
31
  "json_class" => self.class.name,
32
32
  "name" => name,
33
33
  "sample_sheet" => sample_sheet,
34
- "samples" => samples.each_key.map{|k| samples[k].to_json }
34
+ "samples" => samples#each_key.map{|k| samples[k].to_json }
35
35
  }.to_json(*a)
36
36
  end
37
37
  end
data/lib/bio/ngs/illumina/sample.rb CHANGED
@@ -12,6 +12,19 @@ module Bio
12
12
  metadata[:type]=:file
13
13
  metadata[:format]=:fastq
14
14
  end
15
+
16
+ def to_json(*a)
17
+ {
18
+ "json_class" => self.class.name,
19
+ "name" => name,
20
+ "metadata" => metadata
21
+ #{}"filenames" => filenames_paths
22
+ }.to_json(*a)
23
+ end
24
+
25
+ def self.json_create(o)
26
+ me = new(o["name"], o["metadata"]["path"],o["metadata"]["parent"])
27
+ end
15
28
  end #File
16
29
 
17
30
  class Sample < Meta::Pool
@@ -62,7 +75,7 @@ module Bio
62
75
  self.add MetaReads.new(SecureRandom.uuid, metadata)
63
76
  end
64
77
 
65
- #REMOVE # def get(tag=filtered)
78
+ #REMOVE # def get(tag=filtered)
66
79
  # @files.get(tag)
67
80
  # end
68
81
 
@@ -72,12 +85,17 @@ module Bio
72
85
  end.flatten
73
86
  end
74
87
 
75
- # def to_json(*a)
76
- # {
77
- # "json_class" => self.class.name,
78
- # "name" => name,
79
- # "filenames" => filenames_paths
80
- # }.to_json(*a)
88
+ def to_json(*a)
89
+ {
90
+ "json_class" => self.class.name,
91
+ "name" => name,
92
+ "metadata" => metadata,
93
+ "files" => pool
94
+ }.to_json(*a)
95
+ end
96
+
97
+ # def self.json_create(o)
98
+ # me = new(o["name"], o["metadata"]["path"],o["metadata"]["parent"])
81
99
  # end
82
100
  end #Sample
83
101
  end #Illumina
data/lib/meta.rb CHANGED
@@ -64,12 +64,24 @@ module Meta
64
64
  class Pool < Data
65
65
  include Enumerable
66
66
  # include Data
67
- attr_accessor :pool
67
+ attr_accessor :pool
68
68
  def initialize(name=SecureRandom.uuid)
69
69
  super(name)
70
70
  @pool = {}
71
71
  end
72
72
 
73
+ def to_json(*a)
74
+ {
75
+ "json_class" => self.class.name,
76
+ "name" => name,
77
+ "pool" => pool
78
+ #{}"filenames" => filenames_paths
79
+ }.to_json(*a)
80
+ end
81
+
82
+ def self.json_create(o)
83
+ me = new(o["name"], o["metadata"]["path"],o["metadata"]["parent"])
84
+ end
73
85
 
74
86
  def each &block
75
87
  @pool.each_pair{|name, member| block.call(member)}
@@ -97,14 +109,18 @@ module Meta
97
109
  @pool.keys
98
110
  end
99
111
 
100
- def get(name_or_tag_or_value=nil)
112
+ def get(name_or_tag_or_value, value=nil)
101
113
  # TODO implement recursive query or passing multiple values as hash, insercet or etc.....
102
114
  # if name_or_tag_or_value.is_a? Hash
103
115
  # name_or_tag_or_value.each_pair do |tag, value|
104
116
  #
105
117
  # end
106
118
  # else
107
- get_by_name(name_or_tag_or_value) || get_by_tag(name_or_tag_or_value) || get_by_value(name_or_tag_or_value) || get_down_to_childer(name_or_tag_or_value)
119
+ if value
120
+ get_by_tag_and_value(name_or_tag_or_value, value)
121
+ else
122
+ get_by_name(name_or_tag_or_value) || get_by_tag(name_or_tag_or_value) || get_by_value(name_or_tag_or_value) || get_down_to_childer(name_or_tag_or_value)
123
+ end
108
124
  # end
109
125
  end #get
110
126
 
@@ -142,6 +158,9 @@ module Meta
142
158
  ret_pool unless ret_pool.empty?
143
159
  end
144
160
 
161
+
162
+
163
+
145
164
  private
146
165
  def get_generic(type, data)
147
166
  ret_pool = Pool.new
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: 0.4.6.alpha.02
4
+ version: 0.4.7.alpha.02
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: 2012-05-21 00:00:00.000000000 Z
13
+ date: 2012-05-25 00:00:00.000000000 Z
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
16
  name: bio
17
- requirement: &2153665000 !ruby/object:Gem::Requirement
17
+ requirement: &2152729020 !ruby/object:Gem::Requirement
18
18
  none: false
19
19
  requirements:
20
20
  - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
22
22
  version: 1.4.2
23
23
  type: :runtime
24
24
  prerelease: false
25
- version_requirements: *2153665000
25
+ version_requirements: *2152729020
26
26
  - !ruby/object:Gem::Dependency
27
27
  name: bio-samtools
28
- requirement: &2153664500 !ruby/object:Gem::Requirement
28
+ requirement: &2152728500 !ruby/object:Gem::Requirement
29
29
  none: false
30
30
  requirements:
31
31
  - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
33
33
  version: 0.3.2
34
34
  type: :runtime
35
35
  prerelease: false
36
- version_requirements: *2153664500
36
+ version_requirements: *2152728500
37
37
  - !ruby/object:Gem::Dependency
38
38
  name: thor
39
- requirement: &2153795800 !ruby/object:Gem::Requirement
39
+ requirement: &2152727960 !ruby/object:Gem::Requirement
40
40
  none: false
41
41
  requirements:
42
42
  - - =
@@ -44,10 +44,10 @@ dependencies:
44
44
  version: 0.14.6
45
45
  type: :runtime
46
46
  prerelease: false
47
- version_requirements: *2153795800
47
+ version_requirements: *2152727960
48
48
  - !ruby/object:Gem::Dependency
49
49
  name: rubyvis
50
- requirement: &2153795320 !ruby/object:Gem::Requirement
50
+ requirement: &2152727380 !ruby/object:Gem::Requirement
51
51
  none: false
52
52
  requirements:
53
53
  - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
55
55
  version: 0.5.0
56
56
  type: :runtime
57
57
  prerelease: false
58
- version_requirements: *2153795320
58
+ version_requirements: *2152727380
59
59
  - !ruby/object:Gem::Dependency
60
60
  name: daemons
61
- requirement: &2153794840 !ruby/object:Gem::Requirement
61
+ requirement: &2152726800 !ruby/object:Gem::Requirement
62
62
  none: false
63
63
  requirements:
64
64
  - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
66
66
  version: 1.1.0
67
67
  type: :runtime
68
68
  prerelease: false
69
- version_requirements: *2153794840
69
+ version_requirements: *2152726800
70
70
  - !ruby/object:Gem::Dependency
71
71
  name: ruby-ensembl-api
72
- requirement: &2153794300 !ruby/object:Gem::Requirement
72
+ requirement: &2152726260 !ruby/object:Gem::Requirement
73
73
  none: false
74
74
  requirements:
75
75
  - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
77
77
  version: 1.0.1
78
78
  type: :runtime
79
79
  prerelease: false
80
- version_requirements: *2153794300
80
+ version_requirements: *2152726260
81
81
  - !ruby/object:Gem::Dependency
82
82
  name: activerecord
83
- requirement: &2153793160 !ruby/object:Gem::Requirement
83
+ requirement: &2152725720 !ruby/object:Gem::Requirement
84
84
  none: false
85
85
  requirements:
86
86
  - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
88
88
  version: 3.0.5
89
89
  type: :runtime
90
90
  prerelease: false
91
- version_requirements: *2153793160
91
+ version_requirements: *2152725720
92
92
  - !ruby/object:Gem::Dependency
93
93
  name: sqlite3
94
- requirement: &2153791580 !ruby/object:Gem::Requirement
94
+ requirement: &2152725140 !ruby/object:Gem::Requirement
95
95
  none: false
96
96
  requirements:
97
97
  - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
99
99
  version: 1.3.3
100
100
  type: :runtime
101
101
  prerelease: false
102
- version_requirements: *2153791580
102
+ version_requirements: *2152725140
103
103
  - !ruby/object:Gem::Dependency
104
104
  name: bio-blastxmlparser
105
- requirement: &2153790980 !ruby/object:Gem::Requirement
105
+ requirement: &2152740860 !ruby/object:Gem::Requirement
106
106
  none: false
107
107
  requirements:
108
108
  - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
110
110
  version: '0'
111
111
  type: :runtime
112
112
  prerelease: false
113
- version_requirements: *2153790980
113
+ version_requirements: *2152740860
114
114
  - !ruby/object:Gem::Dependency
115
115
  name: progressbar
116
- requirement: &2153790500 !ruby/object:Gem::Requirement
116
+ requirement: &2152740240 !ruby/object:Gem::Requirement
117
117
  none: false
118
118
  requirements:
119
119
  - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
121
121
  version: 0.9.0
122
122
  type: :runtime
123
123
  prerelease: false
124
- version_requirements: *2153790500
124
+ version_requirements: *2152740240
125
125
  - !ruby/object:Gem::Dependency
126
126
  name: rake
127
- requirement: &2153789980 !ruby/object:Gem::Requirement
127
+ requirement: &2152739680 !ruby/object:Gem::Requirement
128
128
  none: false
129
129
  requirements:
130
130
  - - =
@@ -132,10 +132,10 @@ dependencies:
132
132
  version: 0.9.2.2
133
133
  type: :runtime
134
134
  prerelease: false
135
- version_requirements: *2153789980
135
+ version_requirements: *2152739680
136
136
  - !ruby/object:Gem::Dependency
137
137
  name: json
138
- requirement: &2153789440 !ruby/object:Gem::Requirement
138
+ requirement: &2152739120 !ruby/object:Gem::Requirement
139
139
  none: false
140
140
  requirements:
141
141
  - - ! '>='
@@ -143,10 +143,10 @@ dependencies:
143
143
  version: '0'
144
144
  type: :runtime
145
145
  prerelease: false
146
- version_requirements: *2153789440
146
+ version_requirements: *2152739120
147
147
  - !ruby/object:Gem::Dependency
148
148
  name: parallel
149
- requirement: &2153788960 !ruby/object:Gem::Requirement
149
+ requirement: &2152738540 !ruby/object:Gem::Requirement
150
150
  none: false
151
151
  requirements:
152
152
  - - ! '>='
@@ -154,10 +154,10 @@ dependencies:
154
154
  version: '0'
155
155
  type: :runtime
156
156
  prerelease: false
157
- version_requirements: *2153788960
157
+ version_requirements: *2152738540
158
158
  - !ruby/object:Gem::Dependency
159
159
  name: shoulda
160
- requirement: &2153788480 !ruby/object:Gem::Requirement
160
+ requirement: &2152738020 !ruby/object:Gem::Requirement
161
161
  none: false
162
162
  requirements:
163
163
  - - ! '>='
@@ -165,10 +165,10 @@ dependencies:
165
165
  version: '0'
166
166
  type: :development
167
167
  prerelease: false
168
- version_requirements: *2153788480
168
+ version_requirements: *2152738020
169
169
  - !ruby/object:Gem::Dependency
170
170
  name: bundler
171
- requirement: &2153787960 !ruby/object:Gem::Requirement
171
+ requirement: &2152737500 !ruby/object:Gem::Requirement
172
172
  none: false
173
173
  requirements:
174
174
  - - ~>
@@ -176,10 +176,10 @@ dependencies:
176
176
  version: 1.1.0
177
177
  type: :development
178
178
  prerelease: false
179
- version_requirements: *2153787960
179
+ version_requirements: *2152737500
180
180
  - !ruby/object:Gem::Dependency
181
181
  name: jeweler
182
- requirement: &2153846060 !ruby/object:Gem::Requirement
182
+ requirement: &2152736960 !ruby/object:Gem::Requirement
183
183
  none: false
184
184
  requirements:
185
185
  - - ~>
@@ -187,10 +187,10 @@ dependencies:
187
187
  version: 1.8.3
188
188
  type: :development
189
189
  prerelease: false
190
- version_requirements: *2153846060
190
+ version_requirements: *2152736960
191
191
  - !ruby/object:Gem::Dependency
192
192
  name: rcov
193
- requirement: &2153845580 !ruby/object:Gem::Requirement
193
+ requirement: &2152736400 !ruby/object:Gem::Requirement
194
194
  none: false
195
195
  requirements:
196
196
  - - ~>
@@ -198,10 +198,10 @@ dependencies:
198
198
  version: 0.9.11
199
199
  type: :development
200
200
  prerelease: false
201
- version_requirements: *2153845580
201
+ version_requirements: *2152736400
202
202
  - !ruby/object:Gem::Dependency
203
203
  name: bio
204
- requirement: &2153844960 !ruby/object:Gem::Requirement
204
+ requirement: &2152735800 !ruby/object:Gem::Requirement
205
205
  none: false
206
206
  requirements:
207
207
  - - ! '>='
@@ -209,10 +209,10 @@ dependencies:
209
209
  version: 1.4.2
210
210
  type: :development
211
211
  prerelease: false
212
- version_requirements: *2153844960
212
+ version_requirements: *2152735800
213
213
  - !ruby/object:Gem::Dependency
214
214
  name: thor
215
- requirement: &2153844140 !ruby/object:Gem::Requirement
215
+ requirement: &2152735180 !ruby/object:Gem::Requirement
216
216
  none: false
217
217
  requirements:
218
218
  - - =
@@ -220,10 +220,10 @@ dependencies:
220
220
  version: 0.14.6
221
221
  type: :development
222
222
  prerelease: false
223
- version_requirements: *2153844140
223
+ version_requirements: *2152735180
224
224
  - !ruby/object:Gem::Dependency
225
225
  name: ffi
226
- requirement: &2153843400 !ruby/object:Gem::Requirement
226
+ requirement: &2152734620 !ruby/object:Gem::Requirement
227
227
  none: false
228
228
  requirements:
229
229
  - - ! '>='
@@ -231,10 +231,10 @@ dependencies:
231
231
  version: 1.0.6
232
232
  type: :development
233
233
  prerelease: false
234
- version_requirements: *2153843400
234
+ version_requirements: *2152734620
235
235
  - !ruby/object:Gem::Dependency
236
236
  name: rubyvis
237
- requirement: &2153842920 !ruby/object:Gem::Requirement
237
+ requirement: &2152734120 !ruby/object:Gem::Requirement
238
238
  none: false
239
239
  requirements:
240
240
  - - ! '>='
@@ -242,10 +242,10 @@ dependencies:
242
242
  version: 0.5.0
243
243
  type: :development
244
244
  prerelease: false
245
- version_requirements: *2153842920
245
+ version_requirements: *2152734120
246
246
  - !ruby/object:Gem::Dependency
247
247
  name: rspec
248
- requirement: &2153842440 !ruby/object:Gem::Requirement
248
+ requirement: &2152733600 !ruby/object:Gem::Requirement
249
249
  none: false
250
250
  requirements:
251
251
  - - ! '>='
@@ -253,10 +253,10 @@ dependencies:
253
253
  version: 2.5.0
254
254
  type: :development
255
255
  prerelease: false
256
- version_requirements: *2153842440
256
+ version_requirements: *2152733600
257
257
  - !ruby/object:Gem::Dependency
258
258
  name: daemons
259
- requirement: &2153841880 !ruby/object:Gem::Requirement
259
+ requirement: &2152775800 !ruby/object:Gem::Requirement
260
260
  none: false
261
261
  requirements:
262
262
  - - ! '>='
@@ -264,10 +264,10 @@ dependencies:
264
264
  version: 1.1.0
265
265
  type: :development
266
266
  prerelease: false
267
- version_requirements: *2153841880
267
+ version_requirements: *2152775800
268
268
  - !ruby/object:Gem::Dependency
269
269
  name: bio-samtools
270
- requirement: &2153841380 !ruby/object:Gem::Requirement
270
+ requirement: &2152775280 !ruby/object:Gem::Requirement
271
271
  none: false
272
272
  requirements:
273
273
  - - ! '>='
@@ -275,10 +275,10 @@ dependencies:
275
275
  version: 0.3.2
276
276
  type: :development
277
277
  prerelease: false
278
- version_requirements: *2153841380
278
+ version_requirements: *2152775280
279
279
  - !ruby/object:Gem::Dependency
280
280
  name: ruby-ensembl-api
281
- requirement: &2153840900 !ruby/object:Gem::Requirement
281
+ requirement: &2152774760 !ruby/object:Gem::Requirement
282
282
  none: false
283
283
  requirements:
284
284
  - - ! '>='
@@ -286,10 +286,10 @@ dependencies:
286
286
  version: 1.0.1
287
287
  type: :development
288
288
  prerelease: false
289
- version_requirements: *2153840900
289
+ version_requirements: *2152774760
290
290
  - !ruby/object:Gem::Dependency
291
291
  name: activerecord
292
- requirement: &2153840400 !ruby/object:Gem::Requirement
292
+ requirement: &2152774240 !ruby/object:Gem::Requirement
293
293
  none: false
294
294
  requirements:
295
295
  - - ! '>='
@@ -297,10 +297,10 @@ dependencies:
297
297
  version: 3.0.5
298
298
  type: :development
299
299
  prerelease: false
300
- version_requirements: *2153840400
300
+ version_requirements: *2152774240
301
301
  - !ruby/object:Gem::Dependency
302
302
  name: sqlite3
303
- requirement: &2153839920 !ruby/object:Gem::Requirement
303
+ requirement: &2152773740 !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: *2153839920
311
+ version_requirements: *2152773740
312
312
  - !ruby/object:Gem::Dependency
313
313
  name: bio-blastxmlparser
314
- requirement: &2153839360 !ruby/object:Gem::Requirement
314
+ requirement: &2152773180 !ruby/object:Gem::Requirement
315
315
  none: false
316
316
  requirements:
317
317
  - - ! '>='
@@ -319,10 +319,10 @@ dependencies:
319
319
  version: '0'
320
320
  type: :development
321
321
  prerelease: false
322
- version_requirements: *2153839360
322
+ version_requirements: *2152773180
323
323
  - !ruby/object:Gem::Dependency
324
324
  name: progressbar
325
- requirement: &2153838840 !ruby/object:Gem::Requirement
325
+ requirement: &2152772640 !ruby/object:Gem::Requirement
326
326
  none: false
327
327
  requirements:
328
328
  - - ! '>='
@@ -330,10 +330,10 @@ dependencies:
330
330
  version: 0.9.0
331
331
  type: :development
332
332
  prerelease: false
333
- version_requirements: *2153838840
333
+ version_requirements: *2152772640
334
334
  - !ruby/object:Gem::Dependency
335
335
  name: json
336
- requirement: &2153838360 !ruby/object:Gem::Requirement
336
+ requirement: &2152772040 !ruby/object:Gem::Requirement
337
337
  none: false
338
338
  requirements:
339
339
  - - ! '>='
@@ -341,10 +341,10 @@ dependencies:
341
341
  version: '0'
342
342
  type: :development
343
343
  prerelease: false
344
- version_requirements: *2153838360
344
+ version_requirements: *2152772040
345
345
  - !ruby/object:Gem::Dependency
346
346
  name: rake
347
- requirement: &2153897220 !ruby/object:Gem::Requirement
347
+ requirement: &2152770800 !ruby/object:Gem::Requirement
348
348
  none: false
349
349
  requirements:
350
350
  - - =
@@ -352,10 +352,10 @@ dependencies:
352
352
  version: 0.9.2.2
353
353
  type: :development
354
354
  prerelease: false
355
- version_requirements: *2153897220
355
+ version_requirements: *2152770800
356
356
  - !ruby/object:Gem::Dependency
357
357
  name: parallel
358
- requirement: &2153896700 !ruby/object:Gem::Requirement
358
+ requirement: &2152769720 !ruby/object:Gem::Requirement
359
359
  none: false
360
360
  requirements:
361
361
  - - ! '>='
@@ -363,7 +363,7 @@ dependencies:
363
363
  version: '0'
364
364
  type: :development
365
365
  prerelease: false
366
- version_requirements: *2153896700
366
+ version_requirements: *2152769720
367
367
  description: bio-ngs provides a framework for handling NGS data with BioRuby
368
368
  email: francesco.strozzi@gmail.com
369
369
  executables:
@@ -497,7 +497,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
497
497
  version: '0'
498
498
  segments:
499
499
  - 0
500
- hash: -1070352367343550027
500
+ hash: -2512494530563499590
501
501
  required_rubygems_version: !ruby/object:Gem::Requirement
502
502
  none: false
503
503
  requirements: