bio-fastqc 0.7.2 → 0.8.0

Sign up to get free protection for your applications and to get access to all the features.
Files changed (4) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/lib/bio/fastqc/semantics.rb +64 -48
  4. metadata +2 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: ca7ee6aa02b7e7b658b0ffaf6c7036225868dd0e
4
- data.tar.gz: 275ff7f63f708b9eaa01c279e4b8fbbbabc49208
3
+ metadata.gz: 6cbdb6a0b5125d4d90dc3e5b17f451b6a35db13f
4
+ data.tar.gz: 2bf19899ae60a2ce06f129adcffb2b14ba345191
5
5
  SHA512:
6
- metadata.gz: f932cb789116a17c3dc21c460e8ed3a653fb5edbe08818c94cd6925210425bf25cf7a8d71db6fb5f48296ca62d44d2b8730a56a3a09284b433adddbcf51c2d6c
7
- data.tar.gz: e9aefcb4429a33f9bf2f0d58a57ac45f91cf0c55050a18c80614111be81a963bde73846440bbdcddc63a3b3caed60ed875626508a936fdbfb323b11b10e451fc
6
+ metadata.gz: 3a29404861f22e429d96f6253a7f8d3a4b3bb2c6960343bf21e627603f1f3276709004ed2e5c001d02ac1456c20d13e5e89a354b6a82d099fe085e73b86abc52
7
+ data.tar.gz: c2de3c14c3d844792e1ac00e1ed5c7107754886ebdfb98be6a07071b497da108a7e6ee0ad153cf27e41380984eecbe289d8692f74032c82d9382f3202b0b5e22
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.7.2
1
+ 0.8.0
data/lib/bio/fastqc/semantics.rb CHANGED
@@ -13,7 +13,7 @@ module Bio
13
13
  end
14
14
 
15
15
  def rdf_version
16
- "0.1.1"
16
+ "0.1.2"
17
17
  end
18
18
 
19
19
  def turtle
@@ -28,10 +28,12 @@ module Bio
28
28
  {
29
29
  "uo" => "http://purl.obolibrary.org/obo/",
30
30
  "rdf" => "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
31
+ "rdfs" => "http://www.w3.org/2000/01/rdf-schema#",
31
32
  "dcterms" => "http://purl.org/dc/terms/",
32
33
  "pav" => "http://purl.org/pav/",
33
34
  "foaf" => "http://xmlns.com/foaf/0.1/",
34
35
  "sos" => "http://purl.jp/bio/01/quanto/ontology/sos#",
36
+ "quanto" => "http://purl.jp/bio/01/quanto/resource/",
35
37
  }
36
38
  end
37
39
 
@@ -47,12 +49,16 @@ module Bio
47
49
  "http://purl.jp/bio/01/quanto"
48
50
  end
49
51
 
52
+ def sra_identifier
53
+ @fastqc_object[:filename].split(".")[0].split("_")[0]
54
+ end
55
+
50
56
  def identifier_literal
51
57
  @id ? @id : "QNT" + @fastqc_object[:filename].split(".")[0]
52
58
  end
53
59
 
54
60
  def identifier_uri
55
- uri_base + "/resource/" + identifier_literal
61
+ "quanto:" + identifier_literal
56
62
  end
57
63
 
58
64
  def object_core
@@ -63,10 +69,19 @@ module Bio
63
69
  "dcterms:identifier" => identifier_literal,
64
70
  "dcterms:contributor" => ["Tazro Ohta", "Shuichi Kawashima"],
65
71
  "dcterms:created" => Time.now.strftime("%Y-%m-%d"),
66
- "dcterms:license" => "http://creativecommons.org/licenses/by-sa/2.1/jp/deed.en",
67
- "dcterms:publisher" => "http://dbcls.rois.ac.jp/",
72
+ "dcterms:license" => {
73
+ "@id" => "http://creativecommons.org/licenses/by-sa/4.0/",
74
+ },
75
+ "dcterms:publisher" => {
76
+ "@id" => "http://dbcls.rois.ac.jp/",
77
+ },
68
78
  "pav:version" => rdf_version,
69
- "foaf:page" => "http://quanto.dbcls.jp",
79
+ "foaf:page" => {
80
+ "@id" => "http://quanto.dbcls.jp",
81
+ },
82
+ "rdfs:seeAlso" => {
83
+ "@id" => "http://identifiers.org/insdc.sra/" + sra_identifier,
84
+ },
70
85
  }
71
86
  end
72
87
 
@@ -144,7 +159,7 @@ module Bio
144
159
  {
145
160
  "totalSequences" => {
146
161
  "@type" => "SequenceReadAmount",
147
- "hasUnit" => "uo:CountUnit",
162
+ "hasUnit" => "uo:UO_0000244",
148
163
  "rdf:value" => @fastqc_object[:total_sequences],
149
164
  }
150
165
  }
@@ -154,7 +169,7 @@ module Bio
154
169
  {
155
170
  "filteredSequences" => {
156
171
  "@type" => "SequenceReadAmount",
157
- "hasUnit" => "uo:CountUnit",
172
+ "hasUnit" => "uo:UO_0000244",
158
173
  "rdf:value" => @fastqc_object[:filtered_sequences],
159
174
  }
160
175
  }
@@ -164,7 +179,7 @@ module Bio
164
179
  {
165
180
  "sequenceLength" => {
166
181
  "@type" => "SequenceReadLength",
167
- "hasUnit" => "uo:CountUnit",
182
+ "hasUnit" => "uo:UO_0000244",
168
183
  "rdf:value" => @fastqc_object[:sequence_length],
169
184
  }
170
185
  }
@@ -173,8 +188,8 @@ module Bio
173
188
  def percent_gc
174
189
  {
175
190
  "percentGC" => {
176
- "@type" => "SequenceBaseAmount",
177
- "hasUnit" => "uo:CountUnit",
191
+ "@type" => "BaseRatio",
192
+ "hasUnit" => "uo:UO_0000187",
178
193
  "rdf:value" => @fastqc_object[:percent_gc],
179
194
  }
180
195
  }
@@ -206,32 +221,32 @@ module Bio
206
221
  "basePosition" => base,
207
222
  "meanBaseCallQuality" => {
208
223
  "@type" => "PhredQualityScore",
209
- "hasUnit" => "uo:CountUnit",
224
+ "hasUnit" => "uo:UO_0000189",
210
225
  "rdf:value" => mean,
211
226
  },
212
227
  "medianBaseCallQuality" => {
213
228
  "@type" => "PhredQualityScore",
214
- "hasUnit" => "uo:CountUnit",
229
+ "hasUnit" => "uo:UO_0000189",
215
230
  "rdf:value" => median,
216
231
  },
217
232
  "baseCallQualityLowerQuartile" => {
218
233
  "@type" => "PhredQualityScore",
219
- "hasUnit" => "uo:CountUnit",
234
+ "hasUnit" => "uo:UO_0000189",
220
235
  "rdf:value" => lower_quartile,
221
236
  },
222
237
  "baseCallQualityUpperQuartile" => {
223
238
  "@type" => "PhredQualityScore",
224
- "hasUnit" => "uo:CountUnit",
239
+ "hasUnit" => "uo:UO_0000189",
225
240
  "rdf:value" => upper_quartile,
226
241
  },
227
242
  "baseCallQuality10thPercentile" => {
228
243
  "@type" => "PhredQualityScore",
229
- "hasUnit" => "uo:CountUnit",
244
+ "hasUnit" => "uo:UO_0000189",
230
245
  "rdf:value" => tenth_percentile,
231
246
  },
232
247
  "baseCallQuality90thPercentile" => {
233
248
  "@type" => "PhredQualityScore",
234
- "hasUnit" => "uo:CountUnit",
249
+ "hasUnit" => "uo:UO_0000189",
235
250
  "rdf:value" => ninetieth_percentile,
236
251
  },
237
252
  }
@@ -258,12 +273,12 @@ module Bio
258
273
  "rowIndex" => i,
259
274
  "baseCallQuality" => {
260
275
  "@type" => "PhredQualityScore",
261
- "hasUnit" => "uo:CountUnit",
276
+ "hasUnit" => "uo:UO_0000189",
262
277
  "rdf:value" => quality,
263
278
  },
264
279
  "sequenceReadCount" => {
265
280
  "@type" => "SequenceReadAmount",
266
- "hasUnit" => "uo:CountUnit",
281
+ "hasUnit" => "uo:UO_0000244",
267
282
  "rdf:value" => count,
268
283
  },
269
284
  }
@@ -292,23 +307,23 @@ module Bio
292
307
  "rowIndex" => i,
293
308
  "basePosition" => base,
294
309
  "percentGuanine" => {
295
- "@type" => "SequenceBaseAmount",
296
- "hasUnit" => "uo:Percentage",
310
+ "@type" => "BaseRatio",
311
+ "hasUnit" => "uo:UO_0000187",
297
312
  "rdf:value" => guanine,
298
313
  },
299
314
  "percentAdenine" => {
300
- "@type" => "SequenceBaseAmount",
301
- "hasUnit" => "uo:Percentage",
315
+ "@type" => "BaseRatio",
316
+ "hasUnit" => "uo:UO_0000187",
302
317
  "rdf:value" => adenine,
303
318
  },
304
319
  "percentThymine" => {
305
- "@type" => "SequenceBaseAmount",
306
- "hasUnit" => "uo:Percentage",
320
+ "@type" => "BaseRatio",
321
+ "hasUnit" => "uo:UO_0000187",
307
322
  "rdf:value" => thymine,
308
323
  },
309
324
  "percentCytosine" => {
310
- "@type" => "SequenceBaseAmount",
311
- "hasUnit" => "uo:Percentage",
325
+ "@type" => "BaseRatio",
326
+ "hasUnit" => "uo:UO_0000187",
312
327
  "rdf:value" => chytosine,
313
328
  },
314
329
  }
@@ -330,13 +345,13 @@ module Bio
330
345
  "@type" => "Row",
331
346
  "rowIndex" => i,
332
347
  "percentGC" => {
333
- "@type" => "SequenceBaseAmount",
334
- "hasunit" => "uo:Percent",
348
+ "@type" => "BaseRatio",
349
+ "hasunit" => "uo:UO_0000187",
335
350
  "rdf:value" => gc_content,
336
351
  },
337
352
  "sequenceReadCount" => {
338
353
  "@type" => "SequenceReadAmount",
339
- "hasUnit" => "uo:CountUnit",
354
+ "hasUnit" => "uo:UO_0000244",
340
355
  "rdf:value" => count,
341
356
  },
342
357
  }
@@ -362,8 +377,8 @@ module Bio
362
377
  "rowIndex" => i,
363
378
  "basePosition" => base,
364
379
  "nCount" => {
365
- "@type" => "SequenceBaseAmount",
366
- "hasUnit" => "uo:Percentage",
380
+ "@type" => "BaseRatio",
381
+ "hasUnit" => "uo:UO_0000187",
367
382
  "rdf:value" => n_count,
368
383
  },
369
384
  }
@@ -387,12 +402,12 @@ module Bio
387
402
 
388
403
  "sequenceReadLength" => {
389
404
  "@type" => "SequenceReadLength",
390
- "hasUnit" => "uo:CountUnit",
405
+ "hasUnit" => "uo:UO_0000244",
391
406
  "rdf:value" => length,
392
407
  },
393
408
  "sequenceReadCount" => {
394
409
  "@type" => "SequenceReadAmount",
395
- "hasUnit" => "uo:CountUnit",
410
+ "hasUnit" => "uo:UO_0000244",
396
411
  "rdf:value" => count,
397
412
  },
398
413
  }
@@ -420,12 +435,12 @@ module Bio
420
435
 
421
436
  "sequenceDuplicationLevel" => {
422
437
  "@type" => "SequenceDuplicationLevel",
423
- "hasUnit" => "uo:CountUnit",
438
+ "hasUnit" => "uo:UO_0000189",
424
439
  "rdf:value" => duplication_level,
425
440
  },
426
441
  "sequenceReadRelativeCount" => {
427
442
  "@type" => "SequenceReadAmount",
428
- "hasUnit" => "uo:CountUnit",
443
+ "hasUnit" => "uo:UO_0000244",
429
444
  "rdf:value" => relative_count,
430
445
  },
431
446
  }
@@ -451,12 +466,12 @@ module Bio
451
466
  "overrepresentedSequence" => sequence,
452
467
  "sequenceReadCount" => {
453
468
  "@type" => "SequenceReadAmount",
454
- "hasUnit" => "uo:CountUnit",
469
+ "hasUnit" => "uo:UO_0000244",
455
470
  "rdf:value" => count,
456
471
  },
457
472
  "sequenceReadPercentage" => {
458
- "@type" => "SequenceReadAmount",
459
- "hasUnit" => "uo:Percentage",
473
+ "@type" => "SequenceReadRatio",
474
+ "hasUnit" => "uo:UO_0000187",
460
475
  "rdf:value" => percentage,
461
476
  },
462
477
  "possibleSourceOfSequence" => possible_source,
@@ -488,7 +503,7 @@ module Bio
488
503
  "kmerSequence" => sequence,
489
504
  "sequenceReadCount" => {
490
505
  "@type" => "SequenceReadAmount",
491
- "hasUnit" => "uo:CountUnit",
506
+ "hasUnit" => "uo:UO_0000244",
492
507
  "rdf:value" => count,
493
508
  },
494
509
  "observedPerExpectedOverall" => {
@@ -510,7 +525,7 @@ module Bio
510
525
  {
511
526
  "minSequenceLength" => {
512
527
  "@type" => "SequenceReadLength",
513
- "hasUnit" => "uo:CountUnit",
528
+ "hasUnit" => "uo:UO_0000244",
514
529
  "rdf:value" => @fastqc_object[:min_length],
515
530
  }
516
531
  }
@@ -520,7 +535,7 @@ module Bio
520
535
  {
521
536
  "maxSequenceLength" => {
522
537
  "@type" => "SequenceReadLength",
523
- "hasUnit" => "uo:CountUnit",
538
+ "hasUnit" => "uo:UO_0000244",
524
539
  "rdf:value" => @fastqc_object[:max_length],
525
540
  }
526
541
  }
@@ -530,7 +545,7 @@ module Bio
530
545
  {
531
546
  "meanSequenceLength" => {
532
547
  "@type" => "SequenceReadLength",
533
- "hasUnit" => "uo:CountUnit",
548
+ "hasUnit" => "uo:UO_0000244",
534
549
  "rdf:value" => @fastqc_object[:mean_sequence_length],
535
550
  }
536
551
  }
@@ -540,7 +555,7 @@ module Bio
540
555
  {
541
556
  "medianSequenceLength" => {
542
557
  "@type" => "SequenceReadLength",
543
- "hasUnit" => "uo:CountUnit",
558
+ "hasUnit" => "uo:UO_0000244",
544
559
  "rdf:value" => @fastqc_object[:median_sequence_length],
545
560
  }
546
561
  }
@@ -550,7 +565,7 @@ module Bio
550
565
  {
551
566
  "overallMeanBaseCallQuality" => {
552
567
  "@type" => "PhredQualityScore",
553
- "hasUnit" => "uo:CountUnit",
568
+ "hasUnit" => "uo:UO_0000189",
554
569
  "rdf:value" => @fastqc_object[:overall_mean_quality_score],
555
570
  }
556
571
  }
@@ -560,7 +575,7 @@ module Bio
560
575
  {
561
576
  "overallMedianBaseCallQuality" => {
562
577
  "@type" => "PhredQualityScore",
563
- "hasUnit" => "uo:CountUnit",
578
+ "hasUnit" => "uo:UO_0000189",
564
579
  "rdf:value" => @fastqc_object[:overall_median_quality_score],
565
580
  }
566
581
  }
@@ -569,8 +584,8 @@ module Bio
569
584
  def overall_n_content
570
585
  {
571
586
  "overallNContent" => {
572
- "@type" => "SequenceBaseAmount",
573
- "hasUnit" => "uo:Percentage",
587
+ "@type" => "BaseRatio",
588
+ "hasUnit" => "uo:UO_0000187",
574
589
  "rdf:value" => @fastqc_object[:overall_n_content],
575
590
  }
576
591
  }
@@ -662,8 +677,9 @@ module Bio
662
677
  def sos_class_for_values
663
678
  [
664
679
  "PhredQualityScore",
665
- "SequenceBaseAmount",
680
+ "BaseRatio",
666
681
  "SequenceReadAmount",
682
+ "SequenceReadRatio",
667
683
  "SequenceReadLength",
668
684
  "SequenceDuplicationLevel",
669
685
  ]
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-fastqc
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.7.2
4
+ version: 0.8.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Tazro Inutano Ohta
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2016-07-07 00:00:00.000000000 Z
11
+ date: 2016-07-08 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rubyzip