genevalidator 1.6.1 → 1.6.2

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 (131) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +3 -1
  3. data/.travis.yml +2 -0
  4. data/README.md +78 -30
  5. data/Rakefile +11 -8
  6. data/aux/app_template_footer.erb +1 -6
  7. data/aux/app_template_header.erb +12 -32
  8. data/aux/files/css/style.css +2 -8
  9. data/aux/files/js/plots.js +564 -576
  10. data/aux/files/js/script.js +10 -0
  11. data/aux/json_footer.erb +8 -0
  12. data/aux/json_header.erb +19 -0
  13. data/aux/json_query.erb +14 -0
  14. data/aux/template_footer.erb +9 -58
  15. data/aux/template_header.erb +18 -58
  16. data/aux/template_query.erb +8 -36
  17. data/bin/genevalidator +45 -32
  18. data/genevalidator.gemspec +11 -7
  19. data/lib/genevalidator.rb +75 -455
  20. data/lib/genevalidator/arg_validation.rb +78 -107
  21. data/lib/genevalidator/blast.rb +57 -60
  22. data/lib/genevalidator/clusterization.rb +15 -15
  23. data/lib/genevalidator/exceptions.rb +32 -5
  24. data/lib/genevalidator/get_raw_sequences.rb +70 -33
  25. data/lib/genevalidator/hsp.rb +1 -4
  26. data/lib/genevalidator/json_to_gv_results.rb +109 -0
  27. data/lib/genevalidator/output.rb +177 -185
  28. data/lib/genevalidator/pool.rb +2 -1
  29. data/lib/genevalidator/sequences.rb +3 -3
  30. data/lib/genevalidator/tabular_parser.rb +24 -18
  31. data/lib/genevalidator/validation.rb +279 -0
  32. data/lib/genevalidator/validation_alignment.rb +31 -47
  33. data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
  34. data/lib/genevalidator/validation_duplication.rb +23 -19
  35. data/lib/genevalidator/validation_gene_merge.rb +30 -65
  36. data/lib/genevalidator/validation_length_cluster.rb +14 -53
  37. data/lib/genevalidator/validation_length_rank.rb +10 -11
  38. data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
  39. data/lib/genevalidator/validation_report.rb +2 -5
  40. data/lib/genevalidator/validation_test.rb +8 -4
  41. data/lib/genevalidator/version.rb +1 -1
  42. data/test/test_all_validations.rb +51 -66
  43. data/test/test_blast.rb +68 -51
  44. data/test/test_clusterization.rb +1 -1
  45. data/test/test_clusterization_2d.rb +19 -13
  46. data/test/test_extended_array_methods.rb +1 -1
  47. data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
  48. data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
  49. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
  50. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
  51. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
  52. data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
  53. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
  54. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
  55. data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
  56. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
  57. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
  58. data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
  59. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
  60. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
  61. data/test/test_sequences.rb +46 -41
  62. data/test/test_validation_open_reading_frame.rb +318 -202
  63. data/test/test_validations.rb +48 -32
  64. metadata +76 -102
  65. data/doc/AliasDuplicationError.html +0 -134
  66. data/doc/AlignmentValidation.html +0 -1687
  67. data/doc/AlignmentValidationOutput.html +0 -659
  68. data/doc/Blast.html +0 -1905
  69. data/doc/BlastRFValidationOutput.html +0 -545
  70. data/doc/BlastReadingFrameValidation.html +0 -370
  71. data/doc/BlastUtils.html +0 -875
  72. data/doc/ClasspathError.html +0 -134
  73. data/doc/Cluster.html +0 -1316
  74. data/doc/DuplciationValidationOutput.html +0 -564
  75. data/doc/DuplicationValidation.html +0 -920
  76. data/doc/DuplicationValidationOutput.html +0 -564
  77. data/doc/FileNotFoundException.html +0 -134
  78. data/doc/GeneMergeValidation.html +0 -935
  79. data/doc/GeneMergeValidationOutput.html +0 -652
  80. data/doc/HierarchicalClusterization.html +0 -994
  81. data/doc/Hsp.html +0 -1485
  82. data/doc/InconsistentTabularFormat.html +0 -135
  83. data/doc/LengthClusterValidation.html +0 -982
  84. data/doc/LengthClusterValidationOutput.html +0 -515
  85. data/doc/LengthRankValidation.html +0 -496
  86. data/doc/LengthRankValidationOutput.html +0 -517
  87. data/doc/NoInternetError.html +0 -135
  88. data/doc/NoMafftInstallationError.html +0 -134
  89. data/doc/NoPIdentError.html +0 -134
  90. data/doc/NoValidationError.html +0 -134
  91. data/doc/NotEnoughHitsError.html +0 -135
  92. data/doc/ORFValidationOutput.html +0 -593
  93. data/doc/OpenReadingFrameValidation.html +0 -1107
  94. data/doc/OtherError.html +0 -123
  95. data/doc/Output.html +0 -1540
  96. data/doc/Pair.html +0 -309
  97. data/doc/PairCluster.html +0 -767
  98. data/doc/Plot.html +0 -837
  99. data/doc/QueryError.html +0 -134
  100. data/doc/ReportClassError.html +0 -135
  101. data/doc/Sequence.html +0 -1299
  102. data/doc/SequenceTypeError.html +0 -135
  103. data/doc/TabularEntry.html +0 -837
  104. data/doc/TabularParser.html +0 -1104
  105. data/doc/Validation.html +0 -2147
  106. data/doc/ValidationClassError.html +0 -134
  107. data/doc/ValidationOutput.html +0 -460
  108. data/doc/ValidationReport.html +0 -940
  109. data/doc/ValidationTest.html +0 -939
  110. data/doc/_index.html +0 -449
  111. data/doc/class_list.html +0 -54
  112. data/doc/css/common.css +0 -1
  113. data/doc/css/full_list.css +0 -57
  114. data/doc/css/style.css +0 -338
  115. data/doc/file.README.html +0 -151
  116. data/doc/file_list.html +0 -56
  117. data/doc/frames.html +0 -26
  118. data/doc/index.html +0 -151
  119. data/doc/js/app.js +0 -214
  120. data/doc/js/full_list.js +0 -178
  121. data/doc/js/jquery.js +0 -4
  122. data/doc/method_list.html +0 -1505
  123. data/doc/top-level-namespace.html +0 -112
  124. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
  125. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
  126. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
  127. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
  128. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
  129. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
  130. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
  131. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx +0 -3751
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160
- </li>
161
-
162
-
163
- <li class="public ">
164
- <span class="summary_signature">
165
-
166
- <a href="#hsp_list-instance_method" title="#hsp_list (instance method)">- (Object) <strong>hsp_list</strong> </a>
167
-
168
-
169
-
170
- </span>
171
-
172
-
173
-
174
-
175
-
176
-
177
-
178
-
179
-
180
-
181
-
182
-
183
- <span class="summary_desc"><div class='inline'>
184
- <p>array of Hsp objects.</p>
185
- </div></span>
186
-
187
- </li>
188
-
189
-
190
- <li class="public ">
191
- <span class="summary_signature">
192
-
193
- <a href="#identifier-instance_method" title="#identifier (instance method)">- (Object) <strong>identifier</strong> </a>
194
-
195
-
196
-
197
- </span>
198
-
199
-
200
-
201
-
202
-
203
-
204
-
205
-
206
-
207
-
208
-
209
-
210
- <span class="summary_desc"><div class='inline'>
211
- <p>Returns the value of attribute identifier.</p>
212
- </div></span>
213
-
214
- </li>
215
-
216
-
217
- <li class="public ">
218
- <span class="summary_signature">
219
-
220
- <a href="#length_protein-instance_method" title="#length_protein (instance method)">- (Object) <strong>length_protein</strong> </a>
221
-
222
-
223
-
224
- </span>
225
-
226
-
227
-
228
-
229
-
230
-
231
-
232
-
233
-
234
-
235
-
236
-
237
- <span class="summary_desc"><div class='inline'>
238
- <p>Returns the value of attribute length_protein.</p>
239
- </div></span>
240
-
241
- </li>
242
-
243
-
244
- <li class="public ">
245
- <span class="summary_signature">
246
-
247
- <a href="#nucleotide_rf-instance_method" title="#nucleotide_rf (instance method)">- (Object) <strong>nucleotide_rf</strong> </a>
248
-
249
-
250
-
251
- </span>
252
-
253
-
254
-
255
-
256
-
257
-
258
-
259
-
260
-
261
-
262
-
263
-
264
- <span class="summary_desc"><div class='inline'>
265
- <p>used only for nucleotides.</p>
266
- </div></span>
267
-
268
- </li>
269
-
270
-
271
- <li class="public ">
272
- <span class="summary_signature">
273
-
274
- <a href="#protein_translation-instance_method" title="#protein_translation (instance method)">- (Object) <strong>protein_translation</strong> </a>
275
-
276
-
277
-
278
- </span>
279
-
280
-
281
-
282
-
283
-
284
-
285
-
286
-
287
-
288
-
289
-
290
-
291
- <span class="summary_desc"><div class='inline'>
292
- <p>used only for nucleotides.</p>
293
- </div></span>
294
-
295
- </li>
296
-
297
-
298
- <li class="public ">
299
- <span class="summary_signature">
300
-
301
- <a href="#raw_sequence-instance_method" title="#raw_sequence (instance method)">- (Object) <strong>raw_sequence</strong> </a>
302
-
303
-
304
-
305
- </span>
306
-
307
-
308
-
309
-
310
-
311
-
312
-
313
-
314
-
315
-
316
-
317
-
318
- <span class="summary_desc"><div class='inline'>
319
- <p>Returns the value of attribute raw_sequence.</p>
320
- </div></span>
321
-
322
- </li>
323
-
324
-
325
- <li class="public ">
326
- <span class="summary_signature">
327
-
328
- <a href="#reading_frame-instance_method" title="#reading_frame (instance method)">- (Object) <strong>reading_frame</strong> </a>
329
-
330
-
331
-
332
- </span>
333
-
334
-
335
-
336
-
337
-
338
-
339
-
340
-
341
-
342
-
343
-
344
-
345
- <span class="summary_desc"><div class='inline'>
346
- <p>Returns the value of attribute reading_frame.</p>
347
- </div></span>
348
-
349
- </li>
350
-
351
-
352
- <li class="public ">
353
- <span class="summary_signature">
354
-
355
- <a href="#species-instance_method" title="#species (instance method)">- (Object) <strong>species</strong> </a>
356
-
357
-
358
-
359
- </span>
360
-
361
-
362
-
363
-
364
-
365
-
366
-
367
-
368
-
369
-
370
-
371
-
372
- <span class="summary_desc"><div class='inline'>
373
- <p>Returns the value of attribute species.</p>
374
- </div></span>
375
-
376
- </li>
377
-
378
-
379
- <li class="public ">
380
- <span class="summary_signature">
381
-
382
- <a href="#type-instance_method" title="#type (instance method)">- (Object) <strong>type</strong> </a>
383
-
384
-
385
-
386
- </span>
387
-
388
-
389
-
390
-
391
-
392
-
393
-
394
-
395
-
396
-
397
-
398
-
399
- <span class="summary_desc"><div class='inline'>
400
- <p>protein | mRNA.</p>
401
- </div></span>
402
-
403
- </li>
404
-
405
-
406
- </ul>
407
-
408
-
409
-
410
-
411
-
412
- <h2>
413
- Instance Method Summary
414
- <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
415
- </h2>
416
-
417
- <ul class="summary">
418
-
419
- <li class="public ">
420
- <span class="summary_signature">
421
-
422
- <a href="#get_sequence_by_accession_no-instance_method" title="#get_sequence_by_accession_no (instance method)">- (Object) <strong>get_sequence_by_accession_no</strong>(accno, db) </a>
423
-
424
-
425
-
426
- </span>
427
-
428
-
429
-
430
-
431
-
432
-
433
-
434
-
435
-
436
- <span class="summary_desc"><div class='inline'>
437
- <p>Gets raw sequence by accession number from a givem database Params:
438
- <tt>accno</tt>: accession number as String <tt>db</tt>: database as String
439
- Output: String with the nucleotide sequence corresponding to the accno.</p>
440
- </div></span>
441
-
442
- </li>
443
-
444
-
445
- <li class="public ">
446
- <span class="summary_signature">
447
-
448
- <a href="#get_sequence_from_index_file-instance_method" title="#get_sequence_from_index_file (instance method)">- (Object) <strong>get_sequence_from_index_file</strong>(index_file_name, identifier) </a>
449
-
450
-
451
-
452
- </span>
453
-
454
-
455
-
456
-
457
-
458
-
459
-
460
-
461
-
462
- <span class="summary_desc"><div class='inline'>
463
- <p>Gets raw sequence by fasta identifier from a fasta index file Params:
464
- <tt>index_file_name</tt>: name of the fasta index file <tt>identifier</tt>:
465
- String Output: String with the nucleotide sequence corresponding to the
466
- identifier.</p>
467
- </div></span>
468
-
469
- </li>
470
-
471
-
472
- <li class="public ">
473
- <span class="summary_signature">
474
-
475
- <a href="#init_tabular_attribute-instance_method" title="#init_tabular_attribute (instance method)">- (Object) <strong>init_tabular_attribute</strong>(column, value) </a>
476
-
477
-
478
-
479
- </span>
480
-
481
-
482
-
483
-
484
-
485
-
486
-
487
-
488
-
489
- <span class="summary_desc"><div class='inline'>
490
- <p>Initializes the corresponding attribute of the sequence with respect to the
491
- column name of the tabular blast output.</p>
492
- </div></span>
493
-
494
- </li>
495
-
496
-
497
- <li class="public ">
498
- <span class="summary_signature">
499
-
500
- <a href="#initialize-instance_method" title="#initialize (instance method)">- (Sequence) <strong>initialize</strong> </a>
501
-
502
-
503
-
504
- </span>
505
-
506
-
507
- <span class="note title constructor">constructor</span>
508
-
509
-
510
-
511
-
512
-
513
-
514
-
515
-
516
- <span class="summary_desc"><div class='inline'>
517
- <p>A new instance of Sequence.</p>
518
- </div></span>
519
-
520
- </li>
521
-
522
-
523
- </ul>
524
-
525
-
526
- <div id="constructor_details" class="method_details_list">
527
- <h2>Constructor Details</h2>
528
-
529
- <div class="method_details first">
530
- <h3 class="signature first" id="initialize-instance_method">
531
-
532
- - (<tt><span class='object_link'><a href="" title="Sequence (class)">Sequence</a></span></tt>) <strong>initialize</strong>
533
-
534
-
535
-
536
-
537
-
538
- </h3><div class="docstring">
539
- <div class="discussion">
540
-
541
- <p>Returns a new instance of Sequence</p>
542
-
543
-
544
- </div>
545
- </div>
546
- <div class="tags">
547
-
548
-
549
- </div><table class="source_code">
550
- <tr>
551
- <td>
552
- <pre class="lines">
553
-
554
-
555
- 18
556
- 19
557
- 20
558
- 21
559
- 22
560
- 23</pre>
561
- </td>
562
- <td>
563
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 18</span>
564
-
565
- <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span>
566
- <span class='ivar'>@hsp_list</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
567
- <span class='ivar'>@raw_sequence</span> <span class='op'>=</span> <span class='kw'>nil</span>
568
- <span class='ivar'>@protein_translation</span> <span class='op'>=</span> <span class='kw'>nil</span>
569
- <span class='ivar'>@nucleotide_rf</span> <span class='op'>=</span> <span class='kw'>nil</span>
570
- <span class='kw'>end</span></pre>
571
- </td>
572
- </tr>
573
- </table>
574
- </div>
575
-
576
- </div>
577
-
578
- <div id="instance_attr_details" class="attr_details">
579
- <h2>Instance Attribute Details</h2>
580
-
581
-
582
- <span id="accession_no=-instance_method"></span>
583
- <div class="method_details first">
584
- <h3 class="signature first" id="accession_no-instance_method">
585
-
586
- - (<tt>Object</tt>) <strong>accession_no</strong>
587
-
588
-
589
-
590
-
591
-
592
- </h3><div class="docstring">
593
- <div class="discussion">
594
-
595
- <p>Returns the value of attribute accession_no</p>
596
-
597
-
598
- </div>
599
- </div>
600
- <div class="tags">
601
-
602
-
603
- </div><table class="source_code">
604
- <tr>
605
- <td>
606
- <pre class="lines">
607
-
608
-
609
- 9
610
- 10
611
- 11</pre>
612
- </td>
613
- <td>
614
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 9</span>
615
-
616
- <span class='kw'>def</span> <span class='id identifier rubyid_accession_no'>accession_no</span>
617
- <span class='ivar'>@accession_no</span>
618
- <span class='kw'>end</span></pre>
619
- </td>
620
- </tr>
621
- </table>
622
- </div>
623
-
624
-
625
- <span id="definition=-instance_method"></span>
626
- <div class="method_details ">
627
- <h3 class="signature " id="definition-instance_method">
628
-
629
- - (<tt>Object</tt>) <strong>definition</strong>
630
-
631
-
632
-
633
-
634
-
635
- </h3><div class="docstring">
636
- <div class="discussion">
637
-
638
- <p>Returns the value of attribute definition</p>
639
-
640
-
641
- </div>
642
- </div>
643
- <div class="tags">
644
-
645
-
646
- </div><table class="source_code">
647
- <tr>
648
- <td>
649
- <pre class="lines">
650
-
651
-
652
- 6
653
- 7
654
- 8</pre>
655
- </td>
656
- <td>
657
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 6</span>
658
-
659
- <span class='kw'>def</span> <span class='id identifier rubyid_definition'>definition</span>
660
- <span class='ivar'>@definition</span>
661
- <span class='kw'>end</span></pre>
662
- </td>
663
- </tr>
664
- </table>
665
- </div>
666
-
667
-
668
- <span id="hsp_list=-instance_method"></span>
669
- <div class="method_details ">
670
- <h3 class="signature " id="hsp_list-instance_method">
671
-
672
- - (<tt>Object</tt>) <strong>hsp_list</strong>
673
-
674
-
675
-
676
-
677
-
678
- </h3><div class="docstring">
679
- <div class="discussion">
680
-
681
- <p>array of Hsp objects</p>
682
-
683
-
684
- </div>
685
- </div>
686
- <div class="tags">
687
-
688
-
689
- </div><table class="source_code">
690
- <tr>
691
- <td>
692
- <pre class="lines">
693
-
694
-
695
- 12
696
- 13
697
- 14</pre>
698
- </td>
699
- <td>
700
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 12</span>
701
-
702
- <span class='kw'>def</span> <span class='id identifier rubyid_hsp_list'>hsp_list</span>
703
- <span class='ivar'>@hsp_list</span>
704
- <span class='kw'>end</span></pre>
705
- </td>
706
- </tr>
707
- </table>
708
- </div>
709
-
710
-
711
- <span id="identifier=-instance_method"></span>
712
- <div class="method_details ">
713
- <h3 class="signature " id="identifier-instance_method">
714
-
715
- - (<tt>Object</tt>) <strong>identifier</strong>
716
-
717
-
718
-
719
-
720
-
721
- </h3><div class="docstring">
722
- <div class="discussion">
723
-
724
- <p>Returns the value of attribute identifier</p>
725
-
726
-
727
- </div>
728
- </div>
729
- <div class="tags">
730
-
731
-
732
- </div><table class="source_code">
733
- <tr>
734
- <td>
735
- <pre class="lines">
736
-
737
-
738
- 7
739
- 8
740
- 9</pre>
741
- </td>
742
- <td>
743
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 7</span>
744
-
745
- <span class='kw'>def</span> <span class='id identifier rubyid_identifier'>identifier</span>
746
- <span class='ivar'>@identifier</span>
747
- <span class='kw'>end</span></pre>
748
- </td>
749
- </tr>
750
- </table>
751
- </div>
752
-
753
-
754
- <span id="length_protein=-instance_method"></span>
755
- <div class="method_details ">
756
- <h3 class="signature " id="length_protein-instance_method">
757
-
758
- - (<tt>Object</tt>) <strong>length_protein</strong>
759
-
760
-
761
-
762
-
763
-
764
- </h3><div class="docstring">
765
- <div class="discussion">
766
-
767
- <p>Returns the value of attribute length_protein</p>
768
-
769
-
770
- </div>
771
- </div>
772
- <div class="tags">
773
-
774
-
775
- </div><table class="source_code">
776
- <tr>
777
- <td>
778
- <pre class="lines">
779
-
780
-
781
- 10
782
- 11
783
- 12</pre>
784
- </td>
785
- <td>
786
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 10</span>
787
-
788
- <span class='kw'>def</span> <span class='id identifier rubyid_length_protein'>length_protein</span>
789
- <span class='ivar'>@length_protein</span>
790
- <span class='kw'>end</span></pre>
791
- </td>
792
- </tr>
793
- </table>
794
- </div>
795
-
796
-
797
- <span id="nucleotide_rf=-instance_method"></span>
798
- <div class="method_details ">
799
- <h3 class="signature " id="nucleotide_rf-instance_method">
800
-
801
- - (<tt>Object</tt>) <strong>nucleotide_rf</strong>
802
-
803
-
804
-
805
-
806
-
807
- </h3><div class="docstring">
808
- <div class="discussion">
809
-
810
- <p>used only for nucleotides</p>
811
-
812
-
813
- </div>
814
- </div>
815
- <div class="tags">
816
-
817
-
818
- </div><table class="source_code">
819
- <tr>
820
- <td>
821
- <pre class="lines">
822
-
823
-
824
- 16
825
- 17
826
- 18</pre>
827
- </td>
828
- <td>
829
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 16</span>
830
-
831
- <span class='kw'>def</span> <span class='id identifier rubyid_nucleotide_rf'>nucleotide_rf</span>
832
- <span class='ivar'>@nucleotide_rf</span>
833
- <span class='kw'>end</span></pre>
834
- </td>
835
- </tr>
836
- </table>
837
- </div>
838
-
839
-
840
- <span id="protein_translation=-instance_method"></span>
841
- <div class="method_details ">
842
- <h3 class="signature " id="protein_translation-instance_method">
843
-
844
- - (<tt>Object</tt>) <strong>protein_translation</strong>
845
-
846
-
847
-
848
-
849
-
850
- </h3><div class="docstring">
851
- <div class="discussion">
852
-
853
- <p>used only for nucleotides</p>
854
-
855
-
856
- </div>
857
- </div>
858
- <div class="tags">
859
-
860
-
861
- </div><table class="source_code">
862
- <tr>
863
- <td>
864
- <pre class="lines">
865
-
866
-
867
- 15
868
- 16
869
- 17</pre>
870
- </td>
871
- <td>
872
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 15</span>
873
-
874
- <span class='kw'>def</span> <span class='id identifier rubyid_protein_translation'>protein_translation</span>
875
- <span class='ivar'>@protein_translation</span>
876
- <span class='kw'>end</span></pre>
877
- </td>
878
- </tr>
879
- </table>
880
- </div>
881
-
882
-
883
- <span id="raw_sequence=-instance_method"></span>
884
- <div class="method_details ">
885
- <h3 class="signature " id="raw_sequence-instance_method">
886
-
887
- - (<tt>Object</tt>) <strong>raw_sequence</strong>
888
-
889
-
890
-
891
-
892
-
893
- </h3><div class="docstring">
894
- <div class="discussion">
895
-
896
- <p>Returns the value of attribute raw_sequence</p>
897
-
898
-
899
- </div>
900
- </div>
901
- <div class="tags">
902
-
903
-
904
- </div><table class="source_code">
905
- <tr>
906
- <td>
907
- <pre class="lines">
908
-
909
-
910
- 14
911
- 15
912
- 16</pre>
913
- </td>
914
- <td>
915
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 14</span>
916
-
917
- <span class='kw'>def</span> <span class='id identifier rubyid_raw_sequence'>raw_sequence</span>
918
- <span class='ivar'>@raw_sequence</span>
919
- <span class='kw'>end</span></pre>
920
- </td>
921
- </tr>
922
- </table>
923
- </div>
924
-
925
-
926
- <span id="reading_frame=-instance_method"></span>
927
- <div class="method_details ">
928
- <h3 class="signature " id="reading_frame-instance_method">
929
-
930
- - (<tt>Object</tt>) <strong>reading_frame</strong>
931
-
932
-
933
-
934
-
935
-
936
- </h3><div class="docstring">
937
- <div class="discussion">
938
-
939
- <p>Returns the value of attribute reading_frame</p>
940
-
941
-
942
- </div>
943
- </div>
944
- <div class="tags">
945
-
946
-
947
- </div><table class="source_code">
948
- <tr>
949
- <td>
950
- <pre class="lines">
951
-
952
-
953
- 11
954
- 12
955
- 13</pre>
956
- </td>
957
- <td>
958
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 11</span>
959
-
960
- <span class='kw'>def</span> <span class='id identifier rubyid_reading_frame'>reading_frame</span>
961
- <span class='ivar'>@reading_frame</span>
962
- <span class='kw'>end</span></pre>
963
- </td>
964
- </tr>
965
- </table>
966
- </div>
967
-
968
-
969
- <span id="species=-instance_method"></span>
970
- <div class="method_details ">
971
- <h3 class="signature " id="species-instance_method">
972
-
973
- - (<tt>Object</tt>) <strong>species</strong>
974
-
975
-
976
-
977
-
978
-
979
- </h3><div class="docstring">
980
- <div class="discussion">
981
-
982
- <p>Returns the value of attribute species</p>
983
-
984
-
985
- </div>
986
- </div>
987
- <div class="tags">
988
-
989
-
990
- </div><table class="source_code">
991
- <tr>
992
- <td>
993
- <pre class="lines">
994
-
995
-
996
- 8
997
- 9
998
- 10</pre>
999
- </td>
1000
- <td>
1001
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 8</span>
1002
-
1003
- <span class='kw'>def</span> <span class='id identifier rubyid_species'>species</span>
1004
- <span class='ivar'>@species</span>
1005
- <span class='kw'>end</span></pre>
1006
- </td>
1007
- </tr>
1008
- </table>
1009
- </div>
1010
-
1011
-
1012
- <span id="type=-instance_method"></span>
1013
- <div class="method_details ">
1014
- <h3 class="signature " id="type-instance_method">
1015
-
1016
- - (<tt>Object</tt>) <strong>type</strong>
1017
-
1018
-
1019
-
1020
-
1021
-
1022
- </h3><div class="docstring">
1023
- <div class="discussion">
1024
-
1025
- <p>protein | mRNA</p>
1026
-
1027
-
1028
- </div>
1029
- </div>
1030
- <div class="tags">
1031
-
1032
-
1033
- </div><table class="source_code">
1034
- <tr>
1035
- <td>
1036
- <pre class="lines">
1037
-
1038
-
1039
- 5
1040
- 6
1041
- 7</pre>
1042
- </td>
1043
- <td>
1044
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 5</span>
1045
-
1046
- <span class='kw'>def</span> <span class='id identifier rubyid_type'>type</span>
1047
- <span class='ivar'>@type</span>
1048
- <span class='kw'>end</span></pre>
1049
- </td>
1050
- </tr>
1051
- </table>
1052
- </div>
1053
-
1054
- </div>
1055
-
1056
-
1057
- <div id="instance_method_details" class="method_details_list">
1058
- <h2>Instance Method Details</h2>
1059
-
1060
-
1061
- <div class="method_details first">
1062
- <h3 class="signature first" id="get_sequence_by_accession_no-instance_method">
1063
-
1064
- - (<tt>Object</tt>) <strong>get_sequence_by_accession_no</strong>(accno, db)
1065
-
1066
-
1067
-
1068
-
1069
-
1070
- </h3><div class="docstring">
1071
- <div class="discussion">
1072
-
1073
- <p>Gets raw sequence by accession number from a givem database Params:
1074
- <tt>accno</tt>: accession number as String <tt>db</tt>: database as String
1075
- Output: String with the nucleotide sequence corresponding to the accno</p>
1076
-
1077
-
1078
- </div>
1079
- </div>
1080
- <div class="tags">
1081
-
1082
-
1083
- </div><table class="source_code">
1084
- <tr>
1085
- <td>
1086
- <pre class="lines">
1087
-
1088
-
1089
- 67
1090
- 68
1091
- 69
1092
- 70
1093
- 71
1094
- 72
1095
- 73
1096
- 74
1097
- 75
1098
- 76
1099
- 77
1100
- 78
1101
- 79
1102
- 80
1103
- 81
1104
- 82
1105
- 83
1106
- 84
1107
- 85
1108
- 86
1109
- 87
1110
- 88
1111
- 89
1112
- 90
1113
- 91</pre>
1114
- </td>
1115
- <td>
1116
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 67</span>
1117
-
1118
- <span class='kw'>def</span> <span class='id identifier rubyid_get_sequence_by_accession_no'>get_sequence_by_accession_no</span><span class='lparen'>(</span><span class='id identifier rubyid_accno'>accno</span><span class='comma'>,</span> <span class='id identifier rubyid_db'>db</span><span class='rparen'>)</span>
1119
-
1120
- <span class='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
1121
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>&amp;retmax=1&amp;usehistory=y&amp;term=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_accno'>accno</span><span class='rbrace'>}</span><span class='tstring_content'>/</span><span class='tstring_end'>&quot;</span></span>
1122
- <span class='id identifier rubyid_result'>result</span> <span class='op'>=</span> <span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span><span class='lparen'>(</span><span class='const'>URI</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='rparen'>)</span><span class='rparen'>)</span>
1123
-
1124
- <span class='id identifier rubyid_result2'>result2</span> <span class='op'>=</span> <span class='id identifier rubyid_result'>result</span>
1125
- <span class='id identifier rubyid_queryKey'>queryKey</span> <span class='op'>=</span> <span class='id identifier rubyid_result2'>result2</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>&lt;\bQueryKey\b&gt;([\w\W\d]+)&lt;\/\bQueryKey\b&gt;</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
1126
- <span class='id identifier rubyid_webEnv'>webEnv</span> <span class='op'>=</span> <span class='id identifier rubyid_result'>result</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>&lt;\bWebEnv\b&gt;([\w\W\d]+)&lt;\/\bWebEnv\b&gt;</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
1127
-
1128
- <span class='id identifier rubyid_uri'>uri</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
1129
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>retmode=text&amp;retstart=0&amp;retmax=1&amp;db=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'>&amp;query_key=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_queryKey'>queryKey</span><span class='rbrace'>}</span><span class='tstring_content'>&amp;WebEnv=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_webEnv'>webEnv</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
1130
- <span class='id identifier rubyid_result'>result</span> <span class='op'>=</span> <span class='const'>Net</span><span class='op'>::</span><span class='const'>HTTP</span><span class='period'>.</span><span class='id identifier rubyid_get'>get</span><span class='lparen'>(</span><span class='const'>URI</span><span class='period'>.</span><span class='id identifier rubyid_parse'>parse</span><span class='lparen'>(</span><span class='id identifier rubyid_uri'>uri</span><span class='rparen'>)</span><span class='rparen'>)</span>
1131
-
1132
- <span class='comment'>#parse FASTA output
1133
- </span> <span class='id identifier rubyid_rec'>rec</span><span class='op'>=</span><span class='id identifier rubyid_result'>result</span>
1134
- <span class='id identifier rubyid_nl'>nl</span> <span class='op'>=</span> <span class='id identifier rubyid_rec'>rec</span><span class='period'>.</span><span class='id identifier rubyid_index'>index</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1135
- <span class='id identifier rubyid_header'>header</span> <span class='op'>=</span> <span class='id identifier rubyid_rec'>rec</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_nl'>nl</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
1136
- <span class='id identifier rubyid_seq'>seq</span> <span class='op'>=</span> <span class='id identifier rubyid_rec'>rec</span><span class='lbracket'>[</span><span class='id identifier rubyid_nl'>nl</span><span class='op'>+</span><span class='int'>1</span><span class='op'>..</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span>
1137
- <span class='ivar'>@raw_sequence</span> <span class='op'>=</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_gsub!'>gsub!</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\n</span><span class='regexp_end'>/</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span>
1138
- <span class='kw'>unless</span> <span class='ivar'>@raw_sequence</span><span class='period'>.</span><span class='id identifier rubyid_index'>index</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>ERROR</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span> <span class='op'>==</span> <span class='kw'>nil</span>
1139
- <span class='ivar'>@raw_sequence</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
1140
- <span class='kw'>end</span>
1141
- <span class='ivar'>@raw_sequence</span>
1142
- <span class='kw'>end</span></pre>
1143
- </td>
1144
- </tr>
1145
- </table>
1146
- </div>
1147
-
1148
- <div class="method_details ">
1149
- <h3 class="signature " id="get_sequence_from_index_file-instance_method">
1150
-
1151
- - (<tt>Object</tt>) <strong>get_sequence_from_index_file</strong>(index_file_name, identifier)
1152
-
1153
-
1154
-
1155
-
1156
-
1157
- </h3><div class="docstring">
1158
- <div class="discussion">
1159
-
1160
- <p>Gets raw sequence by fasta identifier from a fasta index file Params:
1161
- <tt>index_file_name</tt>: name of the fasta index file <tt>identifier</tt>:
1162
- String Output: String with the nucleotide sequence corresponding to the
1163
- identifier</p>
1164
-
1165
-
1166
- </div>
1167
- </div>
1168
- <div class="tags">
1169
-
1170
-
1171
- </div><table class="source_code">
1172
- <tr>
1173
- <td>
1174
- <pre class="lines">
1175
-
1176
-
1177
- 40
1178
- 41
1179
- 42
1180
- 43
1181
- 44
1182
- 45
1183
- 46
1184
- 47
1185
- 48
1186
- 49
1187
- 50
1188
- 51
1189
- 52
1190
- 53
1191
- 54
1192
- 55
1193
- 56
1194
- 57
1195
- 58</pre>
1196
- </td>
1197
- <td>
1198
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 40</span>
1199
-
1200
- <span class='kw'>def</span> <span class='id identifier rubyid_get_sequence_from_index_file'>get_sequence_from_index_file</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file_name'>index_file_name</span><span class='comma'>,</span> <span class='id identifier rubyid_identifier'>identifier</span><span class='rparen'>)</span>
1201
- <span class='kw'>begin</span>
1202
- <span class='id identifier rubyid_index'>index</span> <span class='op'>=</span> <span class='const'>Bio</span><span class='op'>::</span><span class='const'>FlatFileIndex</span><span class='op'>::</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file_name'>index_file_name</span><span class='rparen'>)</span>
1203
-
1204
- <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_identifier'>identifier</span>
1205
-
1206
- <span class='id identifier rubyid_results'>results</span> <span class='op'>=</span> <span class='id identifier rubyid_index'>index</span><span class='period'>.</span><span class='id identifier rubyid_search'>search</span><span class='lparen'>(</span><span class='id identifier rubyid_identifier'>identifier</span><span class='rparen'>)</span>
1207
- <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Results: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_results'>results</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
1208
- <span class='id identifier rubyid_results'>results</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_str'>str</span><span class='op'>|</span>
1209
- <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_str'>str</span>
1210
- <span class='kw'>end</span>
1211
- <span class='id identifier rubyid_index'>index</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
1212
-
1213
- <span class='comment'>#fasta_sequence = index.get_by_id(identifier) # returned as fasta string
1214
- </span> <span class='comment'>#return fasta_sequence
1215
- </span> <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
1216
- <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>.</span><span class='tstring_end'>&quot;</span></span>
1217
- <span class='kw'>end</span>
1218
- <span class='kw'>end</span></pre>
1219
- </td>
1220
- </tr>
1221
- </table>
1222
- </div>
1223
-
1224
- <div class="method_details ">
1225
- <h3 class="signature " id="init_tabular_attribute-instance_method">
1226
-
1227
- - (<tt>Object</tt>) <strong>init_tabular_attribute</strong>(column, value)
1228
-
1229
-
1230
-
1231
-
1232
-
1233
- </h3><div class="docstring">
1234
- <div class="discussion">
1235
-
1236
- <p>Initializes the corresponding attribute of the sequence with respect to the
1237
- column name of the tabular blast output</p>
1238
-
1239
-
1240
- </div>
1241
- </div>
1242
- <div class="tags">
1243
-
1244
-
1245
- </div><table class="source_code">
1246
- <tr>
1247
- <td>
1248
- <pre class="lines">
1249
-
1250
-
1251
- 96
1252
- 97
1253
- 98
1254
- 99
1255
- 100
1256
- 101
1257
- 102
1258
- 103
1259
- 104
1260
- 105
1261
- 106
1262
- 107
1263
- 108
1264
- 109</pre>
1265
- </td>
1266
- <td>
1267
- <pre class="code"><span class="info file"># File 'lib/genevalidator/sequences.rb', line 96</span>
1268
-
1269
- <span class='kw'>def</span> <span class='id identifier rubyid_init_tabular_attribute'>init_tabular_attribute</span><span class='lparen'>(</span><span class='id identifier rubyid_column'>column</span><span class='comma'>,</span> <span class='id identifier rubyid_value'>value</span><span class='rparen'>)</span>
1270
- <span class='kw'>case</span> <span class='id identifier rubyid_column'>column</span>
1271
- <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sseqid</span><span class='tstring_end'>&quot;</span></span>
1272
- <span class='comment'>#@definition = value
1273
- </span> <span class='ivar'>@identifier</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span>
1274
- <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>qseqid</span><span class='tstring_end'>&quot;</span></span>
1275
- <span class='comment'>#@definition = value
1276
- </span> <span class='ivar'>@identifier</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span>
1277
- <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sacc</span><span class='tstring_end'>&quot;</span></span>
1278
- <span class='ivar'>@accession_no</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span>
1279
- <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>slen</span><span class='tstring_end'>&quot;</span></span>
1280
- <span class='ivar'>@length_protein</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
1281
- <span class='kw'>end</span>
1282
- <span class='kw'>end</span></pre>
1283
- </td>
1284
- </tr>
1285
- </table>
1286
- </div>
1287
-
1288
- </div>
1289
-
1290
- </div>
1291
-
1292
- <div id="footer">
1293
- Generated on Sat Sep 28 07:01:32 2013 by
1294
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
1295
- 0.8.7.2 (ruby-1.9.3).
1296
- </div>
1297
-
1298
- </body>
1299
- </html>