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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- Generated on Sat Sep 28 07:01:32 2013 by
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- <a href="#inside_cluster-instance_method" title="#inside_cluster (instance method)">- (Object) <strong>inside_cluster</strong>(value) </a>
317
-
318
-
319
-
320
- </span>
321
-
322
-
323
-
324
-
325
-
326
-
327
-
328
-
329
-
330
- <span class="summary_desc"><div class='inline'>
331
- <p>Returns whether the value is inside the cluster Params: <tt>value</tt>:
332
- value to compare Output: :ok or :shorter or :longer.</p>
333
- </div></span>
334
-
335
- </li>
336
-
337
-
338
- <li class="public ">
339
- <span class="summary_signature">
340
-
341
- <a href="#mean-instance_method" title="#mean (instance method)">- (Object) <strong>mean</strong> </a>
342
-
343
-
344
-
345
- </span>
346
-
347
-
348
-
349
-
350
-
351
-
352
-
353
-
354
-
355
- <span class="summary_desc"><div class='inline'>
356
- <p>Returns the weighted mean value of the cluster.</p>
357
- </div></span>
358
-
359
- </li>
360
-
361
-
362
- <li class="public ">
363
- <span class="summary_signature">
364
-
365
- <a href="#print-instance_method" title="#print (instance method)">- (Object) <strong>print</strong> </a>
366
-
367
-
368
-
369
- </span>
370
-
371
-
372
-
373
-
374
-
375
-
376
-
377
-
378
-
379
- <span class="summary_desc"><div class='inline'>
380
- <p>Prints the current cluster.</p>
381
- </div></span>
382
-
383
- </li>
384
-
385
-
386
- <li class="public ">
387
- <span class="summary_signature">
388
-
389
- <a href="#standard_deviation-instance_method" title="#standard_deviation (instance method)">- (Object) <strong>standard_deviation</strong>(lengths = nil) </a>
390
-
391
-
392
-
393
- </span>
394
-
395
-
396
-
397
-
398
-
399
-
400
-
401
-
402
-
403
- <span class="summary_desc"><div class='inline'>
404
- <p>Returns the standard deviation of a set of values Params: <tt>lengths</tt>:
405
- a vector of values (optional, by default it takes the values in the
406
- cluster).</p>
407
- </div></span>
408
-
409
- </li>
410
-
411
-
412
- <li class="public ">
413
- <span class="summary_signature">
414
-
415
- <a href="#t_test-instance_method" title="#t_test (instance method)">- (Object) <strong>t_test</strong>(clusters, queryLength) </a>
416
-
417
-
418
-
419
- </span>
420
-
421
-
422
-
423
-
424
-
425
-
426
-
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-
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-
429
- <span class="summary_desc"><div class='inline'>
430
- <p>Returns the p-value of a t-test <tt>clusters</tt>: a list of Cluster
431
- objects <tt>querylength</tt>: a reference Sequence object.</p>
432
- </div></span>
433
-
434
- </li>
435
-
436
-
437
- <li class="public ">
438
- <span class="summary_signature">
439
-
440
- <a href="#wilcox_test-instance_method" title="#wilcox_test (instance method)">- (Object) <strong>wilcox_test</strong>(clusters, queryLength) </a>
441
-
442
-
443
-
444
- </span>
445
-
446
-
447
-
448
-
449
-
450
-
451
-
452
-
453
-
454
- <span class="summary_desc"><div class='inline'>
455
- <p>Returns the p-value of a wilcox test <tt>clusters</tt>: a list of Cluster
456
- objects <tt>querylength</tt>: a reference Sequence object.</p>
457
- </div></span>
458
-
459
- </li>
460
-
461
-
462
- <li class="public ">
463
- <span class="summary_signature">
464
-
465
- <a href="#wss-instance_method" title="#wss (instance method)">- (Object) <strong>wss</strong>(lengths = nil) </a>
466
-
467
-
468
-
469
- </span>
470
-
471
-
472
-
473
-
474
-
475
-
476
-
477
-
478
-
479
- <span class="summary_desc"><div class='inline'>
480
- <p>Returns within cluster sum of squares.</p>
481
- </div></span>
482
-
483
- </li>
484
-
485
-
486
- </ul>
487
-
488
-
489
- <div id="constructor_details" class="method_details_list">
490
- <h2>Constructor Details</h2>
491
-
492
- <div class="method_details first">
493
- <h3 class="signature first" id="initialize-instance_method">
494
-
495
- - (<tt><span class='object_link'><a href="" title="Cluster (class)">Cluster</a></span></tt>) <strong>initialize</strong>(lengths)
496
-
497
-
498
-
499
-
500
-
501
- </h3><div class="docstring">
502
- <div class="discussion">
503
-
504
- <p>Returns a new instance of Cluster</p>
505
-
506
-
507
- </div>
508
- </div>
509
- <div class="tags">
510
-
511
-
512
- </div><table class="source_code">
513
- <tr>
514
- <td>
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- <pre class="lines">
516
-
517
-
518
- 170
519
- 171
520
- 172</pre>
521
- </td>
522
- <td>
523
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 170</span>
524
-
525
- <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_lengths'>lengths</span><span class='rparen'>)</span>
526
- <span class='ivar'>@lengths</span> <span class='op'>=</span> <span class='id identifier rubyid_lengths'>lengths</span>
527
- <span class='kw'>end</span></pre>
528
- </td>
529
- </tr>
530
- </table>
531
- </div>
532
-
533
- </div>
534
-
535
- <div id="instance_attr_details" class="attr_details">
536
- <h2>Instance Attribute Details</h2>
537
-
538
-
539
- <span id="lengths=-instance_method"></span>
540
- <div class="method_details first">
541
- <h3 class="signature first" id="lengths-instance_method">
542
-
543
- - (<tt>Object</tt>) <strong>lengths</strong>
544
-
545
-
546
-
547
-
548
-
549
- </h3><div class="docstring">
550
- <div class="discussion">
551
-
552
- <p>a hash map containing the pair (length, no_occurences)</p>
553
-
554
-
555
- </div>
556
- </div>
557
- <div class="tags">
558
-
559
-
560
- </div><table class="source_code">
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- <tr>
562
- <td>
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- <pre class="lines">
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-
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-
566
- 168
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- 169
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- 170</pre>
569
- </td>
570
- <td>
571
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 168</span>
572
-
573
- <span class='kw'>def</span> <span class='id identifier rubyid_lengths'>lengths</span>
574
- <span class='ivar'>@lengths</span>
575
- <span class='kw'>end</span></pre>
576
- </td>
577
- </tr>
578
- </table>
579
- </div>
580
-
581
- </div>
582
-
583
-
584
- <div id="instance_method_details" class="method_details_list">
585
- <h2>Instance Method Details</h2>
586
-
587
-
588
- <div class="method_details first">
589
- <h3 class="signature first" id="add-instance_method">
590
-
591
- - (<tt>Object</tt>) <strong>add</strong>(cluster)
592
-
593
-
594
-
595
-
596
-
597
- </h3><div class="docstring">
598
- <div class="discussion">
599
-
600
- <p>Merges the current cluster with the one given as parameter
601
- <tt>clusters</tt> vector of Cluster objects</p>
602
-
603
-
604
- </div>
605
- </div>
606
- <div class="tags">
607
-
608
-
609
- </div><table class="source_code">
610
- <tr>
611
- <td>
612
- <pre class="lines">
613
-
614
-
615
- 325
616
- 326
617
- 327
618
- 328
619
- 329</pre>
620
- </td>
621
- <td>
622
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 325</span>
623
-
624
- <span class='kw'>def</span> <span class='id identifier rubyid_add'>add</span><span class='lparen'>(</span><span class='id identifier rubyid_cluster'>cluster</span><span class='rparen'>)</span>
625
- <span class='id identifier rubyid_cluster'>cluster</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</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_elem'>elem</span><span class='op'>|</span>
626
- <span class='id identifier rubyid_lengths'>lengths</span><span class='lbracket'>[</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
627
- <span class='kw'>end</span>
628
- <span class='kw'>end</span></pre>
629
- </td>
630
- </tr>
631
- </table>
632
- </div>
633
-
634
- <div class="method_details ">
635
- <h3 class="signature " id="density-instance_method">
636
-
637
- - (<tt>Object</tt>) <strong>density</strong>
638
-
639
-
640
-
641
-
642
-
643
- </h3><div class="docstring">
644
- <div class="discussion">
645
-
646
- <p>Returns the density of the cluster: how many values it contains</p>
647
-
648
-
649
- </div>
650
- </div>
651
- <div class="tags">
652
-
653
-
654
- </div><table class="source_code">
655
- <tr>
656
- <td>
657
- <pre class="lines">
658
-
659
-
660
- 190
661
- 191
662
- 192
663
- 193
664
- 194
665
- 195
666
- 196
667
- 197</pre>
668
- </td>
669
- <td>
670
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 190</span>
671
-
672
- <span class='kw'>def</span> <span class='id identifier rubyid_density'>density</span>
673
- <span class='id identifier rubyid_d'>d</span> <span class='op'>=</span> <span class='int'>0</span>
674
- <span class='id identifier rubyid_lengths'>lengths</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_elem'>elem</span><span class='op'>|</span>
675
- <span class='id identifier rubyid_d'>d</span> <span class='op'>+=</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
676
- <span class='kw'>end</span>
677
- <span class='id identifier rubyid_d'>d</span>
678
-
679
- <span class='kw'>end</span></pre>
680
- </td>
681
- </tr>
682
- </table>
683
- </div>
684
-
685
- <div class="method_details ">
686
- <h3 class="signature " id="deviation-instance_method">
687
-
688
- - (<tt>Object</tt>) <strong>deviation</strong>(clusters, queryLength)
689
-
690
-
691
-
692
-
693
-
694
- </h3><div class="docstring">
695
- <div class="discussion">
696
-
697
- <p>Returns the deviation of a value from the values in all clusters Params:
698
- <tt>clusters</tt>: a list of Cluster objects <tt>queryLength</tt>: a
699
- reference Sequence object</p>
700
-
701
-
702
- </div>
703
- </div>
704
- <div class="tags">
705
-
706
-
707
- </div><table class="source_code">
708
- <tr>
709
- <td>
710
- <pre class="lines">
711
-
712
-
713
- 266
714
- 267
715
- 268
716
- 269
717
- 270
718
- 271
719
- 272
720
- 273
721
- 274</pre>
722
- </td>
723
- <td>
724
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 266</span>
725
-
726
- <span class='kw'>def</span> <span class='id identifier rubyid_deviation'>deviation</span><span class='lparen'>(</span><span class='id identifier rubyid_clusters'>clusters</span><span class='comma'>,</span> <span class='id identifier rubyid_queryLength'>queryLength</span><span class='rparen'>)</span>
727
- <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='id identifier rubyid_clusters'>clusters</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_c'>c</span><span class='op'>|</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
728
- <span class='id identifier rubyid_raw_hits'>raw_hits</span> <span class='op'>=</span> <span class='id identifier rubyid_clusters'>clusters</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_c'>c</span><span class='op'>|</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>[</span><span class='tstring_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><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>]</span><span class='tstring_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>
729
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sd = sd(c(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='rbrace'>}</span><span class='tstring_content'>))</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
730
- <span class='id identifier rubyid_sd'>sd</span> <span class='op'>=</span> <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_pull'>pull</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sd</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
731
- <span class='id identifier rubyid_sd'>sd</span> <span class='op'>=</span> <span class='id identifier rubyid_standard_deviation'>standard_deviation</span><span class='lparen'>(</span><span class='id identifier rubyid_hits'>hits</span><span class='rparen'>)</span>
732
- <span class='lparen'>(</span><span class='id identifier rubyid_queryLength'>queryLength</span> <span class='op'>-</span> <span class='id identifier rubyid_mean'>mean</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_abs'>abs</span> <span class='op'>/</span> <span class='id identifier rubyid_sd'>sd</span>
733
-
734
- <span class='kw'>end</span></pre>
735
- </td>
736
- </tr>
737
- </table>
738
- </div>
739
-
740
- <div class="method_details ">
741
- <h3 class="signature " id="distance-instance_method">
742
-
743
- - (<tt>Object</tt>) <strong>distance</strong>(cluster, method = 0)
744
-
745
-
746
-
747
-
748
-
749
- </h3><div class="docstring">
750
- <div class="discussion">
751
-
752
- <p>Returns the euclidian distance between the current cluster and the one
753
- given as parameter Params: <tt>cluster</tt>: Cluster object
754
- <tt>method</tt>: 0 or 1 method = 0: do not into condseideration duplicate
755
- values method = 1: average linkage clusterization</p>
756
-
757
-
758
- </div>
759
- </div>
760
- <div class="tags">
761
-
762
-
763
- </div><table class="source_code">
764
- <tr>
765
- <td>
766
- <pre class="lines">
767
-
768
-
769
- 205
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- 206
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786
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- 223
788
- 224
789
- 225</pre>
790
- </td>
791
- <td>
792
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 205</span>
793
-
794
- <span class='kw'>def</span> <span class='id identifier rubyid_distance'>distance</span><span class='lparen'>(</span><span class='id identifier rubyid_cluster'>cluster</span><span class='comma'>,</span> <span class='id identifier rubyid_method'>method</span> <span class='op'>=</span> <span class='int'>0</span><span class='rparen'>)</span>
795
- <span class='id identifier rubyid_d'>d</span> <span class='op'>=</span> <span class='int'>0</span>
796
- <span class='id identifier rubyid_norm'>norm</span> <span class='op'>=</span> <span class='int'>0</span>
797
-
798
- <span class='id identifier rubyid_cluster'>cluster</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</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_elem1'>elem1</span><span class='op'>|</span>
799
- <span class='id identifier rubyid_lengths'>lengths</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_elem2'>elem2</span><span class='op'>|</span>
800
- <span class='kw'>if</span> <span class='id identifier rubyid_method'>method</span> <span class='op'>==</span> <span class='int'>1</span>
801
- <span class='id identifier rubyid_d'>d</span> <span class='op'>+=</span> <span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>*</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>*</span> <span class='lparen'>(</span><span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_abs'>abs</span>
802
- <span class='id identifier rubyid_norm'>norm</span> <span class='op'>+=</span> <span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>*</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
803
- <span class='kw'>else</span>
804
- <span class='id identifier rubyid_d'>d</span> <span class='op'>+=</span> <span class='lparen'>(</span><span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_abs'>abs</span>
805
- <span class='id identifier rubyid_norm'>norm</span> <span class='op'>=</span> <span class='id identifier rubyid_cluster'>cluster</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>*</span> <span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
806
- <span class='kw'>end</span>
807
- <span class='kw'>end</span>
808
- <span class='kw'>end</span>
809
-
810
- <span class='comment'>#group average distance
811
- </span> <span class='id identifier rubyid_d'>d</span> <span class='op'>/=</span> <span class='lparen'>(</span><span class='id identifier rubyid_norm'>norm</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
812
- <span class='kw'>return</span> <span class='id identifier rubyid_d'>d</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>4</span><span class='rparen'>)</span>
813
-
814
- <span class='kw'>end</span></pre>
815
- </td>
816
- </tr>
817
- </table>
818
- </div>
819
-
820
- <div class="method_details ">
821
- <h3 class="signature " id="get_limits-instance_method">
822
-
823
- - (<tt>Object</tt>) <strong>get_limits</strong>
824
-
825
-
826
-
827
-
828
-
829
- </h3><div class="docstring">
830
- <div class="discussion">
831
-
832
- <p>Returns the interval limits of the current cluster</p>
833
-
834
-
835
- </div>
836
- </div>
837
- <div class="tags">
838
-
839
-
840
- </div><table class="source_code">
841
- <tr>
842
- <td>
843
- <pre class="lines">
844
-
845
-
846
- 343
847
- 344
848
- 345</pre>
849
- </td>
850
- <td>
851
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 343</span>
852
-
853
- <span class='kw'>def</span> <span class='id identifier rubyid_get_limits'>get_limits</span>
854
- <span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_elem'>elem</span><span class='op'>|</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_minmax'>minmax</span>
855
- <span class='kw'>end</span></pre>
856
- </td>
857
- </tr>
858
- </table>
859
- </div>
860
-
861
- <div class="method_details ">
862
- <h3 class="signature " id="inside_cluster-instance_method">
863
-
864
- - (<tt>Object</tt>) <strong>inside_cluster</strong>(value)
865
-
866
-
867
-
868
-
869
-
870
- </h3><div class="docstring">
871
- <div class="discussion">
872
-
873
- <p>Returns whether the value is inside the cluster Params: <tt>value</tt>:
874
- value to compare Output: :ok or :shorter or :longer</p>
875
-
876
-
877
- </div>
878
- </div>
879
- <div class="tags">
880
-
881
-
882
- </div><table class="source_code">
883
- <tr>
884
- <td>
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- <pre class="lines">
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- 358
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895
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- 363
899
- 364
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- 365
901
- 366
902
- 367
903
- 368
904
- 369</pre>
905
- </td>
906
- <td>
907
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 353</span>
908
-
909
- <span class='kw'>def</span> <span class='id identifier rubyid_inside_cluster'>inside_cluster</span><span class='lparen'>(</span><span class='id identifier rubyid_value'>value</span><span class='rparen'>)</span>
910
- <span class='id identifier rubyid_limits'>limits</span> <span class='op'>=</span> <span class='id identifier rubyid_get_limits'>get_limits</span>
911
- <span class='id identifier rubyid_left'>left</span> <span class='op'>=</span> <span class='id identifier rubyid_limits'>limits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
912
- <span class='id identifier rubyid_right'>right</span> <span class='op'>=</span> <span class='id identifier rubyid_limits'>limits</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
913
-
914
- <span class='kw'>if</span> <span class='id identifier rubyid_left'>left</span> <span class='op'>&lt;=</span> <span class='id identifier rubyid_value'>value</span> <span class='kw'>and</span> <span class='id identifier rubyid_right'>right</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_value'>value</span>
915
- <span class='symbol'>:ok</span>
916
- <span class='kw'>end</span>
917
-
918
- <span class='kw'>if</span> <span class='id identifier rubyid_left'>left</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_value'>value</span>
919
- <span class='symbol'>:shorter</span>
920
- <span class='kw'>end</span>
921
-
922
- <span class='kw'>if</span> <span class='id identifier rubyid_right'>right</span> <span class='op'>&lt;=</span> <span class='id identifier rubyid_value'>value</span>
923
- <span class='symbol'>:longer</span>
924
- <span class='kw'>end</span>
925
- <span class='kw'>end</span></pre>
926
- </td>
927
- </tr>
928
- </table>
929
- </div>
930
-
931
- <div class="method_details ">
932
- <h3 class="signature " id="mean-instance_method">
933
-
934
- - (<tt>Object</tt>) <strong>mean</strong>
935
-
936
-
937
-
938
-
939
-
940
- </h3><div class="docstring">
941
- <div class="discussion">
942
-
943
- <p>Returns the weighted mean value of the cluster</p>
944
-
945
-
946
- </div>
947
- </div>
948
- <div class="tags">
949
-
950
-
951
- </div><table class="source_code">
952
- <tr>
953
- <td>
954
- <pre class="lines">
955
-
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-
957
- 176
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- 177
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- 179
961
- 180
962
- 181
963
- 182
964
- 183
965
- 184
966
- 185
967
- 186</pre>
968
- </td>
969
- <td>
970
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 176</span>
971
-
972
- <span class='kw'>def</span> <span class='id identifier rubyid_mean'>mean</span>
973
- <span class='id identifier rubyid_mean_len'>mean_len</span> <span class='op'>=</span> <span class='int'>0</span>
974
- <span class='id identifier rubyid_weight'>weight</span> <span class='op'>=</span> <span class='int'>0</span>
975
-
976
- <span class='id identifier rubyid_lengths'>lengths</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_length'>length</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='op'>|</span>
977
- <span class='id identifier rubyid_mean_len'>mean_len</span> <span class='op'>+=</span> <span class='id identifier rubyid_length'>length</span> <span class='op'>*</span> <span class='id identifier rubyid_n'>n</span>
978
- <span class='id identifier rubyid_weight'>weight</span> <span class='op'>+=</span> <span class='id identifier rubyid_n'>n</span>
979
- <span class='kw'>end</span>
980
- <span class='id identifier rubyid_mean_len'>mean_len</span> <span class='op'>/=</span> <span class='id identifier rubyid_weight'>weight</span>
981
-
982
- <span class='kw'>end</span></pre>
983
- </td>
984
- </tr>
985
- </table>
986
- </div>
987
-
988
- <div class="method_details ">
989
- <h3 class="signature " id="print-instance_method">
990
-
991
- - (<tt>Object</tt>) <strong>print</strong>
992
-
993
-
994
-
995
-
996
-
997
- </h3><div class="docstring">
998
- <div class="discussion">
999
-
1000
- <p>Prints the current cluster</p>
1001
-
1002
-
1003
- </div>
1004
- </div>
1005
- <div class="tags">
1006
-
1007
-
1008
- </div><table class="source_code">
1009
- <tr>
1010
- <td>
1011
- <pre class="lines">
1012
-
1013
-
1014
- 333
1015
- 334
1016
- 335
1017
- 336
1018
- 337
1019
- 338
1020
- 339</pre>
1021
- </td>
1022
- <td>
1023
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 333</span>
1024
-
1025
- <span class='kw'>def</span> <span class='id identifier rubyid_print'>print</span>
1026
- <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Cluster: mean = </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_mean'>mean</span><span class='lparen'>(</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='tstring_content'>, density = </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_density'>density</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
1027
- <span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span><span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span><span class='op'>&lt;=&gt;</span><span class='id identifier rubyid_b'>b</span><span class='rbrace'>}</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_elem'>elem</span><span class='op'>|</span>
1028
- <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_elem'>elem</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='embexpr_beg'>#{</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
1029
- <span class='kw'>end</span>
1030
- <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>--------------------------</span><span class='tstring_end'>&quot;</span></span>
1031
- <span class='kw'>end</span></pre>
1032
- </td>
1033
- </tr>
1034
- </table>
1035
- </div>
1036
-
1037
- <div class="method_details ">
1038
- <h3 class="signature " id="standard_deviation-instance_method">
1039
-
1040
- - (<tt>Object</tt>) <strong>standard_deviation</strong>(lengths = nil)
1041
-
1042
-
1043
-
1044
-
1045
-
1046
- </h3><div class="docstring">
1047
- <div class="discussion">
1048
-
1049
- <p>Returns the standard deviation of a set of values Params: <tt>lengths</tt>:
1050
- a vector of values (optional, by default it takes the values in the
1051
- cluster)</p>
1052
-
1053
-
1054
- </div>
1055
- </div>
1056
- <div class="tags">
1057
-
1058
-
1059
- </div><table class="source_code">
1060
- <tr>
1061
- <td>
1062
- <pre class="lines">
1063
-
1064
-
1065
- 247
1066
- 248
1067
- 249
1068
- 250
1069
- 251
1070
- 252
1071
- 253
1072
- 254
1073
- 255
1074
- 256
1075
- 257
1076
- 258
1077
- 259</pre>
1078
- </td>
1079
- <td>
1080
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 247</span>
1081
-
1082
- <span class='kw'>def</span> <span class='id identifier rubyid_standard_deviation'>standard_deviation</span><span class='lparen'>(</span><span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='rparen'>)</span>
1083
- <span class='kw'>if</span> <span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>==</span> <span class='kw'>nil</span>
1084
- <span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>=</span> <span class='ivar'>@lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
1085
- <span class='kw'>end</span>
1086
-
1087
- <span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>=</span> <span class='id identifier rubyid_mean'>mean</span><span class='lparen'>(</span><span class='rparen'>)</span>
1088
- <span class='id identifier rubyid_std_deviation'>std_deviation</span> <span class='op'>=</span> <span class='int'>0</span>
1089
- <span class='id identifier rubyid_lengths'>lengths</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_len'>len</span><span class='op'>|</span>
1090
- <span class='id identifier rubyid_std_deviation'>std_deviation</span> <span class='op'>+=</span> <span class='lparen'>(</span><span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>-</span> <span class='id identifier rubyid_len'>len</span><span class='rparen'>)</span> <span class='op'>*</span> <span class='lparen'>(</span><span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>-</span> <span class='id identifier rubyid_len'>len</span><span class='rparen'>)</span>
1091
- <span class='kw'>end</span>
1092
- <span class='id identifier rubyid_std_deviation'>std_deviation</span> <span class='op'>=</span> <span class='const'>Math</span><span class='period'>.</span><span class='id identifier rubyid_sqrt'>sqrt</span><span class='lparen'>(</span><span class='id identifier rubyid_std_deviation'>std_deviation</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='int'>1</span><span class='rparen'>)</span><span class='rparen'>)</span>
1093
-
1094
- <span class='kw'>end</span></pre>
1095
- </td>
1096
- </tr>
1097
- </table>
1098
- </div>
1099
-
1100
- <div class="method_details ">
1101
- <h3 class="signature " id="t_test-instance_method">
1102
-
1103
- - (<tt>Object</tt>) <strong>t_test</strong>(clusters, queryLength)
1104
-
1105
-
1106
-
1107
-
1108
-
1109
- </h3><div class="docstring">
1110
- <div class="discussion">
1111
-
1112
- <p>Returns the p-value of a t-test <tt>clusters</tt>: a list of Cluster
1113
- objects <tt>querylength</tt>: a reference Sequence object</p>
1114
-
1115
-
1116
- </div>
1117
- </div>
1118
- <div class="tags">
1119
-
1120
-
1121
- </div><table class="source_code">
1122
- <tr>
1123
- <td>
1124
- <pre class="lines">
1125
-
1126
-
1127
- 302
1128
- 303
1129
- 304
1130
- 305
1131
- 306
1132
- 307
1133
- 308
1134
- 309
1135
- 310
1136
- 311
1137
- 312
1138
- 313
1139
- 314
1140
- 315
1141
- 316
1142
- 317
1143
- 318
1144
- 319
1145
- 320</pre>
1146
- </td>
1147
- <td>
1148
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 302</span>
1149
-
1150
- <span class='kw'>def</span> <span class='id identifier rubyid_t_test'>t_test</span><span class='lparen'>(</span><span class='id identifier rubyid_clusters'>clusters</span><span class='comma'>,</span> <span class='id identifier rubyid_queryLength'>queryLength</span><span class='rparen'>)</span>
1151
- <span class='comment'>#normalize the data so that to fit a bell curve
1152
- </span> <span class='comment'>#raw_hits = lengths.map{ |x| a = Array.new(x[1],x[0])}.flatten.to_s.gsub('[','').gsub(']','')
1153
- </span> <span class='id identifier rubyid_raw_hits'>raw_hits</span> <span class='op'>=</span> <span class='id identifier rubyid_clusters'>clusters</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_c'>c</span><span class='op'>|</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>[</span><span class='tstring_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><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>]</span><span class='tstring_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>
1154
-
1155
- <span class='kw'>if</span> <span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
1156
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>library(preprocessCore)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1157
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>x = matrix(c(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='rbrace'>}</span><span class='tstring_content'>), ncol=1)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1158
- <span class='id identifier rubyid_mean_length'>mean_length</span> <span class='op'>=</span> <span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='period'>.</span><span class='id identifier rubyid_sum'>sum</span> <span class='op'>/</span> <span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span>
1159
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>target = rnorm(10000, m=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_mean'>mean</span><span class='rbrace'>}</span><span class='tstring_content'>, sd=sd(c(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='rbrace'>}</span><span class='tstring_content'>)))</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1160
-
1161
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>hits = normalize.quantiles.use.target(x,target,copy=TRUE)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1162
-
1163
- <span class='comment'>#make the t-test and get the p-value
1164
- </span> <span class='const'>R</span><span class='period'>.</span> <span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>pval = t.test(hits - </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_queryLength'>queryLength</span><span class='rbrace'>}</span><span class='tstring_content'>)$p.value</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1165
- <span class='id identifier rubyid_pval'>pval</span> <span class='op'>=</span> <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_pull'>pull</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>pval</span><span class='tstring_end'>&quot;</span></span>
1166
- <span class='kw'>end</span>
1167
-
1168
- <span class='kw'>end</span></pre>
1169
- </td>
1170
- </tr>
1171
- </table>
1172
- </div>
1173
-
1174
- <div class="method_details ">
1175
- <h3 class="signature " id="wilcox_test-instance_method">
1176
-
1177
- - (<tt>Object</tt>) <strong>wilcox_test</strong>(clusters, queryLength)
1178
-
1179
-
1180
-
1181
-
1182
-
1183
- </h3><div class="docstring">
1184
- <div class="discussion">
1185
-
1186
- <p>Returns the p-value of a wilcox test <tt>clusters</tt>: a list of Cluster
1187
- objects <tt>querylength</tt>: a reference Sequence object</p>
1188
-
1189
-
1190
- </div>
1191
- </div>
1192
- <div class="tags">
1193
-
1194
-
1195
- </div><table class="source_code">
1196
- <tr>
1197
- <td>
1198
- <pre class="lines">
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1210
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1211
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1212
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1213
- 292
1214
- 293
1215
- 294
1216
- 295
1217
- 296</pre>
1218
- </td>
1219
- <td>
1220
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 280</span>
1221
-
1222
- <span class='kw'>def</span> <span class='id identifier rubyid_wilcox_test'>wilcox_test</span><span class='lparen'>(</span><span class='id identifier rubyid_clusters'>clusters</span><span class='comma'>,</span> <span class='id identifier rubyid_queryLength'>queryLength</span><span class='rparen'>)</span>
1223
- <span class='id identifier rubyid_raw_hits'>raw_hits</span> <span class='op'>=</span> <span class='id identifier rubyid_clusters'>clusters</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_c'>c</span><span class='op'>|</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>[</span><span class='tstring_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><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>]</span><span class='tstring_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>
1224
-
1225
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>library(preprocessCore)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1226
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>x = matrix(c(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='rbrace'>}</span><span class='tstring_content'>), ncol=1)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1227
- <span class='id identifier rubyid_mean_length'>mean_length</span> <span class='op'>=</span> <span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='period'>.</span><span class='id identifier rubyid_sum'>sum</span> <span class='op'>/</span> <span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span>
1228
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>target = rnorm(10000, m=</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_mean'>mean</span><span class='rbrace'>}</span><span class='tstring_content'>, sd=sd(c(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='rbrace'>}</span><span class='tstring_content'>)))</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1229
-
1230
- <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>hits = normalize.quantiles.use.target(x,target,copy=TRUE)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1231
-
1232
- <span class='comment'>#make the wilcox-test and get the p-value
1233
- </span> <span class='const'>R</span><span class='period'>.</span><span class='id identifier rubyid_eval'>eval</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>hits = c(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_raw_hits'>raw_hits</span><span class='rbrace'>}</span><span class='tstring_content'>)</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
1234
- <span class='comment'>#R. eval(&quot;pval = wilcox.test(hits - #{queryLength})$p.value&quot;)
1235
- </span> <span class='comment'>#pval = R.pull &quot;pval&quot;
1236
- </span> <span class='int'>0</span>
1237
-
1238
- <span class='kw'>end</span></pre>
1239
- </td>
1240
- </tr>
1241
- </table>
1242
- </div>
1243
-
1244
- <div class="method_details ">
1245
- <h3 class="signature " id="wss-instance_method">
1246
-
1247
- - (<tt>Object</tt>) <strong>wss</strong>(lengths = nil)
1248
-
1249
-
1250
-
1251
-
1252
-
1253
- </h3><div class="docstring">
1254
- <div class="discussion">
1255
-
1256
- <p>Returns within cluster sum of squares</p>
1257
-
1258
-
1259
- </div>
1260
- </div>
1261
- <div class="tags">
1262
-
1263
-
1264
- </div><table class="source_code">
1265
- <tr>
1266
- <td>
1267
- <pre class="lines">
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-
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- 234
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1278
- 237
1279
- 238
1280
- 239
1281
- 240
1282
- 241</pre>
1283
- </td>
1284
- <td>
1285
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 229</span>
1286
-
1287
- <span class='kw'>def</span> <span class='id identifier rubyid_wss'>wss</span><span class='lparen'>(</span><span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='rparen'>)</span>
1288
- <span class='kw'>if</span> <span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>==</span> <span class='kw'>nil</span>
1289
- <span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>=</span> <span class='ivar'>@lengths</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
1290
- <span class='kw'>end</span>
1291
-
1292
- <span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>=</span> <span class='id identifier rubyid_mean'>mean</span>
1293
- <span class='id identifier rubyid_ss'>ss</span> <span class='op'>=</span> <span class='int'>0</span>
1294
- <span class='id identifier rubyid_lengths'>lengths</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_len'>len</span><span class='op'>|</span>
1295
- <span class='id identifier rubyid_ss'>ss</span> <span class='op'>+=</span> <span class='lparen'>(</span><span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>-</span> <span class='id identifier rubyid_len'>len</span><span class='rparen'>)</span> <span class='op'>*</span> <span class='lparen'>(</span><span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>-</span> <span class='id identifier rubyid_len'>len</span><span class='rparen'>)</span>
1296
- <span class='kw'>end</span>
1297
- <span class='id identifier rubyid_ss'>ss</span>
1298
-
1299
- <span class='kw'>end</span></pre>
1300
- </td>
1301
- </tr>
1302
- </table>
1303
- </div>
1304
-
1305
- </div>
1306
-
1307
- </div>
1308
-
1309
- <div id="footer">
1310
- Generated on Sat Sep 28 07:01:32 2013 by
1311
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
1312
- 0.8.7.2 (ruby-1.9.3).
1313
- </div>
1314
-
1315
- </body>
1316
- </html>