genevalidator 1.6.1 → 1.6.2

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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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- </td></tr></table>
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- </td></tr></table>
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- </td></tr></table>
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- </td></tr></table>
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- </div></span>
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-
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- </li>
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- <li class="public ">
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- <span class="summary_signature">
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-
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- <a href="#initialize-instance_method" title="#initialize (instance method)">- (LengthClusterValidation) <strong>initialize</strong>(type, prediction, hits, filename) </a>
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-
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- </span>
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-
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-
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- <span class="note title constructor">constructor</span>
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-
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-
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- <span class="summary_desc"><div class='inline'>
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- <p>Initilizes the object Params: <tt>type</tt>: type of the predicted sequence
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- (:nucleotide or :protein) <tt>prediction</tt>: a <tt>Sequence</tt> object
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- representing the blast query <tt>hits</tt>: a vector of <tt>Sequence</tt>
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- objects (usually representig the blast hits).</p>
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- </div></span>
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-
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- </li>
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-
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-
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- <li class="public ">
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- <span class="summary_signature">
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-
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- <a href="#plot_histo_clusters-instance_method" title="#plot_histo_clusters (instance method)">- (Object) <strong>plot_histo_clusters</strong>(output = &quot;#{@filename}_len_clusters.json&quot;, clusters = @clusters, max_density_cluster = @max_density_cluster, prediction = @prediction) </a>
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-
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-
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- </span>
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-
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-
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- <span class="summary_desc"><div class='inline'>
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- <p>Generates a json file containing data used for plotting the histogram of
310
- the length distribution given a lust of Cluster objects <tt>output</tt>:
311
- filename where to save the graph <tt>clusters</tt>: array of
312
- <tt>Cluster</tt> objects <tt>max_density_cluster</tt>: index of the most
313
- dense cluster <tt>prediction</tt>: <tt>Sequence</tt> object Output:
314
- <tt>Plot</tt> object.</p>
315
- </div></span>
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-
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- </li>
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-
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-
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- <li class="public ">
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- <span class="summary_signature">
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-
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- <a href="#plot_len_clusters-instance_method" title="#plot_len_clusters (instance method)">- (Object) <strong>plot_len_clusters</strong>(output = &quot;#{@filename}_len.json&quot;, hits = @hits) </a>
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-
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- </span>
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-
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-
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-
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- <span class="summary_desc"><div class='inline'>
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- <p>Generates a json file cotaining data used for plotting lines corresponding
339
- to the start and end hit offsets Params: <tt>output</tt>: filename where to
340
- save the graph <tt>hits</tt>: array of Sequence objects Output:
341
- <tt>Plot</tt> object.</p>
342
- </div></span>
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-
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- </li>
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-
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-
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- <li class="public ">
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- <span class="summary_signature">
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-
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- <a href="#run-instance_method" title="#run (instance method)">- (Object) <strong>run</strong> </a>
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-
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- </span>
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-
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- <span class="summary_desc"><div class='inline'>
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- <p>Validates the length of the predicted gene by comparing the length of the
366
- prediction to the most dense cluster The most dense cluster is obtained by
367
- hierarchical clusterization Plots are generated if required (see
368
- <tt>plot</tt> variable) Output: <tt>LengthClusterValidationOutput</tt>
369
- object.</p>
370
- </div></span>
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-
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- </li>
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-
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-
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- </ul>
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- <div id="constructor_details" class="method_details_list">
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- <h2>Constructor Details</h2>
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-
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- <div class="method_details first">
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- <h3 class="signature first" id="initialize-instance_method">
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-
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- - (<tt><span class='object_link'><a href="" title="LengthClusterValidation (class)">LengthClusterValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits, filename)
391
-
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-
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-
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-
395
-
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- </h3><div class="docstring">
397
- <div class="discussion">
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-
399
- <p>Initilizes the object Params: <tt>type</tt>: type of the predicted sequence
400
- (:nucleotide or :protein) <tt>prediction</tt>: a <tt>Sequence</tt> object
401
- representing the blast query <tt>hits</tt>: a vector of <tt>Sequence</tt>
402
- objects (usually representig the blast hits)</p>
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-
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-
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- </div>
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- </div>
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- <div class="tags">
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-
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- </div><table class="source_code">
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- <pre class="lines">
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- 60</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 51</span>
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-
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- <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_type'>type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_filename'>filename</span><span class='rparen'>)</span>
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- <span class='kw'>super</span>
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- <span class='ivar'>@filename</span> <span class='op'>=</span> <span class='id identifier rubyid_filename'>filename</span>
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- <span class='ivar'>@short_header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>LengthCluster</span><span class='tstring_end'>&quot;</span></span>
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- <span class='ivar'>@header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Length Cluster</span><span class='tstring_end'>&quot;</span></span>
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- <span class='ivar'>@description</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Check whether the prediction length fits most of the BLAST hit lengths,</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
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- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> by 1D hierarchical clusterization. Meaning of the output displayed: Prediction_len</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
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- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> [Main Cluster Length Interval]</span><span class='tstring_end'>&quot;</span></span>
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- <span class='ivar'>@cli_name</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>lenc</span><span class='tstring_end'>&quot;</span></span>
439
- <span class='kw'>end</span></pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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- </div>
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-
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- <div id="instance_attr_details" class="attr_details">
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- <h2>Instance Attribute Details</h2>
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-
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-
451
- <span id=""></span>
452
- <div class="method_details first">
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- <h3 class="signature first" id="clusters-instance_method">
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-
455
- - (<tt>Object</tt>) <strong>clusters</strong> <span class="extras">(readonly)</span>
456
-
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-
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-
459
-
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-
461
- </h3><div class="docstring">
462
- <div class="discussion">
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-
464
- <p>Returns the value of attribute clusters</p>
465
-
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-
467
- </div>
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- </div>
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- <div class="tags">
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-
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-
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- </div><table class="source_code">
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- <tr>
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- <pre class="lines">
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- 42
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- 43
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- 44</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 42</span>
484
-
485
- <span class='kw'>def</span> <span class='id identifier rubyid_clusters'>clusters</span>
486
- <span class='ivar'>@clusters</span>
487
- <span class='kw'>end</span></pre>
488
- </td>
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- </tr>
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- </table>
491
- </div>
492
-
493
-
494
- <span id=""></span>
495
- <div class="method_details ">
496
- <h3 class="signature " id="filename-instance_method">
497
-
498
- - (<tt>Object</tt>) <strong>filename</strong> <span class="extras">(readonly)</span>
499
-
500
-
501
-
502
-
503
-
504
- </h3><div class="docstring">
505
- <div class="discussion">
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-
507
- <p>Returns the value of attribute filename</p>
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-
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-
510
- </div>
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- </div>
512
- <div class="tags">
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-
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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- 41
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- 42
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- 43</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 41</span>
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-
528
- <span class='kw'>def</span> <span class='id identifier rubyid_filename'>filename</span>
529
- <span class='ivar'>@filename</span>
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- <span class='kw'>end</span></pre>
531
- </td>
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- </tr>
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- </table>
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- </div>
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-
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-
537
- <span id=""></span>
538
- <div class="method_details ">
539
- <h3 class="signature " id="max_density_cluster-instance_method">
540
-
541
- - (<tt>Object</tt>) <strong>max_density_cluster</strong> <span class="extras">(readonly)</span>
542
-
543
-
544
-
545
-
546
-
547
- </h3><div class="docstring">
548
- <div class="discussion">
549
-
550
- <p>Returns the value of attribute max_density_cluster</p>
551
-
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-
553
- </div>
554
- </div>
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- <div class="tags">
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-
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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-
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-
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- 43
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- 44
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- 45</pre>
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- </td>
568
- <td>
569
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 43</span>
570
-
571
- <span class='kw'>def</span> <span class='id identifier rubyid_max_density_cluster'>max_density_cluster</span>
572
- <span class='ivar'>@max_density_cluster</span>
573
- <span class='kw'>end</span></pre>
574
- </td>
575
- </tr>
576
- </table>
577
- </div>
578
-
579
- </div>
580
-
581
-
582
- <div id="instance_method_details" class="method_details_list">
583
- <h2>Instance Method Details</h2>
584
-
585
-
586
- <div class="method_details first">
587
- <h3 class="signature first" id="clusterization_by_length-instance_method">
588
-
589
- - (<tt>Object</tt>) <strong>clusterization_by_length</strong>(debug = false, lst = @hits, predicted_seq = @prediction)
590
-
591
-
592
-
593
-
594
-
595
- </h3><div class="docstring">
596
- <div class="discussion">
597
-
598
- <p>Clusterization by length from a list of sequences Params:</p>
599
- <table class="rdoc-list"><tr><td class="rdoc-term"><p><tt>debug</tt> (optional)</p></td>
600
- <td>
601
- <p>true to display debug information, false by default (optional argument)</p>
602
- </td></tr><tr><td class="rdoc-term"><p><tt>lst</tt></p></td>
603
- <td>
604
- <p>array of <tt>Sequence</tt> objects</p>
605
- </td></tr><tr><td class="rdoc-term"><p><tt>predicted_seq</tt></p></td>
606
- <td>
607
- <p><tt>Sequence</tt> objetc</p>
608
- </td></tr></table>
609
-
610
- <p>Output</p>
611
- <table class="rdoc-list"><tr><td class="rdoc-term"><p>output 1</p></td>
612
- <td>
613
- <p>array of Cluster objects</p>
614
- </td></tr><tr><td class="rdoc-term"><p>output 2</p></td>
615
- <td>
616
- <p>the index of the most dense cluster</p>
617
- </td></tr></table>
618
-
619
-
620
- </div>
621
- </div>
622
- <div class="tags">
623
-
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-
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- </div><table class="source_code">
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- <td>
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- </td>
662
- <td>
663
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 115</span>
664
-
665
- <span class='kw'>def</span> <span class='id identifier rubyid_clusterization_by_length'>clusterization_by_length</span><span class='lparen'>(</span><span class='id identifier rubyid_debug'>debug</span> <span class='op'>=</span> <span class='kw'>false</span><span class='comma'>,</span>
666
- <span class='id identifier rubyid_lst'>lst</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='comma'>,</span>
667
- <span class='id identifier rubyid_predicted_seq'>predicted_seq</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='rparen'>)</span>
668
- <span class='kw'>begin</span>
669
- <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_lst'>lst</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span> <span class='kw'>and</span>
670
- <span class='id identifier rubyid_predicted_seq'>predicted_seq</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span>
671
-
672
- <span class='id identifier rubyid_contents'>contents</span> <span class='op'>=</span> <span class='id identifier rubyid_lst'>lst</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_x'>x</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span> <span class='rbrace'>}</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>
673
-
674
- <span class='id identifier rubyid_hc'>hc</span> <span class='op'>=</span> <span class='const'>HierarchicalClusterization</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_contents'>contents</span><span class='rparen'>)</span>
675
- <span class='id identifier rubyid_clusters'>clusters</span> <span class='op'>=</span> <span class='id identifier rubyid_hc'>hc</span><span class='period'>.</span><span class='id identifier rubyid_hierarchical_clusterization'>hierarchical_clusterization</span>
676
-
677
- <span class='id identifier rubyid_max_density'>max_density</span> <span class='op'>=</span> <span class='int'>0</span><span class='semicolon'>;</span>
678
- <span class='id identifier rubyid_max_density_cluster_idx'>max_density_cluster_idx</span> <span class='op'>=</span> <span class='int'>0</span><span class='semicolon'>;</span>
679
- <span class='id identifier rubyid_clusters'>clusters</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_item'>item</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
680
- <span class='kw'>if</span> <span class='id identifier rubyid_item'>item</span><span class='period'>.</span><span class='id identifier rubyid_density'>density</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_max_density'>max_density</span>
681
- <span class='id identifier rubyid_max_density'>max_density</span> <span class='op'>=</span> <span class='id identifier rubyid_item'>item</span><span class='period'>.</span><span class='id identifier rubyid_density'>density</span>
682
- <span class='id identifier rubyid_max_density_cluster_idx'>max_density_cluster_idx</span> <span class='op'>=</span> <span class='id identifier rubyid_i'>i</span><span class='semicolon'>;</span>
683
- <span class='kw'>end</span>
684
- <span class='kw'>end</span>
685
-
686
- <span class='kw'>return</span> <span class='lbracket'>[</span><span class='id identifier rubyid_clusters'>clusters</span><span class='comma'>,</span> <span class='id identifier rubyid_max_density_cluster_idx'>max_density_cluster_idx</span><span class='rbracket'>]</span>
687
-
688
- <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
689
- <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'>Type 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><span class='op'>&lt;&lt;</span>
690
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> Possible cause: one of the arguments of 'clusterization_by_length'</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
691
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> method has not the proper type.\n</span><span class='tstring_end'>&quot;</span></span>
692
- <span class='id identifier rubyid_exit'>exit</span>
693
- <span class='kw'>end</span>
694
- <span class='kw'>end</span></pre>
695
- </td>
696
- </tr>
697
- </table>
698
- </div>
699
-
700
- <div class="method_details ">
701
- <h3 class="signature " id="plot_histo_clusters-instance_method">
702
-
703
- - (<tt>Object</tt>) <strong>plot_histo_clusters</strong>(output = &quot;#{@filename}_len_clusters.json&quot;, clusters = @clusters, max_density_cluster = @max_density_cluster, prediction = @prediction)
704
-
705
-
706
-
707
-
708
-
709
- </h3><div class="docstring">
710
- <div class="discussion">
711
-
712
- <p>Generates a json file containing data used for plotting the histogram of
713
- the length distribution given a lust of Cluster objects <tt>output</tt>:
714
- filename where to save the graph <tt>clusters</tt>: array of
715
- <tt>Cluster</tt> objects <tt>max_density_cluster</tt>: index of the most
716
- dense cluster <tt>prediction</tt>: <tt>Sequence</tt> object Output:
717
- <tt>Plot</tt> object</p>
718
-
719
-
720
- </div>
721
- </div>
722
- <div class="tags">
723
-
724
-
725
- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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- <td>
752
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 155</span>
753
-
754
- <span class='kw'>def</span> <span class='id identifier rubyid_plot_histo_clusters'>plot_histo_clusters</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>_len_clusters.json</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
755
- <span class='id identifier rubyid_clusters'>clusters</span> <span class='op'>=</span> <span class='ivar'>@clusters</span><span class='comma'>,</span>
756
- <span class='id identifier rubyid_max_density_cluster'>max_density_cluster</span> <span class='op'>=</span> <span class='ivar'>@max_density_cluster</span><span class='comma'>,</span>
757
- <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='rparen'>)</span>
758
-
759
- <span class='id identifier rubyid_f'>f</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
760
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_clusters'>clusters</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_cluster'>cluster</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
761
- <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_collect'>collect</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
762
- <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>key</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>value</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_v'>v</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>main</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>==</span><span class='id identifier rubyid_max_density_cluster'>max_density_cluster</span><span class='rparen'>)</span><span class='rbrace'>}</span>
763
- <span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span><span class='rparen'>)</span>
764
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
765
- <span class='const'>Plot</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</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'>\/([^\/]+)$</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='comma'>,</span>
766
- <span class='symbol'>:bars</span><span class='comma'>,</span>
767
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Length distribution histogram</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
768
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>prediction, black;most dense cluster,red;other hits, blue</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
769
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>length</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
770
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>frequency</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
771
- <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='rparen'>)</span>
772
- <span class='kw'>end</span></pre>
773
- </td>
774
- </tr>
775
- </table>
776
- </div>
777
-
778
- <div class="method_details ">
779
- <h3 class="signature " id="plot_len_clusters-instance_method">
780
-
781
- - (<tt>Object</tt>) <strong>plot_len_clusters</strong>(output = &quot;#{@filename}_len.json&quot;, hits = @hits)
782
-
783
-
784
-
785
-
786
-
787
- </h3><div class="docstring">
788
- <div class="discussion">
789
-
790
- <p>Generates a json file cotaining data used for plotting lines corresponding
791
- to the start and end hit offsets Params: <tt>output</tt>: filename where to
792
- save the graph <tt>hits</tt>: array of Sequence objects Output:
793
- <tt>Plot</tt> object</p>
794
-
795
-
796
- </div>
797
- </div>
798
- <div class="tags">
799
-
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-
801
- </div><table class="source_code">
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- </td>
832
- <td>
833
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 183</span>
834
-
835
- <span class='kw'>def</span> <span class='id identifier rubyid_plot_len_clusters'>plot_len_clusters</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>_len.json</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='rparen'>)</span>
836
-
837
- <span class='id identifier rubyid_f'>f</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span> <span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
838
- <span class='id identifier rubyid_lst'>lst</span> <span class='op'>=</span> <span class='ivar'>@hits</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='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='op'>&lt;=&gt;</span><span class='id identifier rubyid_b'>b</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='rbrace'>}</span>
839
-
840
- <span class='id identifier rubyid_no_lines'>no_lines</span> <span class='op'>=</span> <span class='int'>100</span>
841
- <span class='id identifier rubyid_ratio'>ratio</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>/</span><span class='id identifier rubyid_no_lines'>no_lines</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
842
- <span class='kw'>if</span> <span class='id identifier rubyid_ratio'>ratio</span> <span class='op'>==</span> <span class='int'>0</span>
843
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='lparen'>(</span><span class='id identifier rubyid_lst'>lst</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_hit'>hit</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>gray</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span> <span class='op'>+</span>
844
- <span class='id identifier rubyid_lst'>lst</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_hit'>hit</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</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_hsp'>hsp</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_from'>hit_from</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_to'>hit_to</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>red</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span><span class='rparen'>)</span>
845
- <span class='kw'>else</span>
846
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='lparen'>(</span><span class='id identifier rubyid_lst'>lst</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_hit'>hit</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_i'>i</span><span class='op'>%</span><span class='id identifier rubyid_ratio'>ratio</span><span class='op'>==</span><span class='int'>0</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_hit'>hit</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>gray</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span> <span class='op'>+</span>
847
- <span class='id identifier rubyid_lst'>lst</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_hit'>hit</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_i'>i</span><span class='op'>%</span><span class='id identifier rubyid_ratio'>ratio</span><span class='op'>==</span><span class='int'>0</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_hit'>hit</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</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_hsp'>hsp</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_i'>i</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_from'>hit_from</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_to'>hit_to</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>red</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span><span class='rparen'>)</span>
848
- <span class='kw'>end</span>
849
-
850
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
851
- <span class='const'>Plot</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</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'>\/([^\/]+)$</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='comma'>,</span>
852
- <span class='symbol'>:lines</span><span class='comma'>,</span>
853
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Hits vs prediction</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
854
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>hit length, gray;high-scoring segment pairs (hsp), red</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
855
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>length</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
856
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>idx</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
857
- <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rparen'>)</span>
858
- <span class='kw'>end</span></pre>
859
- </td>
860
- </tr>
861
- </table>
862
- </div>
863
-
864
- <div class="method_details ">
865
- <h3 class="signature " id="run-instance_method">
866
-
867
- - (<tt>Object</tt>) <strong>run</strong>
868
-
869
-
870
-
871
-
872
-
873
- </h3><div class="docstring">
874
- <div class="discussion">
875
-
876
- <p>Validates the length of the predicted gene by comparing the length of the
877
- prediction to the most dense cluster The most dense cluster is obtained by
878
- hierarchical clusterization Plots are generated if required (see
879
- <tt>plot</tt> variable) Output: <tt>LengthClusterValidationOutput</tt>
880
- object</p>
881
-
882
-
883
- </div>
884
- </div>
885
- <div class="tags">
886
-
887
-
888
- </div><table class="source_code">
889
- <tr>
890
- <td>
891
- <pre class="lines">
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928
- </td>
929
- <td>
930
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 70</span>
931
-
932
- <span class='kw'>def</span> <span class='id identifier rubyid_run'>run</span>
933
- <span class='kw'>begin</span>
934
- <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NotEnoughHitsError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;=</span> <span class='int'>5</span>
935
- <span class='id identifier rubyid_raise'>raise</span> <span class='const'>Exception</span> <span class='kw'>unless</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span> <span class='kw'>and</span>
936
- <span class='id identifier rubyid_hits'>hits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span>
937
-
938
- <span class='id identifier rubyid_start'>start</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span>
939
- <span class='comment'># get [clusters, max_density_cluster_idx]
940
- </span> <span class='id identifier rubyid_clusterization'>clusterization</span> <span class='op'>=</span> <span class='id identifier rubyid_clusterization_by_length'>clusterization_by_length</span>
941
-
942
- <span class='ivar'>@clusters</span> <span class='op'>=</span> <span class='id identifier rubyid_clusterization'>clusterization</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
943
- <span class='ivar'>@max_density_cluster</span> <span class='op'>=</span> <span class='id identifier rubyid_clusterization'>clusterization</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
944
- <span class='id identifier rubyid_limits'>limits</span> <span class='op'>=</span> <span class='ivar'>@clusters</span><span class='lbracket'>[</span><span class='ivar'>@max_density_cluster</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_get_limits'>get_limits</span>
945
- <span class='id identifier rubyid_prediction_len'>prediction_len</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span>
946
-
947
- <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>LengthClusterValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_len'>prediction_len</span><span class='comma'>,</span> <span class='id identifier rubyid_limits'>limits</span><span class='rparen'>)</span>
948
- <span class='id identifier rubyid_plot1'>plot1</span> <span class='op'>=</span> <span class='id identifier rubyid_plot_histo_clusters'>plot_histo_clusters</span>
949
- <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_plot_files'>plot_files</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_plot1'>plot1</span><span class='rparen'>)</span>
950
- <span class='id identifier rubyid_plot2'>plot2</span> <span class='op'>=</span> <span class='id identifier rubyid_plot_len_clusters'>plot_len_clusters</span>
951
- <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_plot_files'>plot_files</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_plot2'>plot2</span><span class='rparen'>)</span>
952
- <span class='ivar'>@running_time</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='id identifier rubyid_start'>start</span>
953
-
954
- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
955
-
956
- <span class='comment'># Exception is raised when blast founds no hits
957
- </span> <span class='kw'>rescue</span> <span class='const'>NotEnoughHitsError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
958
- <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Not enough evidence</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:warning</span><span class='rparen'>)</span>
959
- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
960
- <span class='kw'>else</span>
961
- <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unexpected error</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:error</span><span class='rparen'>)</span>
962
- <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>OtherError</span>
963
- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
964
- <span class='kw'>end</span>
965
- <span class='kw'>end</span></pre>
966
- </td>
967
- </tr>
968
- </table>
969
- </div>
970
-
971
- </div>
972
-
973
- </div>
974
-
975
- <div id="footer">
976
- Generated on Sat Sep 28 07:01:33 2013 by
977
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
978
- 0.8.7.2 (ruby-1.9.3).
979
- </div>
980
-
981
- </body>
982
- </html>