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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- <td><table class="rdoc-list"><tr><td class="rdoc-term"><p>array of Cluster objects output 2</p></td>
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- <td>
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- <p>the index of the most dense cluster.</p>
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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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- </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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- <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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- <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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- </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)
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-
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-
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-
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-
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-
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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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- </div><table class="source_code">
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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>
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- <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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-
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- - (<tt>Object</tt>) <strong>clusters</strong> <span class="extras">(readonly)</span>
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-
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-
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-
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-
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-
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- </h3><div class="docstring">
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- <div class="discussion">
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-
464
- <p>Returns the value of attribute clusters</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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-
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- </div><table class="source_code">
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- <pre class="lines">
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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>
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- </td>
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- </tr>
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- </table>
491
- </div>
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-
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-
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>
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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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- 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
-
552
-
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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661
- </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>
751
- <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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- <pre class="lines">
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- <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>