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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- <p>Generates a json file containing data used for plotting the start/end of
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- the matched region offsets in the prediction Param <tt>slope</tt>: slope of
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- the linear regression line <tt>y_intercept</tt>: the ecuation of the line
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- is y= slope*x + y_intercept <tt>output</tt>: location where the plot will
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- be saved in jped file format <tt>hits</tt>: array of Sequence objects.</p>
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- </div></span>
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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="#plot_matched_regions-instance_method" title="#plot_matched_regions (instance method)">- (Object) <strong>plot_matched_regions</strong>(output = &quot;#{filename}_match.json&quot;, hits = @hits, prediction = @prediction) </a>
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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 matched region
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- of the prediction for each hit Param <tt>output</tt>: location where the
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- plot will be saved in jped file format <tt>hits</tt>: array of Sequence
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- objects <tt>prediction</tt>: Sequence objects.</p>
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- </div></span>
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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="#run-instance_method" title="#run (instance method)">- (Object) <strong>run</strong> </a>
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- </span>
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- <span class="summary_desc"><div class='inline'>
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- <p>Validation test for gene merge Output: <tt>GeneMergeValidationOutput</tt>
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- object.</p>
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- </div></span>
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-
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- </li>
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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="#slope-instance_method" title="#slope (instance method)">- (Object) <strong>slope</strong>(hits = @hits) </a>
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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>Caclulates the slope of the regression line give a set of 2d coordonates of
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- the start/stop offests of the hits Param <tt>hits</tt>: array of Sequence
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- objects Code inspired from: <a
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- href="http://engineering.sharethrough.com/blog/2012/09/12/simple-linear-regression-using-ruby">engineering.sharethrough.com/blog/2012/09/12/simple-linear-regression-using-ruby</a>/
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- Output: The ecuation of the regression line: [y slope].</p>
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- </div></span>
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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="GeneMergeValidation (class)">GeneMergeValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits, filename)
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- </h3><div class="docstring">
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- <div class="discussion">
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-
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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) <tt>filename</tt>: name of the
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- input file, used when generatig the plot files</p>
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- </div>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 66</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'>Gene_Merge(slope)</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'>Gene Merge</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 BLAST hits make evidence about a merge of two</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'> genes that match the predicted gene. Meaning of the output displayed:</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'> slope of the linear regression of the relationship between the start and</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'> stop offsets of the hsps (see the plot). Invalid slopes are around 45 degrees.</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'>merge</span><span class='tstring_end'>&quot;</span></span>
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- <span class='kw'>end</span></pre>
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- </table>
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- </div>
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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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- <span id=""></span>
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- <div class="method_details first">
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- <h3 class="signature first" id="filename-instance_method">
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-
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- - (<tt>Object</tt>) <strong>filename</strong> <span class="extras">(readonly)</span>
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-
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- </h3><div class="docstring">
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- <div class="discussion">
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-
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- <p>Returns the value of attribute filename</p>
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- </div>
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- </div>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 57</span>
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-
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- <span class='kw'>def</span> <span class='id identifier rubyid_filename'>filename</span>
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- <span class='ivar'>@filename</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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-
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- <span id=""></span>
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- <div class="method_details ">
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- <h3 class="signature " id="hits-instance_method">
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-
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- - (<tt>Object</tt>) <strong>hits</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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-
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- <p>Returns the value of attribute hits</p>
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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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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 55</span>
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-
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- <span class='kw'>def</span> <span class='id identifier rubyid_hits'>hits</span>
523
- <span class='ivar'>@hits</span>
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- <span class='kw'>end</span></pre>
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- </td>
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- </table>
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- </div>
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-
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-
531
- <span id=""></span>
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- <div class="method_details ">
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- <h3 class="signature " id="prediction-instance_method">
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-
535
- - (<tt>Object</tt>) <strong>prediction</strong> <span class="extras">(readonly)</span>
536
-
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-
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-
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-
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-
541
- </h3><div class="docstring">
542
- <div class="discussion">
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-
544
- <p>Returns the value of attribute prediction</p>
545
-
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-
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- </div>
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- </div>
549
- <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_gene_merge.rb', line 56</span>
564
-
565
- <span class='kw'>def</span> <span class='id identifier rubyid_prediction'>prediction</span>
566
- <span class='ivar'>@prediction</span>
567
- <span class='kw'>end</span></pre>
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- </td>
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- </table>
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- </div>
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-
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- </div>
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- <div id="instance_method_details" class="method_details_list">
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- <h2>Instance Method Details</h2>
578
-
579
-
580
- <div class="method_details first">
581
- <h3 class="signature first" id="plot_2d_start_from-instance_method">
582
-
583
- - (<tt>Object</tt>) <strong>plot_2d_start_from</strong>(slope, y_intercept, output = &quot;#{filename}_match_2d.json&quot;, hits = @hits)
584
-
585
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586
-
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-
588
-
589
- </h3><div class="docstring">
590
- <div class="discussion">
591
-
592
- <p>Generates a json file containing data used for plotting the start/end of
593
- the matched region offsets in the prediction Param <tt>slope</tt>: slope of
594
- the linear regression line <tt>y_intercept</tt>: the ecuation of the line
595
- is y= slope*x + y_intercept <tt>output</tt>: location where the plot will
596
- be saved in jped file format <tt>hits</tt>: array of Sequence objects</p>
597
-
598
-
599
- </div>
600
- </div>
601
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- </div><table class="source_code">
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- <td>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 155</span>
628
-
629
- <span class='kw'>def</span> <span class='id identifier rubyid_plot_2d_start_from'>plot_2d_start_from</span><span class='lparen'>(</span><span class='id identifier rubyid_slope'>slope</span><span class='comma'>,</span> <span class='id identifier rubyid_y_intercept'>y_intercept</span><span class='comma'>,</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='id identifier rubyid_filename'>filename</span><span class='rbrace'>}</span><span class='tstring_content'>_match_2d.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>
630
- <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>
631
- <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_hits'>hits</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='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>x</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_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='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_min'>min</span><span class='comma'>,</span>
632
- <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_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='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span><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>
633
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
634
- <span class='kw'>return</span> <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>
635
- <span class='symbol'>:scatter</span><span class='comma'>,</span>
636
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Start vs end hsp match</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
637
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
638
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>from</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
639
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>to</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
640
- <span class='id identifier rubyid_y_intercept'>y_intercept</span><span class='comma'>,</span>
641
- <span class='id identifier rubyid_slope'>slope</span><span class='rparen'>)</span>
642
-
643
- <span class='kw'>end</span></pre>
644
- </td>
645
- </tr>
646
- </table>
647
- </div>
648
-
649
- <div class="method_details ">
650
- <h3 class="signature " id="plot_matched_regions-instance_method">
651
-
652
- - (<tt>Object</tt>) <strong>plot_matched_regions</strong>(output = &quot;#{filename}_match.json&quot;, hits = @hits, prediction = @prediction)
653
-
654
-
655
-
656
-
657
-
658
- </h3><div class="docstring">
659
- <div class="discussion">
660
-
661
- <p>Generates a json file containing data used for plotting the matched region
662
- of the prediction for each hit Param <tt>output</tt>: location where the
663
- plot will be saved in jped file format <tt>hits</tt>: array of Sequence
664
- objects <tt>prediction</tt>: Sequence objects</p>
665
-
666
-
667
- </div>
668
- </div>
669
- <div class="tags">
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-
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-
672
- </div><table class="source_code">
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- </td>
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- <td>
706
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 120</span>
707
-
708
- <span class='kw'>def</span> <span class='id identifier rubyid_plot_matched_regions'>plot_matched_regions</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='id identifier rubyid_filename'>filename</span><span class='rbrace'>}</span><span class='tstring_content'>_match.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='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='rparen'>)</span>
709
-
710
- <span class='id identifier rubyid_colors'>colors</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>yellow</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</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='rbracket'>]</span>
711
- <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>
712
- <span class='id identifier rubyid_no_lines'>no_lines</span> <span class='op'>=</span> <span class='int'>100</span>
713
- <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>
714
-
715
- <span class='kw'>if</span> <span class='id identifier rubyid_ratio'>ratio</span> <span class='op'>==</span> <span class='int'>0</span>
716
- <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_hits'>hits</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_prediction'>prediction</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>
717
- <span class='id identifier rubyid_hits'>hits</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>
718
- <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_match_query_from'>match_query_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_match_query_to'>match_query_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='embexpr_beg'>#{</span><span class='id identifier rubyid_colors'>colors</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>%</span><span class='int'>2</span><span class='rbracket'>]</span><span class='rbrace'>}</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>
719
- <span class='kw'>else</span>
720
- <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_hits'>hits</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_prediction'>prediction</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>
721
- <span class='id identifier rubyid_hits'>hits</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>
722
- <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_match_query_from'>match_query_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_match_query_to'>match_query_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='embexpr_beg'>#{</span><span class='id identifier rubyid_colors'>colors</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='op'>%</span><span class='int'>2</span><span class='rbracket'>]</span><span class='rbrace'>}</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>
723
- <span class='kw'>end</span>
724
- <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
725
- <span class='kw'>return</span> <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>
726
- <span class='symbol'>:lines</span><span class='comma'>,</span>
727
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Prediction vs hit match</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
728
- <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>prediction, gray; prediction high-scoring alignmet seq, red; prediction high-scoring alignmet seq, yellow</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
729
- <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>
730
- <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>
731
- <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rparen'>)</span>
732
-
733
- <span class='kw'>end</span></pre>
734
- </td>
735
- </tr>
736
- </table>
737
- </div>
738
-
739
- <div class="method_details ">
740
- <h3 class="signature " id="run-instance_method">
741
-
742
- - (<tt>Object</tt>) <strong>run</strong>
743
-
744
-
745
-
746
-
747
-
748
- </h3><div class="docstring">
749
- <div class="discussion">
750
-
751
- <p>Validation test for gene merge Output: <tt>GeneMergeValidationOutput</tt>
752
- object</p>
753
-
754
-
755
- </div>
756
- </div>
757
- <div class="tags">
758
-
759
-
760
- </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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- 111</pre>
796
- </td>
797
- <td>
798
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 82</span>
799
-
800
- <span class='kw'>def</span> <span class='id identifier rubyid_run'>run</span>
801
- <span class='kw'>begin</span>
802
- <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>
803
- <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> <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>
804
-
805
- <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>
806
-
807
- <span class='id identifier rubyid_lm_slope'>lm_slope</span> <span class='op'>=</span> <span class='id identifier rubyid_slope'>slope</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
808
- <span class='id identifier rubyid_y_intercept'>y_intercept</span> <span class='op'>=</span> <span class='id identifier rubyid_slope'>slope</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
809
-
810
- <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>GeneMergeValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_lm_slope'>lm_slope</span><span class='rparen'>)</span>
811
-
812
- <span class='id identifier rubyid_plot1'>plot1</span> <span class='op'>=</span> <span class='id identifier rubyid_plot_2d_start_from'>plot_2d_start_from</span><span class='lparen'>(</span><span class='id identifier rubyid_lm_slope'>lm_slope</span><span class='comma'>,</span> <span class='id identifier rubyid_y_intercept'>y_intercept</span><span class='rparen'>)</span>
813
- <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>
814
- <span class='id identifier rubyid_plot2'>plot2</span> <span class='op'>=</span> <span class='id identifier rubyid_plot_matched_regions'>plot_matched_regions</span>
815
- <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>
816
- <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>
817
- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
818
-
819
- <span class='comment'># Exception is raised when blast founds no hits
820
- </span> <span class='kw'>rescue</span> <span class='const'>NotEnoughHitsError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
821
- <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>
822
- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
823
- <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
824
- <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>
825
- <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>
826
- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
827
- <span class='kw'>end</span>
828
-
829
- <span class='kw'>end</span></pre>
830
- </td>
831
- </tr>
832
- </table>
833
- </div>
834
-
835
- <div class="method_details ">
836
- <h3 class="signature " id="slope-instance_method">
837
-
838
- - (<tt>Object</tt>) <strong>slope</strong>(hits = @hits)
839
-
840
-
841
-
842
-
843
-
844
- </h3><div class="docstring">
845
- <div class="discussion">
846
-
847
- <p>Caclulates the slope of the regression line give a set of 2d coordonates of
848
- the start/stop offests of the hits Param <tt>hits</tt>: array of Sequence
849
- objects Code inspired from: <a
850
- href="http://engineering.sharethrough.com/blog/2012/09/12/simple-linear-regression-using-ruby">engineering.sharethrough.com/blog/2012/09/12/simple-linear-regression-using-ruby</a>/
851
- Output: The ecuation of the regression line: [y slope]</p>
852
-
853
-
854
- </div>
855
- </div>
856
- <div class="tags">
857
-
858
-
859
- </div><table class="source_code">
860
- <tr>
861
- <td>
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- <pre class="lines">
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- 203</pre>
890
- </td>
891
- <td>
892
- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 179</span>
893
-
894
- <span class='kw'>def</span> <span class='id identifier rubyid_slope'>slope</span><span class='lparen'>(</span><span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='rparen'>)</span>
895
-
896
- <span class='id identifier rubyid_pairs'>pairs</span> <span class='op'>=</span> <span class='ivar'>@hits</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='op'>|</span> <span class='const'>Pair</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</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='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_min'>min</span><span class='comma'>,</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='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span><span class='rparen'>)</span><span class='rbrace'>}</span>
897
-
898
- <span class='id identifier rubyid_xx'>xx</span> <span class='op'>=</span> <span class='id identifier rubyid_pairs'>pairs</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_pair'>pair</span><span class='op'>|</span> <span class='id identifier rubyid_pair'>pair</span><span class='period'>.</span><span class='id identifier rubyid_x'>x</span><span class='rbrace'>}</span>
899
- <span class='id identifier rubyid_yy'>yy</span> <span class='op'>=</span> <span class='id identifier rubyid_pairs'>pairs</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_pair'>pair</span><span class='op'>|</span> <span class='id identifier rubyid_pair'>pair</span><span class='period'>.</span><span class='id identifier rubyid_y'>y</span><span class='rbrace'>}</span>
900
-
901
- <span class='comment'># calculate the slope
902
- </span> <span class='id identifier rubyid_x_mean'>x_mean</span> <span class='op'>=</span> <span class='id identifier rubyid_xx'>xx</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span> <span class='op'>+</span> <span class='id identifier rubyid_sum'>sum</span> <span class='rbrace'>}</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_xx'>xx</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
903
- <span class='id identifier rubyid_y_mean'>y_mean</span> <span class='op'>=</span> <span class='id identifier rubyid_yy'>yy</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span> <span class='op'>+</span> <span class='id identifier rubyid_sum'>sum</span> <span class='rbrace'>}</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_yy'>yy</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
904
-
905
- <span class='id identifier rubyid_numerator'>numerator</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='int'>0</span><span class='op'>...</span><span class='id identifier rubyid_xx'>xx</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
906
- <span class='id identifier rubyid_sum'>sum</span> <span class='op'>+</span> <span class='lparen'>(</span><span class='lparen'>(</span><span class='id identifier rubyid_xx'>xx</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_x_mean'>x_mean</span><span class='rparen'>)</span> <span class='op'>*</span> <span class='lparen'>(</span><span class='id identifier rubyid_yy'>yy</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_y_mean'>y_mean</span><span class='rparen'>)</span><span class='rparen'>)</span>
907
- <span class='kw'>end</span>
908
-
909
- <span class='id identifier rubyid_denominator'>denominator</span> <span class='op'>=</span> <span class='id identifier rubyid_xx'>xx</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_x'>x</span><span class='op'>|</span>
910
- <span class='id identifier rubyid_sum'>sum</span> <span class='op'>+</span> <span class='lparen'>(</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span> <span class='op'>-</span> <span class='id identifier rubyid_x_mean'>x_mean</span><span class='rparen'>)</span> <span class='op'>**</span> <span class='int'>2</span><span class='rparen'>)</span>
911
- <span class='kw'>end</span>
912
-
913
- <span class='id identifier rubyid_slope'>slope</span> <span class='op'>=</span> <span class='id identifier rubyid_numerator'>numerator</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_denominator'>denominator</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
914
- <span class='id identifier rubyid_y_intercept'>y_intercept</span> <span class='op'>=</span> <span class='id identifier rubyid_y_mean'>y_mean</span> <span class='op'>-</span> <span class='lparen'>(</span><span class='id identifier rubyid_slope'>slope</span> <span class='op'>*</span> <span class='id identifier rubyid_x_mean'>x_mean</span><span class='rparen'>)</span>
915
-
916
- <span class='kw'>return</span> <span class='lbracket'>[</span><span class='id identifier rubyid_y_intercept'>y_intercept</span><span class='comma'>,</span> <span class='id identifier rubyid_slope'>slope</span><span class='rbracket'>]</span>
917
-
918
- <span class='kw'>end</span></pre>
919
- </td>
920
- </tr>
921
- </table>
922
- </div>
923
-
924
- </div>
925
-
926
- </div>
927
-
928
- <div id="footer">
929
- Generated on Sat Sep 28 07:01:33 2013 by
930
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
931
- 0.8.7.2 (ruby-1.9.3).
932
- </div>
933
-
934
- </body>
935
- </html>