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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- <span class="summary_desc"><div class='inline'>
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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 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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- </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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- </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">
543
-
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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-
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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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- </tr>
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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
-
586
-
587
-
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
- <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 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>