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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- <div id="content"><h1>Class: LengthRankValidation
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- <dt class="r1">Inherits:</dt>
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- <p>Calculates a precentage based on the rank of the predicion among the hit
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- - (<tt><span class='object_link'><a href="" title="LengthRankValidation (class)">LengthRankValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits, threshold = 0.2)
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_rank.rb', line 49</span>
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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_threshold'>threshold</span> <span class='op'>=</span> <span class='float'>0.2</span><span class='rparen'>)</span>
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- <span class='kw'>super</span>
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- <span class='ivar'>@threshold</span> <span class='op'>=</span> <span class='id identifier rubyid_threshold'>threshold</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'>LengthRank</span><span class='tstring_end'>&quot;</span></span>
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- <span class='ivar'>@header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Length Rank</span><span class='tstring_end'>&quot;</span></span>
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- <span class='ivar'>@description</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Check whether the rank of the prediction length lies among 80% of </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'>all the BLAST hit lengths. Meaning of the output displayed: no of extreme length hits / total no of hits</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'>lenr</span><span class='tstring_end'>&quot;</span></span>
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- <span class='kw'>end</span></pre>
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- <p>Returns the value of attribute threshold</p>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_rank.rb', line 41</span>
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- <div class="method_details first">
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- <h3 class="signature first" id="run-instance_method">
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-
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- - (<tt>Object</tt>) <strong>run</strong>(hits = @hits, prediction = @prediction)
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- </h3><div class="docstring">
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- <div class="discussion">
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- <p>Calculates a precentage based on the rank of the predicion among the hit
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- lengths Params: <tt>hits</tt> (optional): a vector of <tt>Sequence</tt>
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- objects <tt>prediction</tt> (optional): a <tt>Sequence</tt> object Output:
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- <tt>LengthRankValidationOutput</tt> object</p>
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- </div>
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- <div class="tags">
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- <td>
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- <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_rank.rb', line 66</span>
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-
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- <span class='kw'>def</span> <span class='id identifier rubyid_run'>run</span><span class='lparen'>(</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>
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- <span class='kw'>begin</span>
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- <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>
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- <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>
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- <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>
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-
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- <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>
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-
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- <span class='id identifier rubyid_lengths'>lengths</span> <span class='op'>=</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_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span> <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_sort'>sort</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span><span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span><span class='op'>&lt;=&gt;</span><span class='id identifier rubyid_b'>b</span><span class='rbrace'>}</span>
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- <span class='id identifier rubyid_len'>len</span> <span class='op'>=</span> <span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
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- <span class='id identifier rubyid_median'>median</span> <span class='op'>=</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>%</span> <span class='int'>2</span> <span class='op'>==</span> <span class='int'>1</span> <span class='op'>?</span>
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- <span class='id identifier rubyid_lengths'>lengths</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span><span class='op'>/</span><span class='int'>2</span><span class='rbracket'>]</span> <span class='op'>:</span>
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- <span class='lparen'>(</span><span class='id identifier rubyid_lengths'>lengths</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span><span class='op'>/</span><span class='int'>2</span> <span class='op'>-</span> <span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>+</span> <span class='id identifier rubyid_lengths'>lengths</span><span class='lbracket'>[</span><span class='id identifier rubyid_len'>len</span><span class='op'>/</span><span class='int'>2</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span> <span class='op'>/</span> <span class='int'>2</span>
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-
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- <span class='id identifier rubyid_predicted_len'>predicted_len</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span>
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-
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- <span class='kw'>if</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='int'>1</span>
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- <span class='id identifier rubyid_msg'>msg</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
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- <span class='id identifier rubyid_percentage'>percentage</span> <span class='op'>=</span> <span class='int'>1</span>
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- <span class='kw'>else</span>
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- <span class='kw'>if</span> <span class='id identifier rubyid_predicted_len'>predicted_len</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_median'>median</span>
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- <span class='id identifier rubyid_rank'>rank</span> <span class='op'>=</span> <span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_predicted_len'>predicted_len</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
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- <span class='id identifier rubyid_percentage'>percentage</span> <span class='op'>=</span> <span class='id identifier rubyid_rank'>rank</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_len'>len</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
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- <span class='id identifier rubyid_msg'>msg</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>TOO_SHORT</span><span class='tstring_end'>&quot;</span></span>
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- <span class='kw'>else</span>
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- <span class='id identifier rubyid_rank'>rank</span> <span class='op'>=</span> <span class='id identifier rubyid_lengths'>lengths</span><span class='period'>.</span><span class='id identifier rubyid_find_all'>find_all</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_predicted_len'>predicted_len</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
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- <span class='id identifier rubyid_percentage'>percentage</span> <span class='op'>=</span> <span class='id identifier rubyid_rank'>rank</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_len'>len</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
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- <span class='id identifier rubyid_msg'>msg</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>TOO_LONG</span><span class='tstring_end'>&quot;</span></span>
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- <span class='kw'>end</span>
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- <span class='kw'>end</span>
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-
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- <span class='kw'>if</span> <span class='id identifier rubyid_percentage'>percentage</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_threshold'>threshold</span>
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- <span class='id identifier rubyid_msg'>msg</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
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- <span class='kw'>end</span>
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-
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- <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>LengthRankValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_msg'>msg</span><span class='comma'>,</span> <span class='id identifier rubyid_percentage'>percentage</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>2</span><span class='rparen'>)</span><span class='rparen'>)</span>
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- <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>
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- <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
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-
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- <span class='comment'># Exception is raised when blast founds no hits
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- </span> <span class='kw'>rescue</span> <span class='const'>NotEnoughHitsError</span><span class='comment'>#Exception
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- </span> <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>
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- <span class='kw'>else</span>
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- <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>
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- <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>
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- <span class='kw'>end</span>
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- <span class='kw'>end</span></pre>
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- <div id="footer">
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- Generated on Sat Sep 28 07:01:33 2013 by
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- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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- 0.8.7.2 (ruby-1.9.3).
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- </div>
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- </body>
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- </html>