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
data/aux/files/js/script.js CHANGED
@@ -58,4 +58,14 @@ $(document).ready(function() {
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  }
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  }
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  });
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+ });
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+
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+ $( document ).on( "click", "td, .plot_btn", function( event ) {
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+ if ($(this).hasClass('success') || $(this).hasClass('danger')){
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+ var title = $(this).attr('title');
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+ var val = title.replace(/[ \/]/g, '');
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+ addData(this, val);
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+ } else if ($(this).hasClass('plot_btn')){
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+ addData(this, 'all');
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+ }
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  });
data/aux/json_footer.erb ADDED
@@ -0,0 +1,8 @@
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+ </tbody></table>
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+ </div>
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+ <% if output_files.length > 1 %>
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+ <nav><ul class="pagination">
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+ <% output_files.each_with_index do |results_html, idx| %>
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+ <li><a href="<%=results_html%>"><%= idx + 1 %></a></li>
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+ <% end %></ul></nav><%end%>
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+ <footer><div class="container center-block"><p class="text-muted text-center">Please cite: "Dragan M, Moghul MI, Priyam A &amp; Wurm Y <em>(in prep)</em> GeneValidator: identify problematic gene predictions"<br/> Developed at <a href="http://yannick.poulet.org" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a> and <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank">Google Summer of Code 2013</a><br/>This page was created by <a href="https://github.com/wurmlab/GeneValidator" target="_blank" >GeneValidator</a> v<%= GeneValidator::VERSION %></p></div></footer></body></html>
data/aux/json_header.erb ADDED
@@ -0,0 +1,19 @@
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+ <!DOCTYPE html><html><head><title>GeneValidator: identify problems with gene predictions</title><meta content="text/html; charset=utf-8" http-equiv="Content-Type"><script type="text/javascript" src="files/js/jquery-2.1.1.min.js"></script><script type="text/javascript" src="files/js/bootstrap.min.js"></script><script type="text/javascript" src="files/js/jquery.tablesorter.min.js"></script><script type="text/javascript" src="files/js/d3.v3.min.js"></script><script type="text/javascript" src="files/js/script.js"></script><script type="text/javascript" src="files/js/plots.js"></script><link href="files/css/bootstrap.min.css" rel="stylesheet" type="text/css"><link href="files/css/font-awesome.min.css" rel="stylesheet" type="text/css"><link href="files/css/style.css" rel="stylesheet" type="text/css"></head>
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+ <body>
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+ <div aria-hidden="true" aria-labelledby="myModalLabel3" class="modal" id="spinner1" role="dialog" tabindex="-1"><div class="modal-dialog"><div class="modal-content"><div class="modal-body text-center"><h2>Loading ...</h2><i class="fa fa-spinner fa-5x fa-spin"></i></div></div></div></div>
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+ <div class="modal fade" id="alert" aria-hidden="true" aria-labelledby="myModalLabel5" role="dialog" tabindex="-1"><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button><h4 class="modal-title">Oops, Something went wrong!</h4></div><div class="modal-body"><p>This operation is not posible. There seems to be too many queries...</p></div><div class="modal-footer"><button type="button" class="btn btn-default" data-dismiss="modal">Close</button></div></div></div></div>
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+ <div class="modal fade" id="browseralert" aria-hidden="true" aria-labelledby="browser" role="dialog" tabindex="-1"><div class="modal-dialog"><div class="modal-content browser-alert"><div class="modal-header"><button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button><h4 class="modal-title">Incompatible Browser - Please use Mozilla Firefox!</h4></div><div class="modal-body" id="browseralertbody"><p id="browseralertText">The plugin that we use to display the validation plots means that your browser is currently unsupported.</p><p>Please use <strong>Mozilla FireFox</strong> to view this file.</p></div></div></div></div>
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+ <div class="container"><span class="menu_icon pull-right"><a href="#" id="show_all_plots" onclick="show_all_plots(this);"><i class="fa fa-2x fa-bar-chart-o"></i><br>Show All Charts</a></span><span class="menu_icon pull-right"><a href="https://github.com/wurmlab/GeneValidator" target="_blank"><i class="fa fa-2x fa-github"></i><br>Source Code</a></span><span class="menu_icon pull-right"><a href="http://wurmlab.github.io/tools/genevalidator/"><i class="fa fa-2x fa-info-circle"></i><br>About</a></span><div class="clearfix"></div><img class="logo" src="files/img/gene.png" alt="logo"><div class="page-title"><h1>Gene Validator <small>v<%= GeneValidator::VERSION %></small></h1><h4 class="subheading">Identify Problems with Gene Predictions</h4></div><br/><br/>
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+ <div id="report"><div id="report_1"></div></div><br><br>
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+ <table id="sortable_table" class="table table-striped table-collapsed table-bordered table-condensed tablesorter"><thead>
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+ <tr id="header"><th>#</th><th>Ranking</th><th>Sequence Definition&nbsp;<span data-toggle="tooltip" title="Query definition as it apears in the input fasta file." data-placement="top"><i class="fa fa-question-circle"></i></span></th><th>No. Hits&nbsp;<span data-toggle="tooltip" title="Number of non-identical hits found by BLAST." data-placement="top"><i class="fa fa-question-circle"></i></span></th>
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+ <% @json_array[0]['validations'].each do |_short_header, item| %>
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+ <th class="sorter-false"><b><%= item['header'] %></b>
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+ <% if item['header'] == "LengthCluster" || item['header'] == "GeneMerge" || item['header'] == "MainORF" || item['header'] == "MissingExtraSequences" %>
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+ <span data-toggle="tooltip" title="Charts available for this validation" data-placement="top"><i class="fa fa-bar-chart-o chartIcon"></i></span>&nbsp;<span data-toggle="tooltip" title="<%=item['description']%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
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+ <% else %>
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+ <span data-toggle="tooltip" title="<%=item['description']%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
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+ <% end %>
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+ </th>
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+ <% end %>
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+ <th class="sorter-false chart-column"></th></tr></thead><tbody>
data/aux/json_query.erb ADDED
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+ <tr data-target="toggle<%= @row['idx'] %>" data-jsonFile="files/json/<%= @config[:filename] %>_<%= @row['idx'] %>.json">
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+ <td title="idx"><%= @row['idx'] %></td>
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+ <td data-score="<%= @row['overall_score'] %>"><div class="ratings"><div class="empty-stars"></div><div class="full-stars" style="width:<%= @row['overall_score'] * 0.85 %>%;"></div></div></td>
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+ <td title="Definition"><%= @row['definition'] %></td>
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+ <td title="No. Hits"><%= @row['no_hits'] %></td>
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+ <% @row['validations'].each do |_short_header, item| %>
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+ <td title="<%=item['header']%>" class="<%=item['status']%>"><%= item['print']%></td>
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+ <% end %>
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+ <% if @row['validations'].select{|_short_header, item| item['graphs'] != nil}.map{|_short_header, item| item['graphs'].length}.inject(0){|r, e| r+e } != 0 %>
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+ <td><button title="Show plots" class="plot_btn btn btn-default"><i class="fa fa-bar-chart-o"></i></button></td>
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+ <% else %>
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+ <td></td>
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+ <% end %>
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+ </tr>
data/aux/template_footer.erb CHANGED
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- </tbody>
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- </table>
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+ </tbody></table>
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  <script>
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  var evaluation_div = document.getElementById('report_1');
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  var content_less = "<br><%= less %><div class=\"clearfix\"></div><br><button type=\"button\" onClick='add_content()' class=\"btn btn-primary btn-sm\"> Show More</button>";
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  var content = "<%= evaluation %> <div class=\"clearfix\"></div><br><button type=\"button\" onClick='evaluation_div.innerHTML=content_less' class=\"btn btn-primary btn-sm\"> Show Less</button>";
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  evaluation_div.innerHTML = content_less;
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  function add_content(){
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- evaluation_div = document.getElementById('report_1')
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+ evaluation_div = document.getElementById('report_1');
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  evaluation_div.innerHTML=content;
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- addPlot('report_1', '<%= plot_statistics.filename %>', '<%= plot_statistics.type %>', '<%= plot_statistics.title %>', '<%= plot_statistics.footer %>', '<%= plot_statistics.xtitle %>', '<%= plot_statistics.ytitle %>');
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+ addOverallPlot('files/json/overview.json');
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  }
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  </script>
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- <div aria-hidden="true" aria-labelledby="myModalLabel3" class="modal" id="spinner1" role="dialog" tabindex="-1">
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- <div class="modal-dialog">
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- <div class="modal-content">
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- <div class="modal-body text-center">
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- <h2>Loading ...</h2>
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- <i class="fa fa-spinner fa-5x fa-spin"></i>
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- </div>
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- </div>
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- </div>
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- </div>
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-
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- <div class="modal fade" id="alert" aria-hidden="true" aria-labelledby="myModalLabel5" role="dialog" tabindex="-1">
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- <div class="modal-dialog">
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- <div class="modal-content">
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- <div class="modal-header">
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- <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
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- <h4 class="modal-title">Oops, Something went wrong!</h4>
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- </div>
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- <div class="modal-body">
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- <p>This operation is not posible. There seems to be too many queries...</p>
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- </div>
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- <div class="modal-footer">
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- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
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- </div>
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- </div>
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- </div>
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- </div>
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-
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- <div class="modal fade" id="browseralert" aria-hidden="true" aria-labelledby="browser" role="dialog" tabindex="-1">
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- <div class="modal-dialog">
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- <div class="modal-content browser-alert">
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- <div class="modal-header">
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- <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
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- <h4 class="modal-title">Incompatible Browser - Please use Mozilla Firefox!</h4>
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- </div>
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- <div class="modal-body" id="browseralertbody">
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- <p id="browseralertText">The plugin that we use to display the validation plots means that your browser is currently unsupported.</p>
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- <p>Please use <strong>Mozilla FireFox</strong> to view this file.</p>
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- </div>
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- </div>
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- </div>
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- </div>
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-
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  </div>
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-
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- <footer >
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- <div class="container center-block">
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- <p class="text-muted text-center">Please cite: "Dragan M, Moghul MI, Priyam A & Wurm Y <em>(in prep)</em> GeneValidator: identify problematic gene predictions"<br/>
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- Developed at <a href="http://yannick.poulet.org" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a> and <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank">Google Summer of Code 2013</a><br/>
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- This page was created by <a href="https://github.com/wurmlab/GeneValidator" target="_blank" >GeneValidator</a> v<%= GeneValidator::VERSION %></p>
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- </div>
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- </footer>
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-
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- </html>
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+ <% if output_files.length > 1 %>
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+ <nav><ul class="pagination">
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+ <% output_files.each_with_index do |results_html, idx| %>
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+ <li><a href="<%=results_html%>"><%= idx + 1 %></a></li>
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+ <% end %></ul></nav><%end%>
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+ <footer><div class="container center-block"><p class="text-muted text-center">Please cite: "Dragan M, Moghul MI, Priyam A &amp; Wurm Y <em>(in prep)</em> GeneValidator: identify problematic gene predictions"<br/> Developed at <a href="http://yannick.poulet.org" target="_blank">Wurm Lab</a>, <a href="http://www.sbcs.qmul.ac.uk" target="_blank">QMUL</a> with funding by <a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank">BBSRC</a> and <a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank">Google Summer of Code 2013</a><br/>This page was created by <a href="https://github.com/wurmlab/GeneValidator" target="_blank" >GeneValidator</a> v<%= GeneValidator::VERSION %></p></div></footer></body></html>
data/aux/template_header.erb CHANGED
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- <!DOCTYPE html>
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- <html>
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- <head>
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- <title>GeneValidator: identify problems with gene predictions</title>
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- <meta content="text/html; charset=utf-8" http-equiv="Content-Type">
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-
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- <script type="text/javascript" src="files/js/jquery-2.1.1.min.js"></script>
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- <script type="text/javascript" src="files/js/bootstrap.min.js"></script>
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- <script type="text/javascript" src="files/js/jquery.tablesorter.min.js"></script>
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- <script type="text/javascript" src="files/js/d3.v3.min.js"></script>
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- <script type="text/javascript" src="files/js/script.js"></script>
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- <script type="text/javascript" src="files/js/plots.js"></script>
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-
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- <link href="files/css/bootstrap.min.css" rel="stylesheet" type="text/css">
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- <link href="files/css/font-awesome.min.css" rel="stylesheet" type="text/css">
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- <link href="files/css/style.css" rel="stylesheet" type="text/css">
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-
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- </head>
1
+ <!DOCTYPE html><html><head><title>GeneValidator: identify problems with gene predictions</title><meta content="text/html; charset=utf-8" http-equiv="Content-Type"><script type="text/javascript" src="files/js/jquery-2.1.1.min.js"></script><script type="text/javascript" src="files/js/bootstrap.min.js"></script><script type="text/javascript" src="files/js/jquery.tablesorter.min.js"></script><script type="text/javascript" src="files/js/d3.v3.min.js"></script><script type="text/javascript" src="files/js/script.js"></script><script type="text/javascript" src="files/js/plots.js"></script><link href="files/css/bootstrap.min.css" rel="stylesheet" type="text/css"><link href="files/css/font-awesome.min.css" rel="stylesheet" type="text/css"><link href="files/css/style.css" rel="stylesheet" type="text/css"></head>
19
2
  <body>
20
- <div class="container">
21
- <span class="menu_icon pull-right"><a href="#" id="show_all_plots" onclick="show_all_plots(this);"><i class="fa fa-2x fa-bar-chart-o"></i><br>Show All Charts</a></span>
22
- <span class="menu_icon pull-right"><a href="https://github.com/wurmlab/GeneValidator" target="_blank"><i class="fa fa-2x fa-github"></i><br>Source Code</a></span>
23
- <span class="menu_icon pull-right"><a href="http://wurmlab.github.io/tools/genevalidator/documentation/v1/"><i class="fa fa-2x fa-info-circle"></i><br>About</a></span>
24
- <div class="clearfix"></div>
25
- <img class="logo" src="files/img/gene.png" alt="logo">
26
- <div class="page-title">
27
- <h1>Gene Validator <small>v<%= GeneValidator::VERSION %></small></h1>
28
- <h4 class="subheading">Identify Problems with Gene Predictions</h4>
29
- </div>
30
- <br/><br/>
31
- <div id="report">
32
- <div id="report_1"></div>
33
- </div>
34
- <br><br>
35
- <table id="sortable_table" class="table table-collapsed table-bordered table-condensed tablesorter">
36
- <thead>
37
- <tr id="header">
38
- <th>#</th>
39
- <th>Ranking</th>
40
- <th>Sequence Definition
41
- <span data-toggle="tooltip" title="Query definition as it apears in the input fasta file." data-placement="top"><i class="fa fa-question-circle"></i></span>
42
- </th>
43
- <th>No. Hits
44
- <span data-toggle="tooltip" title="Number of non-identical hits found by BLAST." data-placement="top"><i class="fa fa-question-circle"></i></span>
45
- </th>
46
- <% @validations.each do |item| %>
47
- <th class="sorter-false">
48
- <b><%= item.header %></b>
49
- <% if item.short_header == "LengthCluster" || item.short_header == "Gene_Merge" || item.short_header == "ORF" || item.short_header == "MA" %>
50
- <span data-toggle="tooltip" title="Charts available for this validation" data-placement="top"><i class="fa fa-bar-chart-o chartIcon"></i></span>&nbsp;<span data-toggle="tooltip" title="<%=item.description%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
51
- <% else %>
52
- <span data-toggle="tooltip" title="<%=item.description%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
53
- <% end %>
54
- </th>
55
- <% end %>
56
- <th class="sorter-false chart-column"></th>
57
- </tr>
58
- </thead>
59
- <tbody>
3
+ <div aria-hidden="true" aria-labelledby="myModalLabel3" class="modal" id="spinner1" role="dialog" tabindex="-1"><div class="modal-dialog"><div class="modal-content"><div class="modal-body text-center"><h2>Loading ...</h2><i class="fa fa-spinner fa-5x fa-spin"></i></div></div></div></div>
4
+ <div class="modal fade" id="alert" aria-hidden="true" aria-labelledby="myModalLabel5" role="dialog" tabindex="-1"><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button><h4 class="modal-title">Oops, Something went wrong!</h4></div><div class="modal-body"><p>This operation is not posible. There seems to be too many queries...</p></div><div class="modal-footer"><button type="button" class="btn btn-default" data-dismiss="modal">Close</button></div></div></div></div>
5
+ <div class="modal fade" id="browseralert" aria-hidden="true" aria-labelledby="browser" role="dialog" tabindex="-1"><div class="modal-dialog"><div class="modal-content browser-alert"><div class="modal-header"><button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button><h4 class="modal-title">Incompatible Browser - Please use Mozilla Firefox!</h4></div><div class="modal-body" id="browseralertbody"><p id="browseralertText">The plugin that we use to display the validation plots means that your browser is currently unsupported.</p><p>Please use <strong>Mozilla FireFox</strong> to view this file.</p></div></div></div></div>
6
+ <div class="container"><span class="menu_icon pull-right"><a href="#" id="show_all_plots" onclick="show_all_plots(this);"><i class="fa fa-2x fa-bar-chart-o"></i><br>Show All Charts</a></span><span class="menu_icon pull-right"><a href="https://github.com/wurmlab/GeneValidator" target="_blank"><i class="fa fa-2x fa-github"></i><br>Source Code</a></span><span class="menu_icon pull-right"><a href="http://wurmlab.github.io/tools/genevalidator/"><i class="fa fa-2x fa-info-circle"></i><br>About</a></span><div class="clearfix"></div><img class="logo" src="files/img/gene.png" alt="logo"><div class="page-title"><h1>Gene Validator <small>v<%= GeneValidator::VERSION %></small></h1><h4 class="subheading">Identify Problems with Gene Predictions</h4></div><br/><br/>
7
+ <div id="report"><div id="report_1"></div></div><br><br>
8
+ <table id="sortable_table" class="table table-striped table-collapsed table-bordered table-condensed tablesorter"><thead>
9
+ <tr id="header"><th>#</th><th>Ranking</th><th>Sequence Definition&nbsp;<span data-toggle="tooltip" title="Query definition as it apears in the input fasta file." data-placement="top"><i class="fa fa-question-circle"></i></span></th><th>No. Hits&nbsp;<span data-toggle="tooltip" title="Number of non-identical hits found by BLAST." data-placement="top"><i class="fa fa-question-circle"></i></span></th>
10
+ <% @validations.each do |item| %>
11
+ <th class="sorter-false"><b><%= item.header %></b>
12
+ <% if item.short_header == "LengthCluster" || item.short_header == "GeneMerge" || item.short_header == "MainORF" || item.short_header == "MissingExtraSequences" %>
13
+ <span data-toggle="tooltip" title="Charts available for this validation" data-placement="top"><i class="fa fa-bar-chart-o chartIcon"></i></span>&nbsp;<span data-toggle="tooltip" title="<%=item.description%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
14
+ <% else %>
15
+ <span data-toggle="tooltip" title="<%=item.description%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
16
+ <% end %>
17
+ </th>
18
+ <% end %>
19
+ <th class="sorter-false chart-column"></th></tr></thead><tbody>
data/aux/template_query.erb CHANGED
@@ -1,42 +1,14 @@
1
- <tr>
2
- <td><%= @idx %></td>
1
+ <tr data-target="toggle<%= @idx %>" data-jsonFile="files/json/<%= @config[:filename] %>_<%= @idx %>.json">
2
+ <td title="idx"><%= @idx %></td>
3
3
  <td data-score="<%= overall_score %>"><div class="ratings"><div class="empty-stars"></div><div class="full-stars" style="width:<%= overall_score * 0.85 %>%;"></div></div></td>
4
- <td title="Definition" class="seq_definition"><%= @prediction_def.scan(/([^ ]+)/)[0][0] %> <%= @prediction_def.scan(/([^ ]+)(.*)/)[0][1] %></td>
4
+ <td title="Definition"><%= @prediction_def %></td>
5
5
  <td title="No. Hits"><%= @nr_hits %></td>
6
6
  <% @validations.each do |item| %>
7
- <% if item.color == 'warning' %>
8
- <td title="<%=item.header%>" class="<%=item.color%>"><%= item.print%></td>
9
- <% elsif item.plot_files != nil %>
10
- <td title="<%=item.header%>" class="<%=item.color%> my-btn-<%=item.color%>" data-approach="<%= item.approach%>" data-explanation="<%= item.explanation%>" data-conclusion="<%= item.conclusion%>" onclick="showDiv(this, '<%= toggle %>');
11
- <% item.plot_files.each do |plot| %>
12
- addPlot('<%= toggle %>', 'files/json/<%= plot.filename %>', '<%= plot.type %>', '<%= plot.title %>', '<%= plot.footer %>', '<%= plot.xtitle %>', '<%= plot.ytitle %>', '<%= plot.aux1 %>', '<%= plot.aux2 %>');
13
- <% end %>AddExplanation(this, '<%=toggle%>');"><%= item.print%></td>
14
- <% elsif item.plot_files == nil %>
15
- <td title="<%=item.header%>" class="<%=item.color%>" data-approach="<%= item.approach%>" data-explanation="<%= item.explanation%>" data-conclusion="<%= item.conclusion%>" onclick="showDiv(this, '<%= toggle %>'); AddExplanation(this,'<%=toggle%>');"><%= item.print%></td>
16
- <% end %>
7
+ <td title="<%=item.header%>" class="<%=item.color%>"><%= item.print%></td>
17
8
  <% end %>
18
-
19
9
  <% if @validations.select{|item| item.plot_files != nil}.map{|item| item.plot_files.length}.inject(0){|r, e| r+e } != 0 %>
20
- <td>
21
- <button title="Show plots" name="plot_btn" class="plot_btn btn btn-default" onclick="showDiv(this, '<%= toggle %>');
22
- <% @validations.each do |item| %>
23
- <% if item.plot_files != nil %>
24
- <% item.plot_files.each do |plot| %> addPlot('<%= toggle %>', 'files/json/<%= plot.filename %>', '<%= plot.type %>', '<%= plot.title %>', '<%= plot.footer %>', '<%= plot.xtitle %>', '<%= plot.ytitle %>', '<%= plot.aux1 %>', '<%= plot.aux2 %>');<% end %>
25
- <% end %>
26
- <% end %>"><i class="fa fa-bar-chart-o"></i></button>
27
- </td>
28
- </tr>
29
- <tr class="tablesorter-childRow" name="plot_row" style="display:none;">
30
- <td colspan="<%=validations.length + 7%>" id="<%=toggle %>row">
31
- <div id="<%=toggle%>" class="expanded-child"></div>
32
- </td>
33
- </tr>
10
+ <td><button title="Show plots" class="plot_btn btn btn-default"><i class="fa fa-bar-chart-o"></i></button></td>
34
11
  <% else %>
35
- <td></td>
36
- </tr>
37
- <tr class="tablesorter-childRow" style="display:none;">
38
- <td colspan="<%=validations.length + 7%>">
39
- <div></div>
40
- </td>
41
- </tr>
42
- <% end %>
12
+ <td></td>
13
+ <% end %>
14
+ </tr>
data/bin/genevalidator CHANGED
@@ -1,6 +1,9 @@
1
1
  #!/usr/bin/env ruby
2
2
  require 'optparse'
3
+
3
4
  require 'genevalidator'
5
+ require 'genevalidator/get_raw_sequences'
6
+ require 'genevalidator/json_to_gv_results'
4
7
  require 'genevalidator/version'
5
8
 
6
9
  opt = {}
@@ -27,8 +30,8 @@ BANNER
27
30
  ' dup = Check for duplications,',
28
31
  ' frame = Open reading frame (ORF) validation,',
29
32
  ' orf = Main ORF validation,',
30
- ' align = Validating based on multiple alignment') do |lst|
31
- opt[:validations] = lst
33
+ ' align = Validating based on multiple alignment') do |val|
34
+ opt[:validations] = val
32
35
  end
33
36
 
34
37
  opt[:db] = 'swissprot -remote'
@@ -39,20 +42,33 @@ BANNER
39
42
  opt[:db] = db
40
43
  end
41
44
 
42
- opts.on('-x', '--blast_xml_file [FILE]',
45
+ opts.on('-e', '--extract_raw_seqs',
46
+ 'Produces a fasta file of the raw sequences of all BLAST hits in the',
47
+ 'supplied BLAST output file. This fasta file can then be provided to',
48
+ 'GeneValidator with the "-r", "--raw_sequences" argument') do
49
+ opt[:extract_raw_seqs] = true
50
+ end
51
+
52
+ opts.on('-j', '--json_file [JSON_FILE]',
53
+ 'Generate GV results from a json file (or a subset of a json file)',
54
+ 'produced from GeneValidator') do |json|
55
+ opt[:json_file] = json
56
+ end
57
+
58
+ opts.on('-x', '--blast_xml_file [BLAST_XML_FILE]',
43
59
  'Provide GeneValidator with a pre-computed BLAST XML output',
44
60
  'file (BLAST -outfmt option 5).') do |blast_xml_file|
45
61
  opt[:blast_xml_file] = blast_xml_file
46
62
  end
47
63
 
48
- opts.on('-t', '--blast_tabular_file [FILE]',
64
+ opts.on('-t', '--blast_tabular_file [BLAST_TABULAR_FILE]',
49
65
  'Provide GeneValidator with a pre-computed BLAST tabular output',
50
66
  'file. (BLAST -outfmt option 6).') do |blast_tabular_file|
51
67
  opt[:blast_tabular_file] = blast_tabular_file
52
68
  end
53
69
 
54
70
  # default blast tabular columns
55
- opts.on('-o', '--blast_tabular_options [Options]',
71
+ opts.on('-o', '--blast_tabular_options [BLAST_TABULAR_OPTIONS]',
56
72
  'Custom format used in BLAST -outfmt argument',
57
73
  'See BLAST+ manual pages for more details') do |blast_table_options|
58
74
  opt[:blast_tabular_options] = blast_table_options
@@ -64,32 +80,18 @@ BANNER
64
80
  'BLAST and Mafft within GeneValidator.') do |num_threads|
65
81
  opt[:num_threads] = num_threads
66
82
  end
67
-
68
- opt[:fast] = false
69
- opts.on('-f', '--fast',
70
- 'Run BLAST on all sequences together (rather than separately)',
71
- 'to speed up the analysis.',
72
- 'However, this means that there will be a longer wait before the',
73
- 'results can be viewed (as GeneValidator will need to run BLAST',
74
- 'on all sequences before producing any results).',
75
- 'The speed difference will be more apparent on larger input files') do
76
- opt[:fast] = true
77
- end
78
-
83
+
79
84
  opts.on('-r', '--raw_sequences [raw_seq]',
80
85
  'Supply a fasta file of the raw sequences of all BLAST hits present',
81
86
  'in the supplied BLAST XML or BLAST tabular file.') do |raw_seq|
82
87
  opt[:raw_sequences] = raw_seq
83
88
  end
84
89
 
85
- opts.on('-m', '--mafft_bin [MAFFT_PATH]',
86
- 'Path to MAFFT bin folder (is added to $PATH variable)') do |mafft|
87
- opt[:mafft_bin] = mafft
88
- end
89
-
90
- opts.on('-b', '--blast_bin [BLAST_PATH]',
91
- 'Path to BLAST+ bin folder (is added to $PATH variable)') do |blast|
92
- opt[:blast_bin] = blast
90
+ opts.on('-b', '--binaries [binaries]', Array,
91
+ 'Path to BLAST and MAFFT bin folders (is added to $PATH variable)',
92
+ 'To be provided as follows:',
93
+ ' $ genevalidator -b /blast/bin/path/ -b /mafft/bin/path/') do |bin|
94
+ (opt[:bin] ||= []).concat(bin)
93
95
  end
94
96
 
95
97
  opts.on('--version', 'The version of GeneValidator that you are running.') do
@@ -98,7 +100,7 @@ BANNER
98
100
  end
99
101
 
100
102
  opts.on('-h', '--help', 'Show this screen.') do
101
- puts opt_parser
103
+ $stderr.puts opt_parser
102
104
  exit
103
105
  end
104
106
  end
@@ -109,8 +111,8 @@ begin
109
111
  $stderr.puts 'Error: you must specify a single fasta input file instead' \
110
112
  ' of ' + ARGV.length.to_s + ".\n"
111
113
  exit 1
112
- elsif ARGV.length == 0
113
- puts opt_parser
114
+ elsif ARGV.length == 0 && opt[:extract_raw_seqs].nil? && opt[:json_file].nil?
115
+ $stderr.puts opt_parser
114
116
  exit 1
115
117
  end
116
118
  rescue OptionParser::ParseError
@@ -118,10 +120,21 @@ rescue OptionParser::ParseError
118
120
  exit 1
119
121
  end
120
122
 
121
- start = Time.now
122
123
  opt[:input_fasta_file] = ARGV[0]
123
124
 
124
- (GeneValidator::Validation.new(opt)).run
125
+ start = Time.now
126
+
127
+ if opt[:extract_raw_seqs] && opt[:raw_sequences].nil?
128
+ GeneValidator.opt = opt
129
+ GeneValidator.config = {}
130
+ GeneValidator::RawSequences.run
131
+ elsif opt[:json_file]
132
+ GeneValidator.opt = opt
133
+ GeneValidator::JsonToGVResults.run
134
+ else
135
+ GeneValidator.init(opt)
136
+ GeneValidator.run
137
+ end
125
138
 
126
- puts "Total running time: #{(Time.now - start).round(3)}s"
127
- puts # a blank line
139
+ $stderr.puts "Total running time: #{(Time.now - start).round(3)}s"
140
+ $stderr.puts # a blank line
data/genevalidator.gemspec CHANGED
@@ -1,4 +1,4 @@
1
- # coding: utf-8
1
+ # coding: utf-8
2
2
  lib = File.expand_path('../lib', __FILE__)
3
3
  $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
4
4
  require 'genevalidator/version'
@@ -7,22 +7,26 @@ Gem::Specification.new do |s|
7
7
  # meta
8
8
  s.name = 'genevalidator'
9
9
  s.version = GeneValidator::VERSION
10
- s.authors = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam', 'Yannick Wurm']
10
+ s.authors = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam',
11
+ 'Yannick Wurm']
11
12
  s.email = 'y.wurm@qmul.ac.uk'
12
13
  s.homepage = 'https://github.com/wurmlab/GeneValidator'
13
14
  s.license = 'AGPL'
14
15
  s.summary = 'Identifying problems with gene predictions.'
15
- s.description = <<DESC
16
- The tool validates the input predicted genes and provides useful information (length validation, gene merge validation, sequence duplication checking, ORF finding) based on the similarities to genes in public databases.
17
- DESC
16
+ s.description = 'The tool validates the input predicted genes and provides' \
17
+ ' useful information (length validation, gene merge'\
18
+ ' validation, sequence duplication checking, ORF finding)' \
19
+ ' based on the similarities to genes in public databases.'
18
20
 
19
- s.required_ruby_version = '>= 2.0.0'
21
+ s.required_ruby_version = '>= 2.0.0'
20
22
  s.add_development_dependency 'bundler', '~> 1.6'
21
23
  s.add_development_dependency 'rake', '~>10.3'
24
+ s.add_development_dependency 'yard', '~> 0.8'
25
+ s.add_development_dependency 'codeclimate-test-reporter', '~> 0.4', '>= 0.4.7'
22
26
  s.add_dependency('bio', '~> 1.4')
23
27
  s.add_dependency('bio-blastxmlparser', '~>2.0')
24
28
  s.add_dependency('minitest', '~> 5.4')
25
- s.add_dependency('statsample', '~> 1.4')
29
+ s.add_dependency('statsample', '1.4') # Updating to 1.5 breaks GV
26
30
 
27
31
  s.files = `git ls-files -z`.split("\x0")
28
32
  s.executables = s.files.grep(%r{^bin/}) { |f| File.basename(f) }