RubyGems - genevalidator - Versions diffs - 1.6.1 → 1.6.2 - Mend

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

checksums.yaml +4 -4
data/.gitignore +3 -1
data/.travis.yml +2 -0
data/README.md +78 -30
data/Rakefile +11 -8
data/aux/app_template_footer.erb +1 -6
data/aux/app_template_header.erb +12 -32
data/aux/files/css/style.css +2 -8
data/aux/files/js/plots.js +564 -576
data/aux/files/js/script.js +10 -0
data/aux/json_footer.erb +8 -0
data/aux/json_header.erb +19 -0
data/aux/json_query.erb +14 -0
data/aux/template_footer.erb +9 -58
data/aux/template_header.erb +18 -58
data/aux/template_query.erb +8 -36
data/bin/genevalidator +45 -32
data/genevalidator.gemspec +11 -7
data/lib/genevalidator.rb +75 -455
data/lib/genevalidator/arg_validation.rb +78 -107
data/lib/genevalidator/blast.rb +57 -60
data/lib/genevalidator/clusterization.rb +15 -15
data/lib/genevalidator/exceptions.rb +32 -5
data/lib/genevalidator/get_raw_sequences.rb +70 -33
data/lib/genevalidator/hsp.rb +1 -4
data/lib/genevalidator/json_to_gv_results.rb +109 -0
data/lib/genevalidator/output.rb +177 -185
data/lib/genevalidator/pool.rb +2 -1
data/lib/genevalidator/sequences.rb +3 -3
data/lib/genevalidator/tabular_parser.rb +24 -18
data/lib/genevalidator/validation.rb +279 -0
data/lib/genevalidator/validation_alignment.rb +31 -47
data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
data/lib/genevalidator/validation_duplication.rb +23 -19
data/lib/genevalidator/validation_gene_merge.rb +30 -65
data/lib/genevalidator/validation_length_cluster.rb +14 -53
data/lib/genevalidator/validation_length_rank.rb +10 -11
data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
data/lib/genevalidator/validation_report.rb +2 -5
data/lib/genevalidator/validation_test.rb +8 -4
data/lib/genevalidator/version.rb +1 -1
data/test/test_all_validations.rb +51 -66
data/test/test_blast.rb +68 -51
data/test/test_clusterization.rb +1 -1
data/test/test_clusterization_2d.rb +19 -13
data/test/test_extended_array_methods.rb +1 -1
data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
data/test/test_sequences.rb +46 -41
data/test/test_validation_open_reading_frame.rb +318 -202
data/test/test_validations.rb +48 -32
metadata +76 -102
data/doc/AliasDuplicationError.html +0 -134
data/doc/AlignmentValidation.html +0 -1687
data/doc/AlignmentValidationOutput.html +0 -659
data/doc/Blast.html +0 -1905
data/doc/BlastRFValidationOutput.html +0 -545
data/doc/BlastReadingFrameValidation.html +0 -370
data/doc/BlastUtils.html +0 -875
data/doc/ClasspathError.html +0 -134
data/doc/Cluster.html +0 -1316
data/doc/DuplciationValidationOutput.html +0 -564
data/doc/DuplicationValidation.html +0 -920
data/doc/DuplicationValidationOutput.html +0 -564
data/doc/FileNotFoundException.html +0 -134
data/doc/GeneMergeValidation.html +0 -935
data/doc/GeneMergeValidationOutput.html +0 -652
data/doc/HierarchicalClusterization.html +0 -994
data/doc/Hsp.html +0 -1485
data/doc/InconsistentTabularFormat.html +0 -135
data/doc/LengthClusterValidation.html +0 -982
data/doc/LengthClusterValidationOutput.html +0 -515
data/doc/LengthRankValidation.html +0 -496
data/doc/LengthRankValidationOutput.html +0 -517
data/doc/NoInternetError.html +0 -135
data/doc/NoMafftInstallationError.html +0 -134
data/doc/NoPIdentError.html +0 -134
data/doc/NoValidationError.html +0 -134
data/doc/NotEnoughHitsError.html +0 -135
data/doc/ORFValidationOutput.html +0 -593
data/doc/OpenReadingFrameValidation.html +0 -1107
data/doc/OtherError.html +0 -123
data/doc/Output.html +0 -1540
data/doc/Pair.html +0 -309
data/doc/PairCluster.html +0 -767
data/doc/Plot.html +0 -837
data/doc/QueryError.html +0 -134
data/doc/ReportClassError.html +0 -135
data/doc/Sequence.html +0 -1299
data/doc/SequenceTypeError.html +0 -135
data/doc/TabularEntry.html +0 -837
data/doc/TabularParser.html +0 -1104
data/doc/Validation.html +0 -2147
data/doc/ValidationClassError.html +0 -134
data/doc/ValidationOutput.html +0 -460
data/doc/ValidationReport.html +0 -940
data/doc/ValidationTest.html +0 -939
data/doc/_index.html +0 -449
data/doc/class_list.html +0 -54
data/doc/css/common.css +0 -1
data/doc/css/full_list.css +0 -57
data/doc/css/style.css +0 -338
data/doc/file.README.html +0 -151
data/doc/file_list.html +0 -56
data/doc/frames.html +0 -26
data/doc/index.html +0 -151
data/doc/js/app.js +0 -214
data/doc/js/full_list.js +0 -178
data/doc/js/jquery.js +0 -4
data/doc/method_list.html +0 -1505
data/doc/top-level-namespace.html +0 -112
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
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 @@ $(document).ready(function() {
       }
     }
   });
+});
+$( document ).on( "click", "td, .plot_btn", function( event ) {
+    if ($(this).hasClass('success') || $(this).hasClass('danger')){
+      var title = $(this).attr('title');
+      var val = title.replace(/[ \/]/g, '');
+      addData(this, val);
+    } else if ($(this).hasClass('plot_btn')){
+      addData(this, 'all');
+    }
 });

data/aux/json_footer.erb ADDED

@@ -0,0 +1,8 @@
+</tbody></table>
+</div>
+<% if output_files.length > 1 %>
+<nav><ul class="pagination">
+<% output_files.each_with_index do |results_html, idx| %>
+<li><a href="<%=results_html%>"><%= idx + 1 %></a></li>
+<% end %></ul></nav><%end%>
+<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 @@
+<!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>
+<body>
+<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>
+<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>
+<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>
+<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/>
+<div id="report"><div id="report_1"></div></div><br><br>
+<table id="sortable_table" class="table table-striped table-collapsed table-bordered table-condensed tablesorter"><thead>
+<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>
+<% @json_array[0]['validations'].each do |_short_header, item| %>
+  <th class="sorter-false"><b><%= item['header'] %></b>
+  <% if item['header'] == "LengthCluster" || item['header'] == "GeneMerge" || item['header'] == "MainORF" || item['header'] == "MissingExtraSequences" %>
+    <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>
+  <% else %>
+     <span data-toggle="tooltip" title="<%=item['description']%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
+  <% end %>
+</th>
+<% end %>
+<th class="sorter-false chart-column"></th></tr></thead><tbody>

data/aux/json_query.erb ADDED

@@ -0,0 +1,14 @@
+<tr data-target="toggle<%= @row['idx'] %>" data-jsonFile="files/json/<%= @config[:filename] %>_<%= @row['idx'] %>.json">
+  <td title="idx"><%= @row['idx'] %></td>
+  <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>
+  <td title="Definition"><%= @row['definition'] %></td>
+  <td title="No. Hits"><%= @row['no_hits'] %></td>
+<% @row['validations'].each do |_short_header, item| %>
+  <td title="<%=item['header']%>" class="<%=item['status']%>"><%= item['print']%></td>
+<% end %>
+<% if @row['validations'].select{|_short_header, item| item['graphs'] != nil}.map{|_short_header, item| item['graphs'].length}.inject(0){|r, e| r+e } != 0 %>
+  <td><button title="Show plots" class="plot_btn btn btn-default"><i class="fa fa-bar-chart-o"></i></button></td>
+<% else %>
+  <td></td>
+<% end %>
+</tr>

data/aux/template_footer.erb CHANGED

@@ -1,68 +1,19 @@
-</tbody>
-</table>
+</tbody></table>
 <script>
   var evaluation_div = document.getElementById('report_1');
   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>";
   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>";
   evaluation_div.innerHTML = content_less;
   function add_content(){
-    evaluation_div = document.getElementById('report_1')
+    evaluation_div = document.getElementById('report_1');
     evaluation_div.innerHTML=content;
-    addPlot('report_1', '<%= plot_statistics.filename %>', '<%= plot_statistics.type %>', '<%= plot_statistics.title %>', '<%= plot_statistics.footer %>', '<%= plot_statistics.xtitle %>', '<%= plot_statistics.ytitle %>');
+    addOverallPlot('files/json/overview.json');
   }
 </script>
-    <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>
-    <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>
-    <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>
 </div>
-<footer >
-  <div class="container center-block">
-  <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/>
-  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>
+<% if output_files.length > 1 %>
+<nav><ul class="pagination">
+<% output_files.each_with_index do |results_html, idx| %>
+<li><a href="<%=results_html%>"><%= idx + 1 %></a></li>
+<% end %></ul></nav><%end%>
+<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

@@ -1,59 +1,19 @@
-<!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>
+<!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>
 <body>
-  <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/documentation/v1/"><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/>
-    <div id="report">
-      <div id="report_1"></div>
-    </div>
-    <br><br>
-      <table id="sortable_table" class="table table-collapsed table-bordered table-condensed tablesorter">
-        <thead>
-          <tr id="header">
-            <th>#</th>
-            <th>Ranking</th>
-            <th>Sequence Definition
-              <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
-              <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>
-            <% @validations.each do |item| %>
-            <th class="sorter-false">
-              <b><%= item.header %></b>
-                <% if item.short_header == "LengthCluster" || item.short_header == "Gene_Merge" || item.short_header == "ORF" || item.short_header == "MA" %>
-                  <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>
-                <% else %>
-                   <span data-toggle="tooltip" title="<%=item.description%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
-                <% end %>
-            </th>
-            <% end %>
-            <th class="sorter-false chart-column"></th>
-          </tr>
-        </thead>
-        <tbody>
+<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>
+<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>
+<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>
+<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/>
+<div id="report"><div id="report_1"></div></div><br><br>
+<table id="sortable_table" class="table table-striped table-collapsed table-bordered table-condensed tablesorter"><thead>
+<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>
+<% @validations.each do |item| %>
+  <th class="sorter-false"><b><%= item.header %></b>
+  <% if item.short_header == "LengthCluster" || item.short_header == "GeneMerge" || item.short_header == "MainORF" || item.short_header == "MissingExtraSequences" %>
+    <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>
+  <% else %>
+     <span data-toggle="tooltip" title="<%=item.description%>" data-placement="top"><i class="fa fa-question-circle"></i></span>
+  <% end %>
+</th>
+<% end %>
+<th class="sorter-false chart-column"></th></tr></thead><tbody>

data/aux/template_query.erb CHANGED

@@ -1,42 +1,14 @@
-<tr>
-  <td><%= @idx %></td>
+<tr data-target="toggle<%= @idx %>" data-jsonFile="files/json/<%= @config[:filename] %>_<%= @idx %>.json">
+  <td title="idx"><%= @idx %></td>
   <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>
-  <td title="Definition" class="seq_definition"><%= @prediction_def.scan(/([^ ]+)/)[0][0] %> <%= @prediction_def.scan(/([^ ]+)(.*)/)[0][1] %></td>
+  <td title="Definition"><%= @prediction_def %></td>
   <td title="No. Hits"><%= @nr_hits %></td>
 <% @validations.each do |item| %>
-  <% if item.color == 'warning' %>
-    <td title="<%=item.header%>" class="<%=item.color%>"><%= item.print%></td>
-  <% elsif item.plot_files != nil %>
-    <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 %>');
-    <% 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 %>AddExplanation(this, '<%=toggle%>');"><%= item.print%></td>
-  <% elsif item.plot_files == nil %>
-    <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>
-  <% end %>
+  <td title="<%=item.header%>" class="<%=item.color%>"><%= item.print%></td>
 <% end %>
 <% if @validations.select{|item| item.plot_files != nil}.map{|item| item.plot_files.length}.inject(0){|r, e| r+e } != 0 %>
-  <td>
-    <button title="Show plots" name="plot_btn" class="plot_btn btn btn-default" onclick="showDiv(this, '<%= toggle %>');
-    <% @validations.each do |item| %>
-      <% if item.plot_files != nil %>
-        <% 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 %>
-      <% end %>
-    <% end %>"><i class="fa fa-bar-chart-o"></i></button>
-  </td>
-</tr>
-<tr class="tablesorter-childRow" name="plot_row" style="display:none;">
-  <td colspan="<%=validations.length + 7%>" id="<%=toggle %>row">
-    <div id="<%=toggle%>" class="expanded-child"></div>
-  </td>
-</tr>
+  <td><button title="Show plots" class="plot_btn btn btn-default"><i class="fa fa-bar-chart-o"></i></button></td>
 <% else %>
-<td></td>
-</tr>
-<tr class="tablesorter-childRow" style="display:none;">
-  <td colspan="<%=validations.length + 7%>">
-    <div></div>
-  </td>
-</tr>
-<% end %>
+  <td></td>
+<% end %>
+</tr>

data/bin/genevalidator CHANGED

@@ -1,6 +1,9 @@
 #!/usr/bin/env ruby
 require 'optparse'
 require 'genevalidator'
+require 'genevalidator/get_raw_sequences'
+require 'genevalidator/json_to_gv_results'
 require 'genevalidator/version'
 opt = {}
@@ -27,8 +30,8 @@ BANNER
           '  dup   = Check for duplications,',
           '  frame = Open reading frame (ORF) validation,',
           '  orf   = Main ORF validation,',
-          '  align = Validating based on multiple alignment') do |lst|
-    opt[:validations] = lst
+          '  align = Validating based on multiple alignment') do |val|
+    opt[:validations] = val
   end
   opt[:db] = 'swissprot -remote'
@@ -39,20 +42,33 @@ BANNER
     opt[:db] = db
   end
-  opts.on('-x', '--blast_xml_file [FILE]',
+  opts.on('-e', '--extract_raw_seqs',
+          'Produces a fasta file of the raw sequences of all BLAST hits in the',
+          'supplied BLAST output file. This fasta file can then be provided to',
+          'GeneValidator with the "-r", "--raw_sequences" argument') do
+    opt[:extract_raw_seqs] = true
+  end
+  opts.on('-j', '--json_file [JSON_FILE]',
+          'Generate GV results from a json file (or a subset of a json file)',
+          'produced from GeneValidator') do |json|
+    opt[:json_file] = json
+  end
+  opts.on('-x', '--blast_xml_file [BLAST_XML_FILE]',
           'Provide GeneValidator with a pre-computed BLAST XML output',
           'file (BLAST -outfmt option 5).') do |blast_xml_file|
     opt[:blast_xml_file] = blast_xml_file
   end
-  opts.on('-t', '--blast_tabular_file [FILE]',
+  opts.on('-t', '--blast_tabular_file [BLAST_TABULAR_FILE]',
           'Provide GeneValidator with a pre-computed BLAST tabular output',
           'file. (BLAST -outfmt option 6).') do |blast_tabular_file|
     opt[:blast_tabular_file] = blast_tabular_file
   end
   # default blast tabular columns
-  opts.on('-o', '--blast_tabular_options [Options]',
+  opts.on('-o', '--blast_tabular_options [BLAST_TABULAR_OPTIONS]',
           'Custom format used in BLAST -outfmt argument',
           'See BLAST+ manual pages for more details') do |blast_table_options|
     opt[:blast_tabular_options] = blast_table_options
@@ -64,32 +80,18 @@ BANNER
           'BLAST and Mafft within GeneValidator.') do |num_threads|
     opt[:num_threads] = num_threads
   end
-  opt[:fast] = false
-  opts.on('-f', '--fast',
-          'Run BLAST on all sequences together (rather than separately)',
-          'to speed up the analysis.',
-          'However, this means that there will be a longer wait before the',
-          'results can be viewed (as GeneValidator will need to run BLAST',
-          'on all sequences before producing any results).',
-          'The speed difference will be more apparent on larger input files') do
-    opt[:fast] = true
-  end
   opts.on('-r', '--raw_sequences [raw_seq]',
           'Supply a fasta file of the raw sequences of all BLAST hits present',
           'in the supplied BLAST XML or BLAST tabular file.') do |raw_seq|
     opt[:raw_sequences] = raw_seq
   end
-  opts.on('-m', '--mafft_bin [MAFFT_PATH]',
-          'Path to MAFFT bin folder (is added to $PATH variable)') do |mafft|
-    opt[:mafft_bin] = mafft
-  end
-  opts.on('-b', '--blast_bin [BLAST_PATH]',
-          'Path to BLAST+ bin folder (is added to $PATH variable)') do |blast|
-    opt[:blast_bin] = blast
+  opts.on('-b', '--binaries [binaries]', Array,
+          'Path to BLAST and MAFFT bin folders (is added to $PATH variable)',
+          'To be provided as follows:',
+          '   $ genevalidator -b /blast/bin/path/ -b /mafft/bin/path/') do |bin|
+    (opt[:bin] ||= []).concat(bin)
   end
   opts.on('--version', 'The version of GeneValidator that you are running.') do
@@ -98,7 +100,7 @@ BANNER
   end
   opts.on('-h', '--help', 'Show this screen.') do
-    puts opt_parser
+    $stderr.puts opt_parser
     exit
   end
 end
@@ -109,8 +111,8 @@ begin
     $stderr.puts 'Error: you must specify a single fasta input file instead' \
                  ' of ' + ARGV.length.to_s + ".\n"
     exit 1
-  elsif ARGV.length == 0
-    puts opt_parser
+  elsif ARGV.length == 0 && opt[:extract_raw_seqs].nil? && opt[:json_file].nil?
+    $stderr.puts opt_parser
     exit 1
   end
 rescue OptionParser::ParseError
@@ -118,10 +120,21 @@ rescue OptionParser::ParseError
   exit 1
 end
-start = Time.now
 opt[:input_fasta_file] = ARGV[0]
-(GeneValidator::Validation.new(opt)).run
+start = Time.now
+if opt[:extract_raw_seqs] && opt[:raw_sequences].nil?
+  GeneValidator.opt    = opt
+  GeneValidator.config = {}
+  GeneValidator::RawSequences.run
+elsif opt[:json_file]
+  GeneValidator.opt = opt
+  GeneValidator::JsonToGVResults.run
+else
+  GeneValidator.init(opt)
+  GeneValidator.run
+end
-puts "Total running time: #{(Time.now - start).round(3)}s"
-puts # a blank line
+$stderr.puts "Total running time: #{(Time.now - start).round(3)}s"
+$stderr.puts # a blank line

data/genevalidator.gemspec CHANGED

@@ -1,4 +1,4 @@
-# coding: utf-8
+# coding: utf-8
 lib = File.expand_path('../lib', __FILE__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require 'genevalidator/version'
@@ -7,22 +7,26 @@ Gem::Specification.new do |s|
   # meta
   s.name        = 'genevalidator'
   s.version     =  GeneValidator::VERSION
-  s.authors     = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam', 'Yannick Wurm']
+  s.authors     = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam',
+                   'Yannick Wurm']
   s.email       = 'y.wurm@qmul.ac.uk'
   s.homepage    = 'https://github.com/wurmlab/GeneValidator'
   s.license     = 'AGPL'
   s.summary     = 'Identifying problems with gene predictions.'
-  s.description = <<DESC
-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.
-DESC
+  s.description = '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.'
-  s.required_ruby_version     = '>= 2.0.0'
+  s.required_ruby_version = '>= 2.0.0'
   s.add_development_dependency 'bundler', '~> 1.6'
   s.add_development_dependency 'rake', '~>10.3'
+  s.add_development_dependency 'yard', '~> 0.8'
+  s.add_development_dependency 'codeclimate-test-reporter', '~> 0.4', '>= 0.4.7'
   s.add_dependency('bio', '~> 1.4')
   s.add_dependency('bio-blastxmlparser', '~>2.0')
   s.add_dependency('minitest', '~> 5.4')
-  s.add_dependency('statsample', '~> 1.4')
+  s.add_dependency('statsample', '1.4') # Updating to 1.5 breaks GV
   s.files         = `git ls-files -z`.split("\x0")
   s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }