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/doc/GeneMergeValidationOutput.html DELETED

@@ -1,652 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: GeneMergeValidationOutput
-    &mdash; Documentation by YARD 0.8.7.2
-</title>
-  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '';
-  framesUrl = "frames.html#!" + escape(window.location.href);
-</script>
-  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="_index.html">Index (G)</a> &raquo;
-    <span class="title">GeneMergeValidationOutput</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: GeneMergeValidationOutput
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></li>
-            <li class="next">GeneMergeValidationOutput</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/validation_gene_merge.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>Class that stores the validation output information</p>
-  </div>
-</div>
-<div class="tags">
-</div>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
-  <ul class="summary">
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#slope-instance_method" title="#slope (instance method)">- (Object) <strong>slope</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute slope.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#threshold_down-instance_method" title="#threshold_down (instance method)">- (Object) <strong>threshold_down</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute threshold_down.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#threshold_up-instance_method" title="#threshold_up (instance method)">- (Object) <strong>threshold_up</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute threshold_up.</p>
-</div></span>
-</li>
-  </ul>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="ValidationReport.html#bg_color-instance_method" title="ValidationReport#bg_color (method)">#bg_color</a></span>, <span class='object_link'><a href="ValidationReport.html#errors-instance_method" title="ValidationReport#errors (method)">#errors</a></span>, <span class='object_link'><a href="ValidationReport.html#expected-instance_method" title="ValidationReport#expected (method)">#expected</a></span>, <span class='object_link'><a href="ValidationReport.html#message-instance_method" title="ValidationReport#message (method)">#message</a></span>, <span class='object_link'><a href="ValidationReport.html#plot_files-instance_method" title="ValidationReport#plot_files (method)">#plot_files</a></span>, <span class='object_link'><a href="ValidationReport.html#result-instance_method" title="ValidationReport#result (method)">#result</a></span>, <span class='object_link'><a href="ValidationReport.html#validation_result-instance_method" title="ValidationReport#validation_result (method)">#validation_result</a></span></p>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#color-instance_method" title="#color (instance method)">- (Object) <strong>color</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (GeneMergeValidationOutput) <strong>initialize</strong>(slope, threshold_down = 0.4, threshold_up = 1.2, expected = :no) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>A new instance of GeneMergeValidationOutput.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#print-instance_method" title="#print (instance method)">- (Object) <strong>print</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#validation-instance_method" title="#validation (instance method)">- (Object) <strong>validation</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-    </ul>
-  <div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <div class="method_details first">
-  <h3 class="signature first" id="initialize-instance_method">
-    - (<tt><span class='object_link'><a href="" title="GeneMergeValidationOutput (class)">GeneMergeValidationOutput</a></span></tt>) <strong>initialize</strong>(slope, threshold_down = 0.4, threshold_up = 1.2, expected = :no)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns a new instance of GeneMergeValidationOutput</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-12
-13
-14
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-16
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-19</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 12</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span> <span class='lparen'>(</span><span class='id identifier rubyid_slope'>slope</span><span class='comma'>,</span> <span class='id identifier rubyid_threshold_down'>threshold_down</span> <span class='op'>=</span> <span class='float'>0.4</span><span class='comma'>,</span> <span class='id identifier rubyid_threshold_up'>threshold_up</span> <span class='op'>=</span> <span class='float'>1.2</span><span class='comma'>,</span> <span class='id identifier rubyid_expected'>expected</span> <span class='op'>=</span> <span class='symbol'>:no</span><span class='rparen'>)</span>
-  <span class='ivar'>@slope</span>          <span class='op'>=</span> <span class='id identifier rubyid_slope'>slope</span>
-  <span class='ivar'>@threshold_down</span> <span class='op'>=</span> <span class='id identifier rubyid_threshold_down'>threshold_down</span>
-  <span class='ivar'>@threshold_up</span>   <span class='op'>=</span> <span class='id identifier rubyid_threshold_up'>threshold_up</span>
-  <span class='ivar'>@result</span>         <span class='op'>=</span> <span class='id identifier rubyid_validation'>validation</span>
-  <span class='ivar'>@expected</span>       <span class='op'>=</span> <span class='id identifier rubyid_expected'>expected</span>
-  <span class='ivar'>@plot_files</span>     <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id=""></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="slope-instance_method">
-    - (<tt>Object</tt>) <strong>slope</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute slope</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-8
-9
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 8</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_slope'>slope</span>
-  <span class='ivar'>@slope</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="threshold_down-instance_method">
-    - (<tt>Object</tt>) <strong>threshold_down</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute threshold_down</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-9
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 9</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_threshold_down'>threshold_down</span>
-  <span class='ivar'>@threshold_down</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="threshold_up-instance_method">
-    - (<tt>Object</tt>) <strong>threshold_up</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute threshold_up</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-10
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-12</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 10</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_threshold_up'>threshold_up</span>
-  <span class='ivar'>@threshold_up</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="color-instance_method">
-    - (<tt>Object</tt>) <strong>color</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-39
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 39</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_color'>color</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_validation'>validation</span> <span class='op'>==</span> <span class='symbol'>:no</span>
-    <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>success</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>else</span>
-    <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>danger</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="print-instance_method">
-    - (<tt>Object</tt>) <strong>print</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-21
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 21</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_print'>print</span>
-  <span class='kw'>if</span> <span class='ivar'>@slope</span><span class='period'>.</span><span class='id identifier rubyid_nan?'>nan?</span>
-    <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>slope=Inf</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>else</span>
-    <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>slope=</span><span class='embexpr_beg'>#{</span><span class='ivar'>@slope</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='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="validation-instance_method">
-    - (<tt>Object</tt>) <strong>validation</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-29
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_gene_merge.rb', line 29</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_validation'>validation</span>
-  <span class='comment'># color gene merge validation
-</span>  <span class='kw'>if</span> <span class='ivar'>@slope</span> <span class='op'>&gt;</span> <span class='id identifier rubyid_threshold_down'>threshold_down</span> <span class='kw'>and</span> <span class='ivar'>@slope</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_threshold_up'>threshold_up</span>
-    <span class='symbol'>:yes</span>
-  <span class='kw'>else</span>
-    <span class='symbol'>:no</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
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-</table>
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-  Generated on Sat Sep 28 07:01:33 2013 by
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-  0.8.7.2 (ruby-1.9.3).
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