genevalidator 1.6.1 → 1.6.2

data/doc/css/common.css

@@ -1 +0,0 @@
-/* Override this file with custom rules */

data/doc/css/full_list.css

@@ -1,57 +0,0 @@
-body {
-  margin: 0;
-  font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
-  font-size: 13px;
-  height: 101%;
-  overflow-x: hidden;
-}
-
-h1 { padding: 12px 10px; padding-bottom: 0; margin: 0; font-size: 1.4em; }
-.clear { clear: both; }
-#search { position: absolute; right: 5px; top: 9px; padding-left: 24px; }
-#content.insearch #search, #content.insearch #noresults { background: url(data:image/gif;base64,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) no-repeat center left; }
-#full_list { padding: 0; list-style: none; margin-left: 0; }
-#full_list ul { padding: 0; }
-#full_list li { padding: 5px; padding-left: 12px; margin: 0; font-size: 1.1em; list-style: none; }
-#noresults { padding: 7px 12px; }
-#content.insearch #noresults { margin-left: 7px; }
-ul.collapsed ul, ul.collapsed li { display: none; }
-ul.collapsed.search_uncollapsed { display: block; }
-ul.collapsed.search_uncollapsed li { display: list-item; }
-li a.toggle { cursor: default; position: relative; left: -5px; top: 4px; text-indent: -999px; width: 10px; height: 9px; margin-left: -10px; display: block; float: left; background: url(data:image/png;base64,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) no-repeat bottom left; }
-li.collapsed a.toggle { opacity: 0.5; cursor: default; background-position: top left; }
-li { color: #888; cursor: pointer; }
-li.deprecated { text-decoration: line-through; font-style: italic; }
-li.r1 { background: #f0f0f0; }
-li.r2 { background: #fafafa; }
-li:hover { background: #ddd; }
-li small:before { content: "("; }
-li small:after { content: ")"; }
-li small.search_info { display: none; }
-a:link, a:visited { text-decoration: none; color: #05a; }
-li.clicked { background: #05a; color: #ccc; }
-li.clicked a:link, li.clicked a:visited { color: #eee; }
-li.clicked a.toggle { opacity: 0.5; background-position: bottom right; }
-li.collapsed.clicked a.toggle { background-position: top right; }
-#search input { border: 1px solid #bbb; -moz-border-radius: 3px; -webkit-border-radius: 3px; }
-#nav { margin-left: 10px; font-size: 0.9em; display: none; color: #aaa; }
-#nav a:link, #nav a:visited { color: #358; }
-#nav a:hover { background: transparent; color: #5af; }
-.frames #nav span:after { content: ' | '; }
-.frames #nav span:last-child:after { content: ''; }
-
-.frames #content h1 { margin-top: 0; }
-.frames li { white-space: nowrap; cursor: normal; }
-.frames li small { display: block; font-size: 0.8em; }
-.frames li small:before { content: ""; }
-.frames li small:after { content: ""; }
-.frames li small.search_info { display: none; }
-.frames #search { width: 170px; position: static; margin: 3px; margin-left: 10px; font-size: 0.9em; color: #888; padding-left: 0; padding-right: 24px; }
-.frames #content.insearch #search { background-position: center right; }
-.frames #search input { width: 110px; }
-.frames #nav { display: block; }
-
-#full_list.insearch li { display: none; }
-#full_list.insearch li.found { display: list-item; padding-left: 10px; }
-#full_list.insearch li a.toggle { display: none; }
-#full_list.insearch li small.search_info { display: block; }

data/doc/css/style.css

@@ -1,338 +0,0 @@
-body {
-  padding: 0 20px;
-  font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
-  font-size: 13px;
-}
-body.frames { padding: 0 5px; }
-h1 { font-size: 25px; margin: 1em 0 0.5em; padding-top: 4px; border-top: 1px dotted #d5d5d5; }
-h1.noborder { border-top: 0px; margin-top: 0; padding-top: 4px; }
-h1.title { margin-bottom: 10px; }
-h1.alphaindex { margin-top: 0; font-size: 22px; }
-h2 {
-  padding: 0;
-  padding-bottom: 3px;
-  border-bottom: 1px #aaa solid;
-  font-size: 1.4em;
-  margin: 1.8em 0 0.5em;
-}
-h2 small { font-weight: normal; font-size: 0.7em; display: block; float: right; }
-.clear { clear: both; }
-.inline { display: inline; }
-.inline p:first-child { display: inline; }
-.docstring h1, .docstring h2, .docstring h3, .docstring h4 { padding: 0; border: 0; border-bottom: 1px dotted #bbb; }
-.docstring h1 { font-size: 1.2em; }
-.docstring h2 { font-size: 1.1em; }
-.docstring h3, .docstring h4 { font-size: 1em; border-bottom: 0; padding-top: 10px; }
-.summary_desc .object_link, .docstring .object_link { font-family: monospace; }
-.rdoc-term { padding-right: 25px; font-weight: bold; }
-.rdoc-list p { margin: 0; padding: 0; margin-bottom: 4px; }
-
-/* style for <table> */
-#filecontents table, .docstring table { border-collapse: collapse; }
-#filecontents table th, #filecontents table td,
-.docstring table th, .docstring table td { border: 1px solid #ccc; padding: 8px; padding-right: 17px; }
-#filecontents table tr:nth-child(odd),
-.docstring table tr:nth-child(odd) { background: #eee; }
-#filecontents table tr:nth-child(even),
-.docstring table tr:nth-child(even) { background: #fff; }
-#filecontents table th, .docstring table th { background: #fff; }
-
-/* style for <ul> */
-#filecontents li > p, .docstring li > p { margin: 0px; }
-#filecontents ul, .docstring ul { padding-left: 20px; }
-/* style for <dl> */
-#filecontents dl, .docstring dl { border: 1px solid #ccc; }
-#filecontents dt, .docstring dt { background: #ddd; font-weight: bold; padding: 3px 5px; }
-#filecontents dd, .docstring dd { padding: 5px 0px; margin-left: 18px; }
-#filecontents dd > p, .docstring dd > p { margin: 0px; }
-
-.note {
-  color: #222;
-  -moz-border-radius: 3px; -webkit-border-radius: 3px;
-  background: #e3e4e3; border: 1px solid #d5d5d5; padding: 7px 10px;
-  display: block;
-}
-.note.todo { background: #ffffc5; border-color: #ececaa; }
-.note.returns_void { background: #efefef; }
-.note.deprecated { background: #ffe5e5; border-color: #e9dada; }
-.note.private { background: #ffffc5; border-color: #ececaa; }
-.note.title { padding: 1px 5px; font-size: 0.9em; font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif; display: inline; }
-.summary_signature + .note.title { margin-left: 7px; }
-h1 .note.title { font-size: 0.5em; font-weight: normal; padding: 3px 5px; position: relative; top: -3px; text-transform: capitalize; }
-.note.title.constructor { color: #fff; background: #6a98d6; border-color: #6689d6; }
-.note.title.writeonly { color: #fff; background: #45a638; border-color: #2da31d; }
-.note.title.readonly { color: #fff; background: #6a98d6; border-color: #6689d6; }
-.note.title.private { background: #d5d5d5; border-color: #c5c5c5; }
-.note.title.not_defined_here { background: transparent; border: none; font-style: italic; }
-.discussion .note { margin-top: 6px; }
-.discussion .note:first-child { margin-top: 0; }
-
-h3.inherited {
-  font-style: italic;
-  font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
-  font-weight: normal;
-  padding: 0;
-  margin: 0;
-  margin-top: 12px;
-  margin-bottom: 3px;
-  font-size: 13px;
-}
-p.inherited {
-  padding: 0;
-  margin: 0;
-  margin-left: 25px;
-}
-
-#filecontents dl.box, dl.box {
-  border: 0;
-  width: 520px;
-  font-size: 1em;
-}
-#filecontents dl.box dt, dl.box dt {
-  float: left;
-  display: block;
-  width: 100px;
-  margin: 0;
-  text-align: right;
-  font-weight: bold;
-  background: transparent;
-  border: 1px solid #aaa;
-  border-width: 1px 0px 0px 1px;
-  padding: 6px 0;
-  padding-right: 10px;
-}
-#filecontents dl.box dd, dl.box dd {
-  float: left;
-  display: block;
-  width: 380px;
-  margin: 0;
-  padding: 6px 0;
-  padding-right: 20px;
-  border: 1px solid #aaa;
-  border-width: 1px 1px 0 0;
-}
-#filecontents dl.box .last, dl.box .last {
-  border-bottom: 1px solid #aaa;
-}
-#filecontents dl.box .r1, dl.box .r1 { background: #eee; }
-
-ul.toplevel { list-style: none; padding-left: 0; font-size: 1.1em; }
-.index_inline_list { padding-left: 0; font-size: 1.1em; }
-.index_inline_list li { list-style: none; display: inline; padding: 7px 12px; line-height: 35px; }
-
-dl.constants { margin-left: 40px; }
-dl.constants dt { font-weight: bold; font-size: 1.1em; margin-bottom: 5px; }
-dl.constants dd { width: 75%; white-space: pre; font-family: monospace; margin-bottom: 18px; }
-
-.summary_desc { margin-left: 32px; display: block; font-family: sans-serif; }
-.summary_desc tt { font-size: 0.9em; }
-dl.constants .note { padding: 2px 6px; padding-right: 12px; margin-top: 6px; }
-dl.constants .docstring { margin-left: 32px; font-size: 0.9em; font-weight: normal; }
-dl.constants .tags { padding-left: 32px; font-size: 0.9em; line-height: 0.8em; }
-dl.constants .discussion *:first-child { margin-top: 0; }
-dl.constants .discussion *:last-child { margin-bottom: 0; }
-
-.method_details { border-top: 1px dotted #aaa; margin-top: 15px; padding-top: 0; }
-.method_details.first { border: 0; }
-p.signature, h3.signature {
-  font-size: 1.1em; font-weight: normal; font-family: Monaco, Consolas, Courier, monospace;
-  padding: 6px 10px; margin-top: 18px;
-  background: #e5e8ff; border: 1px solid #d8d8e5; -moz-border-radius: 3px; -webkit-border-radius: 3px;
-}
-p.signature tt,
-h3.signature tt { font-family: Monaco, Consolas, Courier, monospace; }
-p.signature .overload,
-h3.signature .overload { display: block; }
-p.signature .extras,
-h3.signature .extras { font-weight: normal; font-family: sans-serif; color: #444; font-size: 1em; }
-p.signature .not_defined_here,
-h3.signature .not_defined_here,
-p.signature .aliases,
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-
-.tags .tag_title { font-size: 1em; margin-bottom: 0; font-weight: bold; }
-.tags ul { margin-top: 5px; padding-left: 30px; list-style: square; }
-.tags ul li { margin-bottom: 3px; }
-.tags ul .name { font-family: monospace; font-weight: bold; }
-.tags ul .note { padding: 3px 6px; }
-.tags { margin-bottom: 12px; }
-
-.tags .examples .tag_title { margin-bottom: 10px; font-weight: bold; }
-.tags .examples .inline p { padding: 0; margin: 0; margin-left: 15px; font-weight: bold; font-size: 0.9em; }
-
-.tags .overload .overload_item { list-style: none; margin-bottom: 25px; }
-.tags .overload .overload_item .signature {
-  padding: 2px 8px;
-  background: #e5e8ff; border: 1px solid #d8d8e5; -moz-border-radius: 3px; -webkit-border-radius: 3px;
-}
-.tags .overload .signature { margin-left: -15px; font-family: monospace; display: block; font-size: 1.1em; }
-.tags .overload .docstring { margin-top: 15px; }
-
-.defines { display: none; }
-
-#method_missing_details .notice.this { position: relative; top: -8px; color: #888; padding: 0; margin: 0; }
-
-.showSource { font-size: 0.9em; }
-.showSource a:link, .showSource a:visited { text-decoration: none; color: #666; }
-
-#content a:link, #content a:visited { text-decoration: none; color: #05a; }
-#content a:hover { background: #ffffa5; }
-div.docstring, p.docstring { margin-right: 6em; }
-
-ul.summary {
-  list-style: none;
-  font-family: monospace;
-  font-size: 1em;
-  line-height: 1.5em;
-}
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-  text-decoration: none; font-size: 1.1em;
-}
-ul.summary li { margin-bottom: 5px; }
-.summary .summary_signature {
-  padding: 1px 10px;
-  background: #eaeaff; border: 1px solid #dfdfe5;
-  -moz-border-radius: 3px; -webkit-border-radius: 3px;
-}
-.summary_signature:hover { background: #eeeeff; cursor: pointer; }
-ul.summary.compact li { display: inline-block; margin: 0px 5px 0px 0px; line-height: 2.6em;}
-ul.summary.compact .summary_signature { padding: 5px 7px; padding-right: 4px; }
-#content .summary_signature:hover a:link,
-#content .summary_signature:hover a:visited {
-  background: transparent;
-  color: #48f;
-}
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-p.inherited a { font-family: monospace; font-size: 0.9em; }
-p.inherited { word-spacing: 5px; font-size: 1.2em; }
-
-p.children { font-size: 1.2em; }
-p.children a { font-size: 0.9em; }
-p.children strong { font-size: 0.8em; }
-p.children strong.modules { padding-left: 5px; }
-
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-    <div id="content"><div id='filecontents'><h1>Identify problems with predicted genes</h1>
-
-<p>This is a GSoC 2013 project.<br>
-Details about the project&#39;s progress during the <strong>Coding period</strong> can be found <a href="https://github.com/monicadragan/gene_prediction/wiki/Project-Diary">here</a>.<br>
-We also have a <a href="http://gene-prediction.blogspot.ro/">blog</a>.<br><br>
-<h3><div align = center><font color="blue">Please note that some of the functionalities<br> of this tool are still under development.<br> So, stay tunned!</font></div></h3>
-<br><br></p>
-
-<h3>Authors</h3>
-
-<ul>
-<li>GSoC student: <a href="http://swarm.cs.pub.ro/%7Emdragan/gsoc2013/Monica_Dragan_CV.pdf">Monica Dragan</a> (<a href="mailto:monica.dragan@cti.pub.ro">email</a>)</li>
-<li>Mentors: <a href="https://plus.google.com/114122400102590087616/about">Anurag Priyam</a>(<a href="mailto:anurag08priyam@gmail.com">email</a>) and <a href="http://yannick.poulet.org/">Yannick Wurm</a>(<a href="mailto:y.wurm@qmul.ac.uk">email</a>)</li>
-</ul>
-
-<h3>Abstract</h3>
-
-<p>The goal of GeneValidator is to identify problems with gene predictions and provide useful information based on the similarities to genes in public databases.The results of the prediction validation will make evidence about how the sequencing curation may be done and can be useful in improving / trying new approaches for gene prediction tools. The main target users of this tool are the Biologists who want to validate the data obtained in their own laboratories.</p>
-
-<h3>Current Validations</h3>
-
-<ul>
-<li>Length validation by clusterization</li>
-<li>Length validation by ranking</li>
-<li>Reading frame validation</li>
-<li>Check gene merge</li>
-<li>Check duplications</li>
-<li>Main ORF validation (for nucleotides)</li>
-<li>Validation based on multiple alignment ~ under development</li>
-<li>Codon coverage ~ under development</li>
-</ul>
-
-<h3>Requirements</h3>
-
-<ul>
-<li>Ruby (&gt;= 1.9.3)</li>
-<li>R (&gt;= 2.14.2)</li>
-<li>RubyGems (&gt;= 1.3.6)</li>
-<li>NCBI BLAST+ (&gt;= 2.2.25+)</li>
-<li>MAFFT installation (download it from : <a href="http://mafft.cbrc.jp/alignment/software/">http://mafft.cbrc.jp/alignment/software/</a> ).<br>
-Linux and MacOS are officially supported!</li>
-</ul>
-
-<h3>Installation</h3>
-
-<ol>
-<li><p>Get the source code<br>
-<code>$ git clone git@github.com:monicadragan/gene_prediction.git</code></p></li>
-<li><p>Be sudo and build the gem<br>
-<code>$ sudo rake</code></p></li>
-<li><p>Run GeneValidation<br>
-<code>$ genevalidator [validations] [skip_blast] [start] [tabular] [mafft] [raw_seq] FILE</code> </p></li>
-</ol>
-
-<p>Example that emphasizes all the validations:<br>
-<code>$ genevalidator -x data/all_validations_prot/all_validations_prot.xml data/all_validations_prot/all_validations_prot.fasta</code></p>
-
-<p>Learn more:<br>
-<code>$ genevalidator -h</code></p>
-
-<h3>Outputs</h3>
-
-<p>By running GeneValidator on your dataset you get numbers and plots. Some relevant files will be generated at the same path with the input file. The results are available in 3 formats:
-* console table output 
-* validation results in YAML format (the YAML file has the same name with the input file + YAML extension) 
-* html output with plot visualization (the useful files will be generated in the &#39;html&#39; directory, at the same path with the input file)<br>
-! Note: for the moment check the html output with Firefox browser only !</p>
-
-<p><a href="http://swarm.cs.pub.ro/%7Emdragan/gsoc2013/genevalidator">Have a look at our results!</a></p>
-
-<h3>Other things</h3>
-
-<ol>
-<li><p>Run unit tests<br>
-<code>$ rake test</code></p></li>
-<li><p>Generate documentation<br>
-<code>$ rake doc</code></p></li>
-</ol>
-</div></div>
-
-    <div id="footer">
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