@gmod/jbrowse
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JBrowse - client-side genome browser
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<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>flatfile-to-json.pl · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="### flatfile-to-json.pl"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="flatfile-to-json.pl · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/index.html"/><meta property="og:description" content="### flatfile-to-json.pl"/><meta name="twitter:card" content="summary"/><link rel="shortcut icon" href="/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css"/><link rel="alternate" type="application/atom+xml" href="https://jbrowse.org/blog/atom.xml" title="JBrowse Blog ATOM Feed"/><link rel="alternate" type="application/rss+xml" 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class="navItem" href="/docs/flatfile-to-json.pl.html">flatfile-to-json.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/remove-track.pl.html">remove-track.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/ucsc-to-json.pl.html">ucsc-to-json.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/generate-names.pl.html">generate-names.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/prepare-refseqs.pl.html">prepare-refseqs.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/biodb-to-json.pl.html">biodb-to-json.pl</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">JBrowse Desktop</h3><ul><li class="navListItem"><a class="navItem" href="/docs/jbrowse_desktop.html">JBrowse Desktop</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">FAQ</h3><ul><li class="navListItem"><a class="navItem" href="/docs/faq.html">JBrowse FAQ</a></li></ul></div><div class="navGroup"><h3 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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">flatfile-to-json.pl</h1></header><article><div><span><h3><a class="anchor" aria-hidden="true" id="flatfile-to-jsonpl"></a><a href="#flatfile-to-jsonpl" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>flatfile-to-json.pl</h3>
<p>Each run of this script formats a single track for JBrowse. A <em>flat file</em> is a data set that exists entirely in a single file. For this script, the file must be a <a href="http://gmod.org/wiki/GFF3">GFF3</a>, <a href="http://www.ensembl.org/info/website/upload/bed.html">BED</a>, or GenBank text file.</p>
<p>Basic usage:</p>
<p><code>bin/flatfile-to-json.pl --[gff|gbk|bed] <flat file> --tracklabel <track name> [options]</code></p>
<p>For a full list of the options supported by flatfile-to-json.pl, run it with the --help option</p>
<p><code>bin/flatfile-to-json.pl --help</code></p>
<p>Example</p>
<pre><code class="hljs"> <span class="hljs-string">flatfile-to-</span><span class="hljs-string">json.</span><span class="hljs-string">pl </span>\
( <span class="hljs-built_in">--gff</span> <<span class="hljs-string">GFF3 </span><span class="hljs-string">file></span> | <span class="hljs-built_in">--bed</span> <<span class="hljs-string">BED </span><span class="hljs-string">file></span> | <span class="hljs-built_in">--gbk</span> <<span class="hljs-string">GenBank </span><span class="hljs-string">file></span> ) \
<span class="hljs-built_in">--trackLabel</span> <<span class="hljs-string">track </span><span class="hljs-string">identifier></span> \
[ <span class="hljs-built_in">--trackType</span> <<span class="hljs-string">JS </span><span class="hljs-string">Class></span> ] \
[ <span class="hljs-built_in">--out</span> <<span class="hljs-string">output </span><span class="hljs-string">directory></span> ] \
[ <span class="hljs-built_in">--key</span> <<span class="hljs-string">human-readable </span><span class="hljs-string">track </span><span class="hljs-string">name></span> ] \
[ <span class="hljs-built_in">--className</span> <<span class="hljs-string">CSS </span><span class="hljs-string">class </span><span class="hljs-string">name </span><span class="hljs-string">for </span><span class="hljs-string">displaying </span><span class="hljs-string">features></span> ] \
[ <span class="hljs-built_in">--urltemplate</span> <span class="hljs-string">"http://example.com/idlookup?id={id}"</span> ] \
[ <span class="hljs-built_in">--arrowheadClass</span> <<span class="hljs-string">CSS </span><span class="hljs-string">class></span> ] \
[ <span class="hljs-built_in">--noSubfeatures</span> ] \
[ <span class="hljs-built_in">--subfeatureClasses</span> <span class="hljs-string">'{ JSON-format subfeature class map }'</span> ] \
[ <span class="hljs-built_in">--clientConfig</span> <span class="hljs-string">'{ JSON-format style configuration for this track }'</span> ] \
[ <span class="hljs-built_in">--config</span> <span class="hljs-string">'{ JSON-format extra configuration for this track }'</span> ] \
[ <span class="hljs-built_in">--thinType</span> <<span class="hljs-string">BAM </span>-<span class="hljs-string">thin_type></span> ] \
[ <span class="hljs-built_in">--thicktype</span> <<span class="hljs-string">BAM </span>-<span class="hljs-string">thick_type></span>] \
[ <span class="hljs-built_in">--type</span> <<span class="hljs-string">feature </span><span class="hljs-string">types </span><span class="hljs-string">to </span><span class="hljs-string">process></span> ] \
[ <span class="hljs-built_in">--nclChunk</span> <<span class="hljs-string">chunk </span><span class="hljs-string">size </span><span class="hljs-string">for </span><span class="hljs-string">generated </span><span class="hljs-string">NCLs></span> ] \
[ <span class="hljs-built_in">--compress</span> ] \
[ <span class="hljs-built_in">--sortMem</span> <<span class="hljs-string">memory </span><span class="hljs-string">in </span><span class="hljs-string">bytes </span><span class="hljs-string">to </span><span class="hljs-string">use </span><span class="hljs-string">for </span><span class="hljs-string">sorting></span> ] \
[ <span class="hljs-built_in">--maxLookback</span> <<span class="hljs-string">maximum </span><span class="hljs-string">number </span><span class="hljs-string">of </span><span class="hljs-string">features </span><span class="hljs-string">to </span><span class="hljs-string">buffer </span><span class="hljs-string">in </span><span class="hljs-string">gff3 </span><span class="hljs-string">files></span> ] \
[ <span class="hljs-built_in">--nameAttributes</span> <span class="hljs-string">"name,alias,id"</span> ] \
</code></pre>
<p>The --trackLabel parameter is the only required parameter, and is the "id" to refer to your track by. The displayed name is also whatever --trackLabel is unless --key is specified, in which case, whatever --key is will be used as the displayed name.</p>
<p>By default the output is in a folder called data in your current working directory, or whatever is specified by --out</p>
<p>Using --trackType CanvasFeatures is generally useful since CanvasFeatures are newer than the default HTMLFeatures (aka FeatureTrack)</p>
</span></div></article></div><div class="docs-prevnext"><a class="docs-prev button" href="/docs/paired_reads.html">← Paired read viewing</a><a class="docs-next button" href="/docs/remove-track.pl.html">remove-track.pl →</a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><h5>Docs</h5><a href="/blog">Blog</a><a href="/docs/tutorial.html">Getting Started</a></div><div><h5>Community</h5><a href="https://gitter.im/GMOD/jbrowse">Project Chat</a><a href="https://twitter.com/JBrowseGossip" target="_blank" rel="noreferrer noopener">Twitter</a></div><div><h5>More</h5><a href="https://github.com/GMOD/jbrowse">GitHub</a><a class="github-button" href="https://github.com/GMOD/jbrowse" data-icon="octicon-star" data-count-href="/GMOD/jbrowse/stargazers" data-show-count="true" data-count-aria-label="# stargazers on GitHub" aria-label="Star this project on GitHub">Star</a></div></section><section class="copyright">Copyright © 2019 Evolutionary Software Foundation</section></footer></div></body></html>