@gmod/jbrowse
Version:
JBrowse - client-side genome browser
64 lines (60 loc) • 16.6 kB
HTML
<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>generate-names.pl · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="# Name Searching and Autocompletion"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="generate-names.pl · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/index.html"/><meta property="og:description" content="# Name Searching and Autocompletion"/><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" href="https://jbrowse.org/blog/feed.xml" title="JBrowse Blog RSS Feed"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><link rel="stylesheet" href="/css/main.css"/></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/"><h2 class="headerTitle">JBrowse</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class=""><a href="/blog" target="_self">Blog</a></li><li class="siteNavGroupActive"><a href="/docs/installation.html" target="_self">Documentation</a></li><li class=""><a href="/en/demos.html" target="_self">Demos</a></li><li class=""><a href="/en/developers.html" target="_self">Developers</a></li><li class=""><a href="/en/contact.html" target="_self">Contact</a></li><li class=""><a href="/en/references.html" target="_self">References</a></li><li class=""><a href="/en/help.html" target="_self">Help</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="container docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><i></i></div><h2><i>›</i><span>Command line</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Tutorial</h3><ul><li class="navListItem"><a class="navItem" href="/docs/installation.html">Installation</a></li><li class="navListItem"><a class="navItem" href="/docs/tutorial.html">Indexed file formats tutorial</a></li><li class="navListItem"><a class="navItem" href="/docs/tutorial_classic.html">Classic quick-start guide</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Configuring tracks</h3><ul><li class="navListItem"><a class="navItem" href="/docs/reference_sequence.html">Reference sequence configuration</a></li><li class="navListItem"><a class="navItem" href="/docs/canvas_features.html">CanvasFeatures</a></li><li class="navListItem"><a class="navItem" href="/docs/html_features.html">HTMLFeatures</a></li><li class="navListItem"><a class="navItem" href="/docs/alignments.html">Alignments tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/bigwig.html">Wiggle/BigWig Tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/variants.html">VCF tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/minimal.html">Minimal JBrowse configurations</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced configuration</h3><ul><li class="navListItem"><a class="navItem" href="/docs/embedding.html">Embedding JBrowse</a></li><li class="navListItem"><a class="navItem" href="/docs/mouse_configs.html">Mouse clicks, menus, and popups</a></li><li class="navListItem"><a class="navItem" href="/docs/configuration_file_formats.html">Configuration File Formats</a></li><li class="navListItem"><a class="navItem" href="/docs/dataset_selector.html">Dataset Selector</a></li><li class="navListItem"><a class="navItem" href="/docs/track_selectors.html">Track Selectors</a></li><li class="navListItem"><a class="navItem" href="/docs/track_metadata.html">Track Metadata</a></li><li class="navListItem"><a class="navItem" href="/docs/global_options.html">Global configuration options</a></li><li class="navListItem"><a class="navItem" href="/docs/compression.html">Compressing JBrowse data</a></li><li class="navListItem"><a class="navItem" href="/docs/authentication.html">HTTP authentication for JBrowse</a></li><li class="navListItem"><a class="navItem" href="/docs/paired_reads.html">Paired read viewing</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Command line</h3><ul><li class="navListItem"><a 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 navListItemActive"><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 class="navGroupCategoryTitle">Other topics</h3><ul><li class="navListItem"><a class="navItem" href="/docs/url_strings.html">JBrowse URL parameters</a></li><li class="navListItem"><a class="navItem" href="/docs/image_tracks.html">Pre-rendered Image Tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/feature_coverage.html">Feature Coverage Tracks</a></li><li class="navListItem"><a class="navItem" href="/docs/screenshots.html">Automating screenshots of JBrowse</a></li><li class="navListItem"><a class="navItem" href="/docs/events.html">JBrowse Subscribe/Publish events</a></li><li class="navListItem"><a class="navItem" href="/docs/perl_config.html">Sample configuration bash script</a></li><li class="navListItem"><a class="navItem" href="/docs/data_formats.html">JBrowse REST API and Data APIs</a></li><li class="navListItem"><a class="navItem" href="/docs/plugins.html">Installing and writing plugins</a></li><li class="navListItem"><a class="navItem" href="/docs/cors.html">Cross-origin resource sharing (CORS)</a></li><li class="navListItem"><a class="navItem" href="/docs/sparql.html">SPARQL configuration</a></li><li class="navListItem"><a class="navItem" href="/docs/data_export.html">Data export</a></li><li class="navListItem"><a class="navItem" href="/docs/usage_stats.html">Usage Statistics</a></li></ul></div></div></section></div><script>
document.addEventListener('DOMContentLoaded', function() {
createToggler('#navToggler', '#docsNav', 'docsSliderActive');
createToggler('#tocToggler', 'body', 'tocActive');
const headings = document.querySelector('.toc-headings');
headings && headings.addEventListener('click', function(event) {
if (event.target.tagName === 'A') {
document.body.classList.remove('tocActive');
}
}, false);
function createToggler(togglerSelector, targetSelector, className) {
var toggler = document.querySelector(togglerSelector);
var target = document.querySelector(targetSelector);
toggler.onclick = function(event) {
event.preventDefault();
target.classList.toggle(className);
};
}
});
</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">generate-names.pl</h1></header><article><div><span><h1><a class="anchor" aria-hidden="true" id="name-searching-and-autocompletion"></a><a href="#name-searching-and-autocompletion" 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>Name Searching and Autocompletion</h1>
<p>The JBrowse search box auto-completes the names of features and reference sequences that are typed into it. After loading all feature and reference sequence data into a JBrowse instance (with <code>prepare-refseqs.pl</code>, <code>flatfile-to-json.pl</code>, etc.), <code>generate-names.pl</code> must be run to build the indexes used for name searching and autocompletion.</p>
<h2><a class="anchor" aria-hidden="true" id="autocompletion-configuration"></a><a href="#autocompletion-configuration" 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>Autocompletion Configuration</h2>
<p>Several settings are available to customize the behavior of autocompletion. Most users will not need to configure any of these variables.</p>
<table>
<thead>
<tr><th>Option</th><th>Value</th></tr>
</thead>
<tbody>
<tr><td><code>autocomplete→stopPrefixes</code></td><td>Array of word-prefixes for which autocomplete will be disabled. For example, a value of <code>['foo']</code> will prevent autocompletion when the user as typed 'f', 'fo', or 'foo', but autocompletion will resume when the user types any additional characters.</td></tr>
<tr><td><code>autocomplete→resultLimit</code></td><td>Maximum number of autocompletion results to display. Defaults to 15.</td></tr>
<tr><td><code>autocomplete→tooManyMatchesMessage</code></td><td>Message displayed in the autocompletion dropdown when more than <code>autocomplete→resultLimit</code> matches are displayed. Defaults to 'too many matches to display'.</td></tr>
</tbody>
</table>
<h2><a class="anchor" aria-hidden="true" id="generate-namespl"></a><a href="#generate-namespl" 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>generate-names.pl</h2>
<p>This script builds indexes of features by <em>label</em> (the visible name below a feature in JBrowse) and/or by <em>alias</em> (a secondary name that is not visible in the web browser, but may be present in the JSON used by JBrowse).</p>
<p>To search for a term, type it in the autocompleting text box at the top of the JBrowse window.</p>
<p>Basic syntax:</p>
<p><code>bin/generate-names.pl [options]</code></p>
<p>Note that generate-names.pl does not require any arguments. However, some options are available:</p>
<table>
<thead>
<tr><th>Option</th><th>Value</th></tr>
</thead>
<tbody>
<tr><td>--out</td><td>A path to the output directory (default is 'data/' in the current directory).</td></tr>
<tr><td>--verbose</td><td>This setting causes information about the division of nodes into chunks to be printed to the screen.</td></tr>
<tr><td>--hashBits</td><td>Sets the number of bits, or the filename length. If you get the error "Error reading from name store", try manually setting --hashBits to 16.</td></tr>
<tr><td>--completionLimit</td><td>Defines the number of letters used in the auto-completion. Example: --completionLimit 0 to disable autocompletion.</td></tr>
<tr><td>--incremental</td><td>Incrementally index new tracks. Fixed in version 1.11.6.</td></tr>
<tr><td>--tracks</td><td>A comma separated list of tracks to index. Can be combined with other options such as --incremental and --completionLimit to only provide autocompletion on certain tracks.</td></tr>
<tr><td>--workdir</td><td>Output the temporary files for names generation to a specific directory. Fixed in 1.11.6.</td></tr>
</tbody>
</table>
<p>View bin/generate-names.pl --help for more options. Note that if you are getting 404 errors for names/root.json then JBrowse is falling back to the legacy names store (and failing) so it is likely that you need to retry generate-names.</p>
<h2><a class="anchor" aria-hidden="true" id="indexing-custom-fields-in-gff"></a><a href="#indexing-custom-fields-in-gff" 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>Indexing custom fields in GFF</h2>
<p>By default, the Name, ID, and Alias fields, for all feature types (gene, mRNA, CDs, exon, etc.), are indexed by generate-names.pl</p>
<p>If you want to index more or different custom fields, you can run flatfile-to-json.pl (not generate-names.pl!) with --nameAttributes "name,id,alias,gene_id" for example, then it will also load the "gene_id" field as a name, and then you can re-run generate-names.pl and the gene_id can be searched for.</p>
<p>Also note that if you have a GFF3Tabix track (which is not loaded via flatfile-to-json.pl) then you can add a nameAttributes=name,id,alias,gene_id to the config for example.</p>
<p>If you have a GFF3Tabix track, you can also select the feature types that you want to index, by adding indexedFeatures=gene,mRNA to the config for example. Other feature types will not be indexed.</p>
</span></div></article></div><div class="docs-prevnext"><a class="docs-prev button" href="/docs/ucsc-to-json.pl.html">← ucsc-to-json.pl</a><a class="docs-next button" href="/docs/prepare-refseqs.pl.html">prepare-refseqs.pl →</a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#autocompletion-configuration">Autocompletion Configuration</a></li><li><a href="#generate-namespl">generate-names.pl</a></li><li><a href="#indexing-custom-fields-in-gff">Indexing custom fields in GFF</a></li></ul></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>