<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>taxonomizr: Functions to Work with NCBI Accessions and Taxonomy — taxonomizr-package • taxonomizr</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="taxonomizr: Functions to Work with NCBI Accessions and Taxonomy — taxonomizr-package"><meta property="og:description" content="Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
    

    <div class="container template-reference-topic">
      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">taxonomizr</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.10.6</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu"><li>
      <a href="../articles/usage.html">taxonomizr usage</a>
    </li>
  </ul></li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://github.com/sherrillmix/taxonomizr/" class="external-link">
    <span class="fab fa-github fa-lg"></span>
     
  </a>
</li>
      </ul></div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>taxonomizr: Functions to Work with NCBI Accessions and Taxonomy</h1>
    <small class="dont-index">Source: <a href="https://github.com/sherrillmix/taxonomizr/blob/HEAD/R/taxa.R" class="external-link"><code>R/taxa.R</code></a></small>
    <div class="hidden name"><code>taxonomizr-package.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.</p>
    </div>


    <div id="details">
    <h2>Details</h2>
    <p>taxonomizr provides some simple functions to parse NCBI taxonomy files and accession dumps and efficiently use them to assign taxonomy to accession numbers or taxonomic IDs (<a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/" class="external-link">https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/</a>). This is useful for example to assign taxonomy to BLAST results. This is all done locally after downloading the appropriate files from NCBI using included functions. The major functions are:</p><ul><li><p><code><a href="prepareDatabase.html">prepareDatabase</a></code>: download data from NCBI and prepare SQLite database</p></li>
<li><p><code>link{accessionToTaxa}</code>: convert accession numbers to taxonomic IDs</p></li>
<li><p><code><a href="getTaxonomy.html">getTaxonomy</a></code>: convert taxonomic IDs to taxonomy</p></li>
</ul><p>More specialized functions are:</p><ul><li><p><code><a href="getId.html">getId</a></code>: convert a biological name to taxonomic ID</p></li>
<li><p><code><a href="getAccessions.html">getAccessions</a></code>: find accessions for a given taxonomic ID</p></li>
</ul></div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="prepareDatabase.html">prepareDatabase</a></code>, <code><a href="accessionToTaxa.html">accessionToTaxa</a></code>, <code><a href="getTaxonomy.html">getTaxonomy</a></code></p></div>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p><strong>Maintainer</strong>: Scott Sherrill-Mix <a href="mailto:ssm@msu.edu">ssm@msu.edu</a></p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span>  <span class="kw">if</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readline.html" class="external-link">readline</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>    <span class="st">"This will download a lot data and take a while to process.</span></span></span>
<span class="r-in"><span><span class="st">     Make sure you have space and bandwidth. Type y to continue: "</span></span></span>
<span class="r-in"><span>  <span class="op">)</span><span class="op">!=</span><span class="st">'y'</span><span class="op">)</span></span></span>
<span class="r-in"><span>    <span class="kw"><a href="https://rdrr.io/r/base/stop.html" class="external-link">stop</a></span><span class="op">(</span><span class="st">'This is a stop to make sure no one downloads a bunch of data unintentionally'</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="prepareDatabase.html">prepareDatabase</a></span><span class="op">(</span><span class="st">'accessionTaxa.sql'</span><span class="op">)</span></span></span>
<span class="r-in"><span>  <span class="va">blastAccessions</span><span class="op">&lt;-</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Z17430.1"</span>,<span class="st">"Z17429.1"</span>,<span class="st">"X62402.1"</span><span class="op">)</span></span></span>
<span class="r-in"><span>  <span class="va">ids</span><span class="op">&lt;-</span><span class="fu"><a href="accessionToTaxa.html">accessionToTaxa</a></span><span class="op">(</span><span class="va">blastAccessions</span>,<span class="st">'accessionTaxa.sql'</span><span class="op">)</span></span></span>
<span class="r-in"><span>  <span class="fu"><a href="getTaxonomy.html">getTaxonomy</a></span><span class="op">(</span><span class="va">ids</span>,<span class="st">'accessionTaxa.sql'</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
    </div>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
    </nav></div>
</div>


      <footer><div class="copyright">
  <p></p><p>Developed by Scott Sherrill-Mix.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer></div>

  


  

  </body></html>

