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an annotation file in gtf file format, this function extracts the longest
isoform per gene locus and stores the results in a new fasta file.
This procedure enables easier downstream analyses such as orthology inference etc
when dealing with proteome fasta files which usually include isoform peptides."><meta property="og:image" content="/logo.png"><!-- 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]>
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    <div class="page-header">
    <h1>Retrieve the longest isoforms of several proteome files stored in a folder</h1>
    <small class="dont-index">Source: <a href="https://github.com/drostlab/orthologr/blob/HEAD/R/retrieve_longest_isoforms_all.R" class="external-link"><code>R/retrieve_longest_isoforms_all.R</code></a></small>
    <div class="hidden name"><code>retrieve_longest_isoforms_all.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Based on a fasta file storing the peptide isoforms of gene loci and
an annotation file in <code>gtf</code> file format, this function extracts the longest
isoform per gene locus and stores the results in a new <code>fasta</code> file.
This procedure enables easier downstream analyses such as orthology inference etc
when dealing with proteome <code>fasta</code> files which usually include isoform peptides.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">retrieve_longest_isoforms_all</span><span class="op">(</span></span>
<span>  <span class="va">proteome_folder</span>,</span>
<span>  <span class="va">annotation_folder</span>,</span>
<span>  <span class="va">output_folder</span>,</span>
<span>  annotation_format <span class="op">=</span> <span class="st">"gff"</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>proteome_folder</dt>
<dd><p>file path to proteome in <code>fasta</code> file format.</p></dd>


<dt>annotation_folder</dt>
<dd><p>file path to the corresponding annotation file in <code>gtf</code> file format.</p></dd>


<dt>output_folder</dt>
<dd><p>file path to new file storing only peptide sequences of the longest isoforms.</p></dd>


<dt>annotation_format</dt>
<dd><p>format of <code>annotation_file</code>. Options are:</p><ul><li><p><code>annotation_file = "gff"</code> (default)</p></li>
<li><p><code>annotation_file = "gtf"</code></p></li>
</ul></dd>

</dl></div>
    <div id="author">
    <h2>Author</h2>
    <p>Hajk-Georg Drost</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="va">orgs</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">"Arabidopsis lyrata"</span>, </span></span>
<span class="r-in"><span>          <span class="st">"Capsella rubella"</span>, <span class="st">"Solanum lycopersicum"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># download proteome files for all species          </span></span></span>
<span class="r-in"><span><span class="fu">biomartr</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/biomartr/reference/getProteomeSet.html" class="external-link">getProteomeSet</a></span><span class="op">(</span>db <span class="op">=</span> <span class="st">"refseq"</span>, organisms <span class="op">=</span> <span class="va">orgs</span>, path <span class="op">=</span> <span class="st">"of_proteomes"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># download annotation files for all species          </span></span></span>
<span class="r-in"><span><span class="fu">biomartr</span><span class="fu">::</span><span class="fu"><a href="https://docs.ropensci.org/biomartr/reference/getGFFSet.html" class="external-link">getGFFSet</a></span><span class="op">(</span>db <span class="op">=</span> <span class="st">"refseq"</span>, organisms <span class="op">=</span> <span class="va">orgs</span>, path <span class="op">=</span> <span class="st">"of_gff"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># select longest splice variant per gene locus</span></span></span>
<span class="r-in"><span><span class="fu">retrieve_longest_isoforms_all</span><span class="op">(</span>proteome_folder <span class="op">=</span> <span class="st">"of_proteomes"</span>, </span></span>
<span class="r-in"><span>                              annotation_folder <span class="op">=</span> <span class="st">"of_gff"</span>,</span></span>
<span class="r-in"><span>                              annotation_format <span class="op">=</span> <span class="st">"gff"</span>, </span></span>
<span class="r-in"><span>                              output_folder <span class="op">=</span> <span class="st">"of_proteomes_longest_sv"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
    </div>
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