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<h2 data-number="12.1" class="anchored" data-anchor-id="obigrep-filters-sequence-files-according-to-numerous-conditions"><span class="header-section-number">12.1</span> <code>obigrep</code> – filters sequence files according to numerous conditions</h2>
<p>The <code>obigrep</code> command is somewhat analogous to the standard Unix <code>grep</code> command. It selects a subset of sequence records from a sequence file. A sequence record is a complex object consisting of an identifier, a set of attributes (a key, defined by its name, associated with a value), a definition, and the sequence itself. Instead of working text line by text line like the standard Unix tool, <code>obigrep</code> selection is done sequence record by sequence record. A large number of options allow you to refine the selection on any element of the sequence. <code>obigrep</code> allows you to specify multiple conditions simultaneously (which take on the value <code>TRUE</code> or <code>FALSE</code>) and only those sequence records which meet all conditions (all conditions are <code>TRUE</code>) are selected. <code>obigrep</code> is able to work on two paired read files. The selection criteria apply to one or the other of the readings in each pair depending on the mode chosen (<strong>--paired-mode</strong> option). In all cases the selection is applied in the same way to both files, thus maintaining their consistency.</p>
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<h4 data-number="12.1.1.1" class="anchored" data-anchor-id="selecting-sequences-based-on-their-caracteristics"><span class="header-section-number">12.1.1.1</span> Selecting sequences based on their caracteristics</h4>
<p>Sequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.</p>
<dl>
<dt><strong>--min-count</strong> | <strong>-c</strong> <em>COUNT</em></dt>
<dd>
<p>only sequences reprensenting at least <em>COUNT</em> reads will be selected. That option rely on the <code>count</code> attribute. If the <code>count</code> attribute is not defined for a sequence record, it is assumed equal to <span class="math inline">\(1\)</span>.</p>
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<dt><strong>--max-count</strong> | <strong>-C</strong> <em>COUNT</em></dt>
<dd>
<p>only sequences reprensenting no more than <em>COUNT</em> reads will be selected. That option rely on the <code>count</code> attribute. If the <code>count</code> attribute is not defined for a sequence record, it is assumed equal to <span class="math inline">\(1\)</span>.</p>
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<dt>Example</dt>
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<p>Selecting sequence records representing at least five reads in the dataset.</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-c</span> 5 data_SPER01.fasta <span class="op">&gt;</span> data_norare_SPER01.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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