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<h2 id="toc-title">Table of contents</h2>
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<li><a href="#obigrep-filters-sequence-files-according-to-numerous-conditions" id="toc-obigrep-filters-sequence-files-according-to-numerous-conditions" class="nav-link active" data-scroll-target="#obigrep-filters-sequence-files-according-to-numerous-conditions"><span class="toc-section-number">12.1</span> <code>obigrep</code> – filters sequence files according to numerous conditions</a>
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<li><a href="#the-options-usable-with-obigrep" id="toc-the-options-usable-with-obigrep" class="nav-link" data-scroll-target="#the-options-usable-with-obigrep"><span class="toc-section-number">12.1.1</span> The options usable with <code>obigrep</code></a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></h1>
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<section id="obigrep-filters-sequence-files-according-to-numerous-conditions" class="level2" data-number="12.1">
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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>
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<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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<section id="the-options-usable-with-obigrep" class="level3" data-number="12.1.1">
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<h3 data-number="12.1.1" class="anchored" data-anchor-id="the-options-usable-with-obigrep"><span class="header-section-number">12.1.1</span> The options usable with <code>obigrep</code></h3>
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<section id="selecting-sequences-based-on-their-caracteristics" class="level4" data-number="12.1.1.1">
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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>
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<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>
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<p><strong>Selection based on the sequence</strong></p>
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<p>Sequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (<em>e.g</em> <code>AACCTT</code>). But the usage of regular patterns allows for looking for more complex pattern. As example, <code>A[TG]C+G</code> matches a <code>A</code>, followed by a <code>T</code> or a <code>G</code>, then one or several <code>C</code> and endly a <code>G</code>.</p>
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<dl>
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<dt><strong>--sequence</strong>|<strong>-s</strong> <em>PATTERN</em></dt>
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<dd>
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<p>Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available <a href="https://yourbasic.org/golang/regexp-cheat-sheet/#cheat-sheet">here</a>.</p>
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</dd>
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<dt><em>Examples:</em></dt>
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<dd>
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<p>Selects only the sequence records that contain an <em>EcoRI</em> restriction site.</p>
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</dd>
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</dl>
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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">-s</span> <span class="st">'GAATTC'</span> seq1.fasta <span class="op">></span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>: Selects only the sequence records that contain a stretch of at least 10 <code>A</code>.</p>
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<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'A{10,}'</span> seq1.fasta <span class="op">></span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<p>: Selects only the sequence records that do not contain ambiguous nucleotides.</p>
|
||
<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'^[ACGT]+$'</span> seq1.fasta <span class="op">></span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<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>
|
||
</dd>
|
||
<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>
|
||
</dd>
|
||
<dt><em>Examples</em></dt>
|
||
<dd>
|
||
<p>Selecting sequence records representing at least five reads in the dataset.</p>
|
||
</dd>
|
||
</dl>
|
||
<div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-c</span> 5 data_SPER01.fasta <span class="op">></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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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></span>
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