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<title>3 Reference documentation for the GO OBITools library | The GO OBITools</title>
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<meta name="author" content="SEric Coissac" />
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<meta name="date" content="2022-08-25" />
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<ul class="summary">
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<li class="chapter" data-level="1" data-path="the-obitools.html"><a href="the-obitools.html"><i class="fa fa-check"></i><b>1</b> The OBITools</a>
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<ul>
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<li class="chapter" data-level="1.1" data-path="the-obitools.html"><a href="the-obitools.html#aims-of-obitools"><i class="fa fa-check"></i><b>1.1</b> Aims of <em>OBITools</em></a></li>
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<li class="chapter" data-level="1.2" data-path="the-obitools.html"><a href="the-obitools.html#file-formats-usable-with-obitools"><i class="fa fa-check"></i><b>1.2</b> File formats usable with <em>OBITools</em></a>
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||
<ul>
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<li class="chapter" data-level="1.2.1" data-path="the-obitools.html"><a href="the-obitools.html#the-sequence-files"><i class="fa fa-check"></i><b>1.2.1</b> The sequence files</a></li>
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||
<li class="chapter" data-level="1.2.2" data-path="the-obitools.html"><a href="the-obitools.html#the-iupac-code"><i class="fa fa-check"></i><b>1.2.2</b> The IUPAC Code</a></li>
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||
<li class="chapter" data-level="1.2.3" data-path="the-obitools.html"><a href="the-obitools.html#classical-fasta"><i class="fa fa-check"></i><b>1.2.3</b> The <em>fasta</em> format</a></li>
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||
<li class="chapter" data-level="1.2.4" data-path="the-obitools.html"><a href="the-obitools.html#classical-fastq"><i class="fa fa-check"></i><b>1.2.4</b> The <em>fastq</em> sequence format</a></li>
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||
</ul></li>
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<li class="chapter" data-level="1.3" data-path="the-obitools.html"><a href="the-obitools.html#file-extension"><i class="fa fa-check"></i><b>1.3</b> File extension</a></li>
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<li class="chapter" data-level="1.4" data-path="the-obitools.html"><a href="the-obitools.html#see-also"><i class="fa fa-check"></i><b>1.4</b> See also</a></li>
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<li class="chapter" data-level="1.5" data-path="the-obitools.html"><a href="the-obitools.html#references"><i class="fa fa-check"></i><b>1.5</b> References</a></li>
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||
</ul></li>
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<li class="chapter" data-level="2" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html"><i class="fa fa-check"></i><b>2</b> The <em>OBITools</em> commands</a>
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<ul>
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<li class="chapter" data-level="2.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#specifying-the-input-files-to-obitools-commands"><i class="fa fa-check"></i><b>2.1</b> Specifying the input files to <em>OBITools</em> commands</a></li>
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<li class="chapter" data-level="2.2" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#options-common-to-most-of-the-obitools-commands"><i class="fa fa-check"></i><b>2.2</b> Options common to most of the <em>OBITools</em> commands</a>
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<ul>
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<li class="chapter" data-level="2.2.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#specifying-input-format"><i class="fa fa-check"></i><b>2.2.1</b> Specifying input format</a></li>
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<li class="chapter" data-level="2.2.2" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#specifying-output-format"><i class="fa fa-check"></i><b>2.2.2</b> Specifying output format</a></li>
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<li class="chapter" data-level="2.2.3" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#format-of-the-annotations-in-fasta-and-fastq-files"><i class="fa fa-check"></i><b>2.2.3</b> Format of the annotations in Fasta and Fastq files</a></li>
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||
</ul></li>
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<li class="chapter" data-level="2.3" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#metabarcode-design-and-quality-assessment"><i class="fa fa-check"></i><b>2.3</b> Metabarcode design and quality assessment</a></li>
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<li class="chapter" data-level="2.4" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#file-format-conversions"><i class="fa fa-check"></i><b>2.4</b> File format conversions</a></li>
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<li class="chapter" data-level="2.5" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#sequence-annotations"><i class="fa fa-check"></i><b>2.5</b> Sequence annotations</a></li>
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<li class="chapter" data-level="2.6" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#computations-on-sequences"><i class="fa fa-check"></i><b>2.6</b> Computations on sequences</a>
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<ul>
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<li class="chapter" data-level="2.6.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#obipairing"><i class="fa fa-check"></i><b>2.6.1</b> <code>obipairing</code></a></li>
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||
</ul></li>
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<li class="chapter" data-level="2.7" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#sequence-sampling-and-filtering"><i class="fa fa-check"></i><b>2.7</b> Sequence sampling and filtering</a>
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||
<ul>
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||
<li class="chapter" data-level="2.7.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#utilities"><i class="fa fa-check"></i><b>2.7.1</b> Utilities</a></li>
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||
</ul></li>
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||
</ul></li>
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||
<li class="chapter" data-level="3" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html"><i class="fa fa-check"></i><b>3</b> Reference documentation for the GO <em>OBITools</em> library</a>
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||
<ul>
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<li class="chapter" data-level="3.1" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#biosequence"><i class="fa fa-check"></i><b>3.1</b> BioSequence</a>
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<ul>
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<li class="chapter" data-level="3.1.1" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#creating-new-instances"><i class="fa fa-check"></i><b>3.1.1</b> Creating new instances</a></li>
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||
<li class="chapter" data-level="3.1.2" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#end-of-life-of-a-biosequence-instance"><i class="fa fa-check"></i><b>3.1.2</b> End of life of a <code>BioSequence</code> instance</a></li>
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||
<li class="chapter" data-level="3.1.3" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#accessing-to-the-elements-of-a-sequence"><i class="fa fa-check"></i><b>3.1.3</b> Accessing to the elements of a sequence</a></li>
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||
</ul></li>
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</ul></li>
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<li class="chapter" data-level="4" data-path="annexes.html"><a href="annexes.html"><i class="fa fa-check"></i><b>4</b> Annexes</a>
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<ul>
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<li class="chapter" data-level="4.0.1" data-path="annexes.html"><a href="annexes.html#sequence-attributes"><i class="fa fa-check"></i><b>4.0.1</b> Sequence attributes</a></li>
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||
</ul></li>
|
||
</ul>
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||
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||
</nav>
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</div>
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|
||
<div class="book-body">
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<div class="body-inner">
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<div class="book-header" role="navigation">
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<h1>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">The GO <em>OBITools</em></a>
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</h1>
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</div>
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<div class="page-wrapper" tabindex="-1" role="main">
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<div class="page-inner">
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<section class="normal" id="section-">
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<div id="reference-documentation-for-the-go-obitools-library" class="section level1 hasAnchor" number="3">
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<h1><span class="header-section-number">3</span> Reference documentation for the GO <em>OBITools</em> library<a href="reference-documentation-for-the-go-obitools-library.html#reference-documentation-for-the-go-obitools-library" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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<div id="biosequence" class="section level2 hasAnchor" number="3.1">
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<h2><span class="header-section-number">3.1</span> BioSequence<a href="reference-documentation-for-the-go-obitools-library.html#biosequence" class="anchor-section" aria-label="Anchor link to header"></a></h2>
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<p>The <code>BioSequence</code> class is used to represent biological sequences. It
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allows for storing : - the sequence itself as a <code>[]byte</code> - the
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sequencing quality score as a <code>[]byte</code> if needed - an identifier as a
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<code>string</code> - a definition as a <code>string</code> - a set of <em>(key, value)</em> pairs in
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a <code>map[sting]interface{}</code></p>
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<p>BioSequence is defined in the obiseq module and is included using the
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code</p>
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<div class="sourceCode" id="cb7"><pre class="sourceCode go"><code class="sourceCode go"><span id="cb7-1"><a href="reference-documentation-for-the-go-obitools-library.html#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
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<span id="cb7-2"><a href="reference-documentation-for-the-go-obitools-library.html#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
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<span id="cb7-3"><a href="reference-documentation-for-the-go-obitools-library.html#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span></code></pre></div>
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<div id="creating-new-instances" class="section level3 hasAnchor" number="3.1.1">
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<h3><span class="header-section-number">3.1.1</span> Creating new instances<a href="reference-documentation-for-the-go-obitools-library.html#creating-new-instances" class="anchor-section" aria-label="Anchor link to header"></a></h3>
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<p>To create new instance, use</p>
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<ul>
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<li><code>MakeBioSequence(id string, sequence []byte, definition string) obiseq.BioSequence</code></li>
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<li><code>NewBioSequence(id string, sequence []byte, definition string) *obiseq.BioSequence</code></li>
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</ul>
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<p>Both create a <code>BioSequence</code> instance, but when the first one returns the
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instance, the second returns a pointer on the new instance. Two other
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functions <code>MakeEmptyBioSequence</code>, and <code>NewEmptyBioSequence</code> do the same
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job but provide an uninitialized objects.</p>
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<ul>
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<li><code>id</code> parameters corresponds to the unique identifier of the
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sequence. It mist be a string constituted of a single word (not
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containing any space).</li>
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<li><code>sequence</code> is the DNA sequence itself, provided as a <code>byte</code> array
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(<code>[]byte</code>).</li>
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<li><code>definition</code> is a <code>string</code>, potentially empty, but usualy containing
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a sentence explaining what is that sequence.</li>
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</ul>
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||
<div class="sourceCode" id="cb8"><pre class="sourceCode go"><code class="sourceCode go"><span id="cb8-1"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
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<span id="cb8-2"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
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<span id="cb8-3"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
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<span id="cb8-4"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-4" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb8-5"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-5" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
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<span id="cb8-6"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-6" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewBiosequence<span class="op">(</span></span>
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<span id="cb8-7"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"seq_GH0001"</span><span class="op">,</span></span>
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<span id="cb8-8"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-8" aria-hidden="true" tabindex="-1"></a> bytes<span class="op">.</span>FromString<span class="op">(</span><span class="st">"ACGTGTCAGTCG"</span><span class="op">),</span></span>
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<span id="cb8-9"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"A short test sequence"</span><span class="op">,</span></span>
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<span id="cb8-10"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-10" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
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<span id="cb8-11"><a href="reference-documentation-for-the-go-obitools-library.html#cb8-11" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code></pre></div>
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<p>When formated as fasta the parameters correspond to the following schema</p>
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<pre><code>>id definition containing potentially several words
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sequence</code></pre>
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</div>
|
||
<div id="end-of-life-of-a-biosequence-instance" class="section level3 hasAnchor" number="3.1.2">
|
||
<h3><span class="header-section-number">3.1.2</span> End of life of a <code>BioSequence</code> instance<a href="reference-documentation-for-the-go-obitools-library.html#end-of-life-of-a-biosequence-instance" class="anchor-section" aria-label="Anchor link to header"></a></h3>
|
||
<p>When a <code>BioSequence</code> instance is no more used, it is normally taken in
|
||
charge by the GO garbage collector. You can if you want call the
|
||
<code>Recycle</code> method on the instance to store the allocated memory element
|
||
in a <code>pool</code> to limit allocation effort when many sequences are
|
||
manipulated.</p>
|
||
</div>
|
||
<div id="accessing-to-the-elements-of-a-sequence" class="section level3 hasAnchor" number="3.1.3">
|
||
<h3><span class="header-section-number">3.1.3</span> Accessing to the elements of a sequence<a href="reference-documentation-for-the-go-obitools-library.html#accessing-to-the-elements-of-a-sequence" class="anchor-section" aria-label="Anchor link to header"></a></h3>
|
||
<p>The different elements of an <code>obiseq.BioSequence</code> must be accessed using
|
||
a set of methods. For the three main elements provided during the
|
||
creation of a new instance methodes are :</p>
|
||
<ul>
|
||
<li><code>Id() string</code></li>
|
||
<li><code>Sequence() []byte</code></li>
|
||
<li><code>Definition() string</code></li>
|
||
</ul>
|
||
<p>It exists pending method to change the value of these elements</p>
|
||
<ul>
|
||
<li><code>SetId(id string)</code></li>
|
||
<li><code>SetSequence(sequence []byte)</code></li>
|
||
<li><code>SetDefinition(definition string)</code></li>
|
||
</ul>
|
||
<div class="sourceCode" id="cb10"><pre class="sourceCode go"><code class="sourceCode go"><span id="cb10-1"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||
<span id="cb10-2"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||
<span id="cb10-3"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||
<span id="cb10-4"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||
<span id="cb10-5"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-5" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb10-6"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-6" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||
<span id="cb10-7"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-7" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewBiosequence<span class="op">(</span></span>
|
||
<span id="cb10-8"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"seq_GH0001"</span><span class="op">,</span></span>
|
||
<span id="cb10-9"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-9" aria-hidden="true" tabindex="-1"></a> bytes<span class="op">.</span>FromString<span class="op">(</span><span class="st">"ACGTGTCAGTCG"</span><span class="op">),</span></span>
|
||
<span id="cb10-10"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"A short test sequence"</span><span class="op">,</span></span>
|
||
<span id="cb10-11"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-11" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
|
||
<span id="cb10-12"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-12" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb10-13"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-13" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>Id<span class="op">())</span></span>
|
||
<span id="cb10-14"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-14" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>SetId<span class="op">(</span><span class="st">"SPE01_0001"</span><span class="op">)</span></span>
|
||
<span id="cb10-15"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-15" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>Id<span class="op">())</span></span>
|
||
<span id="cb10-16"><a href="reference-documentation-for-the-go-obitools-library.html#cb10-16" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code></pre></div>
|
||
<div id="different-ways-for-accessing-an-editing-the-sequence" class="section level4 hasAnchor" number="3.1.3.1">
|
||
<h4><span class="header-section-number">3.1.3.1</span> Different ways for accessing an editing the sequence<a href="reference-documentation-for-the-go-obitools-library.html#different-ways-for-accessing-an-editing-the-sequence" class="anchor-section" aria-label="Anchor link to header"></a></h4>
|
||
<p>If <code>Sequence()</code>and <code>SetSequence(sequence []byte)</code> methods are the basic
|
||
ones, several other methods exist.</p>
|
||
<ul>
|
||
<li><code>String() string</code> return the sequence directly converted to a
|
||
<code>string</code> instance.</li>
|
||
<li>The <code>Write</code> method family allows for extending an existing sequence
|
||
following the buffer protocol.
|
||
<ul>
|
||
<li><code>Write(data []byte) (int, error)</code> allows for appending a byte
|
||
array on 3’ end of the sequence.</li>
|
||
<li><code>WriteString(data string) (int, error)</code> allows for appending a
|
||
<code>string</code>.</li>
|
||
<li><code>WriteByte(data byte) error</code> allows for appending a single
|
||
<code>byte</code>.</li>
|
||
</ul></li>
|
||
</ul>
|
||
<p>The <code>Clear</code> method empties the sequence buffer.</p>
|
||
<div class="sourceCode" id="cb11"><pre class="sourceCode go"><code class="sourceCode go"><span id="cb11-1"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||
<span id="cb11-2"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||
<span id="cb11-3"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||
<span id="cb11-4"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||
<span id="cb11-5"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-5" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb11-6"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-6" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||
<span id="cb11-7"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-7" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewEmptyBiosequence<span class="op">()</span></span>
|
||
<span id="cb11-8"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-8" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb11-9"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-9" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>WriteString<span class="op">(</span><span class="st">"accc"</span><span class="op">)</span></span>
|
||
<span id="cb11-10"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-10" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>WriteByte<span class="op">(</span><span class="dt">byte</span><span class="op">(</span><span class="ch">'c'</span><span class="op">))</span></span>
|
||
<span id="cb11-11"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-11" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>String<span class="op">())</span></span>
|
||
<span id="cb11-12"><a href="reference-documentation-for-the-go-obitools-library.html#cb11-12" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code></pre></div>
|
||
</div>
|
||
<div id="sequence-quality-scores" class="section level4 hasAnchor" number="3.1.3.2">
|
||
<h4><span class="header-section-number">3.1.3.2</span> Sequence quality scores<a href="reference-documentation-for-the-go-obitools-library.html#sequence-quality-scores" class="anchor-section" aria-label="Anchor link to header"></a></h4>
|
||
<p>Sequence quality scores cannot be initialized at the time of instance
|
||
creation. You must use dedicated methods to add quality scores to a
|
||
sequence.</p>
|
||
<p>To be coherent the length of both the DNA sequence and que quality score
|
||
sequence must be equal. But assessment of this constraint is realized.
|
||
It is of the programmer responsability to check that invariant.</p>
|
||
<p>While accessing to the quality scores relies on the method
|
||
<code>Quality() []byte</code>, setting the quality need to call one of the
|
||
following method. They run similarly to their sequence dedicated
|
||
conterpart.</p>
|
||
<ul>
|
||
<li><code>SetQualities(qualities Quality)</code></li>
|
||
<li><code>WriteQualities(data []byte) (int, error)</code></li>
|
||
<li><code>WriteByteQualities(data byte) error</code></li>
|
||
</ul>
|
||
<p>In a way analogous to the <code>Clear</code> method, <code>ClearQualities()</code> empties the
|
||
sequence of quality scores.</p>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
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|
||
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