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<a href="./intro.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></a>
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<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">The <em>OBITools</em> commands</span></a>
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<a href="./library.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">3</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#biosequence" id="toc-biosequence" class="nav-link active" data-scroll-target="#biosequence"><span class="toc-section-number">3.1</span> BioSequence</a>
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<li><a href="#creating-new-instances" id="toc-creating-new-instances" class="nav-link" data-scroll-target="#creating-new-instances"><span class="toc-section-number">3.1.1</span> Creating new instances</a></li>
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<li><a href="#end-of-life-of-a-biosequence-instance" id="toc-end-of-life-of-a-biosequence-instance" class="nav-link" data-scroll-target="#end-of-life-of-a-biosequence-instance"><span class="toc-section-number">3.1.2</span> End of life of a <code>BioSequence</code> instance</a></li>
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<li><a href="#accessing-to-the-elements-of-a-sequence" id="toc-accessing-to-the-elements-of-a-sequence" class="nav-link" data-scroll-target="#accessing-to-the-elements-of-a-sequence"><span class="toc-section-number">3.1.3</span> Accessing to the elements of a sequence</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">3</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></h1>
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<section id="biosequence" class="level2" data-number="3.1">
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<h2 data-number="3.1" class="anchored" data-anchor-id="biosequence"><span class="header-section-number">3.1</span> BioSequence</h2>
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<p>The <code>BioSequence</code> class is used to represent biological sequences. It allows for storing : - the sequence itself as a <code>[]byte</code> - the sequencing quality score as a <code>[]byte</code> if needed - an identifier as a <code>string</code> - a definition as a <code>string</code> - a set of <em>(key, value)</em> pairs in a <code>map[sting]interface{}</code></p>
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<p>BioSequence is defined in the obiseq module and is included using the code</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
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<span id="cb1-2"><a href="#cb1-2" 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="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<section id="creating-new-instances" class="level3" data-number="3.1.1">
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<h3 data-number="3.1.1" class="anchored" data-anchor-id="creating-new-instances"><span class="header-section-number">3.1.1</span> Creating new instances</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 instance, the second returns a pointer on the new instance. Two other functions <code>MakeEmptyBioSequence</code>, and <code>NewEmptyBioSequence</code> do the same 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 sequence. It mist be a string constituted of a single word (not containing any space).</li>
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<li><code>sequence</code> is the DNA sequence itself, provided as a <code>byte</code> array (<code>[]byte</code>).</li>
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<li><code>definition</code> is a <code>string</code>, potentially empty, but usualy containing a sentence explaining what is that sequence.</li>
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</ul>
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<div class="sourceCode" id="cb2"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
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<span id="cb2-2"><a href="#cb2-2" 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="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
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<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb2-5"><a href="#cb2-5" 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="cb2-6"><a href="#cb2-6" 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="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"seq_GH0001"</span><span class="op">,</span></span>
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<span id="cb2-8"><a href="#cb2-8" 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="cb2-9"><a href="#cb2-9" 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="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
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<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></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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</section>
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<section id="end-of-life-of-a-biosequence-instance" class="level3" data-number="3.1.2">
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<h3 data-number="3.1.2" class="anchored" data-anchor-id="end-of-life-of-a-biosequence-instance"><span class="header-section-number">3.1.2</span> End of life of a <code>BioSequence</code> instance</h3>
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<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>
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</section>
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<section id="accessing-to-the-elements-of-a-sequence" class="level3" data-number="3.1.3">
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<h3 data-number="3.1.3" class="anchored" data-anchor-id="accessing-to-the-elements-of-a-sequence"><span class="header-section-number">3.1.3</span> Accessing to the elements of a sequence</h3>
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<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>
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<ul>
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<li><code>Id() string</code></li>
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<li><code>Sequence() []byte</code></li>
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<li><code>Definition() string</code></li>
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</ul>
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<p>It exists pending method to change the value of these elements</p>
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<ul>
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<li><code>SetId(id string)</code></li>
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<li><code>SetSequence(sequence []byte)</code></li>
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<li><code>SetDefinition(definition string)</code></li>
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</ul>
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<div class="sourceCode" id="cb4"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
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<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
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<span id="cb4-3"><a href="#cb4-3" 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="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
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<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb4-6"><a href="#cb4-6" 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="cb4-7"><a href="#cb4-7" 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="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"seq_GH0001"</span><span class="op">,</span></span>
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<span id="cb4-9"><a href="#cb4-9" 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>
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<span id="cb4-10"><a href="#cb4-10" 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="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
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<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb4-13"><a href="#cb4-13" 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="cb4-14"><a href="#cb4-14" 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="cb4-15"><a href="#cb4-15" 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="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<section id="different-ways-for-accessing-an-editing-the-sequence" class="level4" data-number="3.1.3.1">
|
||
<h4 data-number="3.1.3.1" class="anchored" data-anchor-id="different-ways-for-accessing-an-editing-the-sequence"><span class="header-section-number">3.1.3.1</span> Different ways for accessing an editing the sequence</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="cb5"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewEmptyBiosequence<span class="op">()</span></span>
|
||
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb5-9"><a href="#cb5-9" 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="cb5-10"><a href="#cb5-10" 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="cb5-11"><a href="#cb5-11" 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="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
</section>
|
||
<section id="sequence-quality-scores" class="level4" data-number="3.1.3.2">
|
||
<h4 data-number="3.1.3.2" class="anchored" data-anchor-id="sequence-quality-scores"><span class="header-section-number">3.1.3.2</span> Sequence quality scores</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>
|
||
|
||
|
||
</section>
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">2</span> <span class="chapter-title">The <em>OBITools</em> commands</span></span>
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<span class="nav-page-text"><span class="chapter-number">4</span> <span class="chapter-title">Annexes</span></span> <i class="bi bi-arrow-right-short"></i>
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