mirror of
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Reduce doc size
Former-commit-id: 6f92f375e9cf92159e769ce562071bb56a871819
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vendor
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*.fastq
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*.fasta
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*.fastq.gz
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*.fasta.gz
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.DS_Store
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*.gml
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*.log
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sample/test.obipcr.log
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Example_Arth03.ngsfilter
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SPER01.csv
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SPER03.csv
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wolf_diet_ngsfilter.txt
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xx
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yyy_geom.csv
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yyy.json
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bug_obimultiplex/toto
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bug_obimultiplex/toto_mapping
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bug_obimultiplex/tutu
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bug_obimultiplex/tutu_mapping
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bug_obipairing/GIT1_GH_ngsfilter.txt
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<div class="container-fluid d-flex justify-content-between">
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<h1 class="quarto-secondary-nav-title">Appendix A — Annexes</h1>
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<div class="pt-lg-2 mt-2 text-left sidebar-header">
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||||
<div class="sidebar-title mb-0 py-0">
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||||
<a href="./">OBITools V4</a>
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</div>
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||||
</div>
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<div class="mt-2 flex-shrink-0 align-items-center">
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<ul class="list-unstyled mt-1">
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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||||
<a href="./index.html" class="sidebar-item-text sidebar-link">Preface</a>
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</div>
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</li>
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||||
<li class="sidebar-item sidebar-item-section">
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<div class="sidebar-item-container">
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||||
<a href="./intro.html" class="sidebar-item-text sidebar-link">The OBITools</a>
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||||
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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||||
<a href="./installation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">Installation of the <em>OBITools</em></span></a>
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||||
</div>
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||||
</li>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./formats.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">File formats usable with <em>OBITools</em></span></a>
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</div>
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||||
</li>
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<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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||||
<a href="./tutorial.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">OBITools V4 Tutorial</span></a>
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||||
</div>
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||||
</li>
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||||
</ul>
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||||
</li>
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||||
<li class="sidebar-item sidebar-item-section">
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<div class="sidebar-item-container">
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<a href="./commands.html" class="sidebar-item-text sidebar-link">The *OBITools V4* commands</a>
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<a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
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<i class="bi bi-chevron-right ms-2"></i>
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</a>
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||||
</div>
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||||
<ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">
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<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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||||
<a href="./inupt.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">Specifying the data input to <em>OBITools</em> commands</span></a>
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||||
</div>
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||||
</li>
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||||
<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
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||||
</div>
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||||
</li>
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||||
<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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<a href="./common_options.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></a>
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||||
</div>
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||||
</li>
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||||
<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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<a href="./expressions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></a>
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</div>
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||||
</li>
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||||
<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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<a href="./comm_metabarcode_design.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span> <span class="chapter-title">Metabarcode design and quality assessment</span></a>
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</div>
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||||
</li>
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||||
<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./comm_reformat.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span> <span class="chapter-title">File format conversions</span></a>
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</div>
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||||
</li>
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||||
<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
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<a href="./comm_annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></a>
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</div>
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</li>
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||||
<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./comm_computation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></a>
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</div>
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</li>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
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</div>
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||||
</li>
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||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
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||||
<a href="./comm_utilities.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></a>
|
||||
</div>
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||||
</li>
|
||||
</ul>
|
||||
</li>
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||||
<li class="sidebar-item sidebar-item-section">
|
||||
<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
|
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</li>
|
||||
<li class="sidebar-item sidebar-item-section">
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||||
<div class="sidebar-item-container">
|
||||
<a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">Appendices</a>
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||||
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<i class="bi bi-chevron-right ms-2"></i>
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|
||||
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||||
<ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">
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||||
<li class="sidebar-item">
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||||
<div class="sidebar-item-container">
|
||||
<a href="./annexes.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">A</span> <span class="chapter-title">Annexes</span></a>
|
||||
</div>
|
||||
</li>
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||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
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<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
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<h2 id="toc-title">Table of contents</h2>
|
||||
|
||||
<ul>
|
||||
<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">A.1</span> Sequence attributes</a></li>
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<h1 class="title d-none d-lg-block">Appendix A — Annexes</h1>
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<section id="sequence-attributes" class="level2" data-number="A.1">
|
||||
<h2 data-number="A.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">A.1</span> Sequence attributes</h2>
|
||||
<p><strong>ali_dir (<code>string</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
<li>The attribute can contain 2 string values <code>left</code> or <code>right</code>.</li>
|
||||
</ul>
|
||||
<p>The alignment generated by <em>obipairing</em> is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction <code>ali_dir</code> is set to <em>left</em>. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, <code>ali_dir</code> is set to <em>right</em>.</p>
|
||||
<p><strong>ali_length (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p>Length of the aligned parts when merging forward and reverse reads</p>
|
||||
<p><strong>count (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obiuniq</em> tool</li>
|
||||
<li>Getter : method <code>Count()</code></li>
|
||||
<li>Setter : method <code>SetCount(int)</code></li>
|
||||
</ul>
|
||||
<p>The <code>count</code> attribute indicates how-many strictly identical reads have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.</p>
|
||||
<p>The <code>Count()</code> method allows to access to the count attribute as an integer value. If the <code>count</code> attribute is not defined for the given sequence, the value <em>1</em> is returned</p>
|
||||
<p><strong>merged_* (<code>map[string]int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obiuniq</em> tool</li>
|
||||
</ul>
|
||||
<p>The <code>-m</code> option of the <em>obiuniq</em> tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when <em>obiuniq</em> is run after running <em>obimultiplex</em>. The actual name of the attribute depends on the name of the monitored attribute. If <code>-m</code> option is used with the attribute <em>sample</em>, then this attribute names <em>merged_sample</em>.</p>
|
||||
<p><strong>mode (<code>string</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
<li>The attribute can contain 2 string values <code>join</code> or <code>alignment</code>.</li>
|
||||
</ul>
|
||||
<p><strong>obitag_ref_index (<code>map[string]string</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obirefidx</em> tool.</li>
|
||||
</ul>
|
||||
<p>It resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode json code-with-copy"><code class="sourceCode json"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">{</span><span class="dt">"0"</span><span class="fu">:</span><span class="st">"9606@Homo sapiens@species"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="dt">"2"</span><span class="fu">:</span><span class="st">"207598@Homininae@subfamily"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="dt">"3"</span><span class="fu">:</span><span class="st">"9604@Hominidae@family"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="dt">"8"</span><span class="fu">:</span><span class="st">"314295@Hominoidea@superfamily"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="dt">"10"</span><span class="fu">:</span><span class="st">"9526@Catarrhini@parvorder"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="dt">"12"</span><span class="fu">:</span><span class="st">"1437010@Boreoeutheria@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="dt">"16"</span><span class="fu">:</span><span class="st">"9347@Eutheria@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="dt">"17"</span><span class="fu">:</span><span class="st">"40674@Mammalia@class"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="dt">"22"</span><span class="fu">:</span><span class="st">"117571@Euteleostomi@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="dt">"25"</span><span class="fu">:</span><span class="st">"7776@Gnathostomata@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> <span class="dt">"29"</span><span class="fu">:</span><span class="st">"33213@Bilateria@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="dt">"30"</span><span class="fu">:</span><span class="st">"6072@Eumetazoa@clade"</span><span class="fu">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p><strong>pairing_mismatches (<code>map[string]string</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_a_single (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_ab_match (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_b_single (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>score (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>score_norm (<code>float</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
<li>The value ranges between 0 and 1.</li>
|
||||
</ul>
|
||||
<p>Score of the alignment between forward and reverse reads expressed as a fraction of identity.</p>
|
||||
|
||||
|
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<h2 id="toc-title">Table of contents</h2>
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<ul>
|
||||
<li><a href="#obipairing" id="toc-obipairing" class="nav-link active" data-scroll-target="#obipairing"><span class="toc-section-number">11.1</span> <code>obipairing</code></a>
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<li><a href="#alignment-procedure" id="toc-alignment-procedure" class="nav-link" data-scroll-target="#alignment-procedure">Alignment procedure</a></li>
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<li><a href="#the-scoring-system" id="toc-the-scoring-system" class="nav-link" data-scroll-target="#the-scoring-system">The scoring system</a></li>
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<li><a href="#obimultiplex" id="toc-obimultiplex" class="nav-link" data-scroll-target="#obimultiplex"><span class="toc-section-number">11.2</span> <code>obimultiplex</code></a></li>
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<li><a href="#obicomplement" id="toc-obicomplement" class="nav-link" data-scroll-target="#obicomplement"><span class="toc-section-number">11.3</span> <code>obicomplement</code></a></li>
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<li><a href="#obiclean" id="toc-obiclean" class="nav-link" data-scroll-target="#obiclean"><span class="toc-section-number">11.4</span> <code>obiclean</code></a></li>
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<li><a href="#obiuniq" id="toc-obiuniq" class="nav-link" data-scroll-target="#obiuniq"><span class="toc-section-number">11.5</span> <code>obiuniq</code></a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></h1>
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<section id="obipairing" class="level2" data-number="11.1">
|
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<h2 data-number="11.1" class="anchored" data-anchor-id="obipairing"><span class="header-section-number">11.1</span> <code>obipairing</code></h2>
|
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<blockquote class="blockquote">
|
||||
<p>Replace the <code>illuminapairedends</code> original <em>OBITools</em></p>
|
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</blockquote>
|
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<section id="alignment-procedure" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="alignment-procedure">Alignment procedure</h3>
|
||||
<p><code>obipairing</code> is introducing a new alignment algorithm compared to the <code>illuminapairedend</code> command of the <code>OBITools V2</code>. Nethertheless this new algorithm has been design to produce the same results than the previous, except in very few cases.</p>
|
||||
<p>The new algorithm is a two-step procedure. First, a FASTN-type algorithm <span class="citation" data-cites="Lipman1985-hw">(<a href="references.html#ref-Lipman1985-hw" role="doc-biblioref">Lipman and Pearson 1985</a>)</span> identifies the best offset between the two matched readings. This identifies the region of overlap.</p>
|
||||
<p>In the second step, the matching regions of the two reads are extracted along with a flanking sequence of <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>Δ</mi><annotation encoding="application/x-tex">\Delta</annotation></semantics></math> base pairs. The two subsequences are then aligned using a “one side free end-gap” dynamic programming algorithm. This latter step is only called if at least one mismatch is detected by the FASTP step.</p>
|
||||
<p>Unless the similarity between the two reads at their overlap region is very low, the addition of the flanking regions in the second step of the alignment ensures the same alignment as if the dynamic programming alignment was performed on the full reads.</p>
|
||||
</section>
|
||||
<section id="the-scoring-system" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="the-scoring-system">The scoring system</h3>
|
||||
<p>In the dynamic programming step, the match and mismatch scores take into account the quality scores of the two aligned nucleotides. By taking these into account, the probability of a true match can be calculated for each aligned base pair.</p>
|
||||
<p>If we consider a nucleotide read with a quality score <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>Q</mi><annotation encoding="application/x-tex">Q</annotation></semantics></math>, the probability of misreading this base (<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>P</mi><mi>E</mi></msub><annotation encoding="application/x-tex">P_E</annotation></semantics></math>) is : <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>E</mi></msub><mo>=</mo><msup><mn>10</mn><mrow><mo>−</mo><mfrac><mi>Q</mi><mn>10</mn></mfrac></mrow></msup></mrow><annotation encoding="application/x-tex">
|
||||
P_E = 10^{-\frac{Q}{10}}
|
||||
</annotation></semantics></math></p>
|
||||
<p>Thus, when a given nucleotide <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is observed with the quality score <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>Q</mi><annotation encoding="application/x-tex">Q</annotation></semantics></math>. The probability that <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is really an <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><mi>X</mi><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mi>E</mi></msub></mrow><annotation encoding="application/x-tex">
|
||||
P(X=X) = 1 - P_E
|
||||
</annotation></semantics></math></p>
|
||||
<p>Otherwise, <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is actually one of the three other possible nucleotides (<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><annotation encoding="application/x-tex">X_{E1}</annotation></semantics></math>, <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><annotation encoding="application/x-tex">X_{E2}</annotation></semantics></math> or <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mn>3</mn></mrow></msub><annotation encoding="application/x-tex">X_{E3}</annotation></semantics></math>). If we suppose that the three reading error have the same probability :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>3</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>3</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mfrac><msub><mi>P</mi><mi>E</mi></msub><mn>3</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P(X=X_{E1}) = P(X=X_{E3}) = P(X=X_{E3}) = \frac{P_E}{3}
|
||||
</annotation></semantics></math></p>
|
||||
<p>At each position in an alignment where the two nucleotides <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> face each other (not a gapped position), the probability of a true match varies depending on whether <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1=X_2</annotation></semantics></math>, an observed match, or <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>≠</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1 \neq X_2</annotation></semantics></math>, an observed mismatch.</p>
|
||||
<p><strong>Probability of a true match when <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1=X_2</annotation></semantics></math></strong></p>
|
||||
<p>That probability can be divided in two parts. First <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> have been correctly read. The corresponding probability is :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><msub><mi>P</mi><mrow><mi>T</mi><mi>M</mi></mrow></msub></mtd><mtd columnalign="left"><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>1</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right"></mtd><mtd columnalign="left"><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msup><mn>10</mn><mrow><mo>−</mo><mfrac><msub><mi>Q</mi><mn>1</mn></msub><mn>10</mn></mfrac></mrow></msup><mo stretchy="true" form="postfix">)</mo></mrow><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msup><mn>10</mn><mrow><mo>−</mo><mfrac><msub><mi>Q</mi><mn>2</mn></msub><mn>10</mn></mfrac></mrow></msup><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P_{TM} &= (1- PE_1)(1-PE_2)\\
|
||||
&=(1 - 10^{-\frac{Q_1}{10} } )(1 - 10^{-\frac{Q_2}{10}} )
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p>Secondly, a match can occure if the true nucleotides read as <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> are not <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> but identical.</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>∩</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>2</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd><mtd columnalign="left"><mo>=</mo><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>9</mn></mfrac></mtd></mtr><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mi>x</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>∩</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>2</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mi>x</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd><mtd columnalign="left"><mo>=</mo><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>3</mn></mfrac></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P(X_1==X_{E1}) \cap P(X_2==X_{E1}) &= \frac{P_{E1} P_{E2}}{9} \\
|
||||
P(X_1==X_{Ex}) \cap P(X_2==X_{Ex}) & = \frac{P_{E1} P_{E2}}{3}
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p>The probability of a true match between <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> when <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1 = X_2</annotation></semantics></math> an observed match :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>M</mi><mi>A</mi><mi>T</mi><mi>C</mi><mi>H</mi><mo stretchy="false" form="prefix">|</mo><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>1</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>3</mn></mfrac></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P(MATCH | X_1 = X_2) = (1- PE_1)(1-PE_2) + \frac{P_{E1} P_{E2}}{3}
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p><strong>Probability of a true match when <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>≠</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1 \neq X_2</annotation></semantics></math></strong></p>
|
||||
<p>That probability can be divided in three parts.</p>
|
||||
<ol type="a">
|
||||
<li><math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> has been correctly read and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> is a sequencing error and is actually equal to <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math>. <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>a</mi></msub><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mn>3</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P_a = (1-P_{E1})\frac{P_{E2}}{3}
|
||||
</annotation></semantics></math></li>
|
||||
<li><math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> has been correctly read and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> is a sequencing error and is actually equal to <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math>. <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>b</mi></msub><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mn>3</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P_b = (1-P_{E2})\frac{P_{E1}}{3}
|
||||
</annotation></semantics></math></li>
|
||||
<li><math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> corresponds to sequencing error but are actually the same base <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mi>x</mi></mrow></msub><annotation encoding="application/x-tex">X_{Ex}</annotation></semantics></math> <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>c</mi></msub><mo>=</mo><mn>2</mn><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>9</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P_c = 2\frac{P_{E1} P_{E2}}{9}
|
||||
</annotation></semantics></math></li>
|
||||
</ol>
|
||||
<p>Consequently : <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>M</mi><mi>A</mi><mi>T</mi><mi>C</mi><mi>H</mi><mo stretchy="false" form="prefix">|</mo><msub><mi>X</mi><mn>1</mn></msub><mo>≠</mo><msub><mi>X</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mn>3</mn></mfrac><mo>+</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mn>3</mn></mfrac><mo>+</mo><mn>2</mn><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>9</mn></mfrac></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P(MATCH | X_1 \neq X_2) = (1-P_{E1})\frac{P_{E2}}{3} + (1-P_{E2})\frac{P_{E1}}{3} + 2\frac{P_{E1} P_{E2}}{9}
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p><strong>Probability of a match under the random model</strong></p>
|
||||
<p>The second considered model is a pure random model where every base is equiprobable, hence having a probability of occurrence of a nucleotide equals <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mn>0.25</mn><annotation encoding="application/x-tex">0.25</annotation></semantics></math>. Under that hypothesis</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>M</mi><mi>A</mi><mi>T</mi><mi>C</mi><mi>H</mi><mo stretchy="false" form="prefix">|</mo><mtext mathvariant="normal">Random model</mtext><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>0.25</mn></mrow><annotation encoding="application/x-tex">
|
||||
P(MATCH | \text{Random model}) = 0.25
|
||||
</annotation></semantics></math></p>
|
||||
<p><strong>The score is a log ration of likelyhood</strong></p>
|
||||
<p>Score is define as the logarithm of the ratio between the likelyhood of the observations considering the sequencer error model over tha likelyhood u</p>
|
||||
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|
||||
<div class="cell-output-display">
|
||||
<div class="quarto-figure quarto-figure-center">
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|
||||
<p><img src="comm_computation_files/figure-html/unnamed-chunk-1-1.png" class="img-fluid figure-img" width="672"></p>
|
||||
<p></p><figcaption class="figure-caption">Evolution of the match and mismatch scores when the quality of base is 20 while the second range from 10 to 40.</figcaption><p></p>
|
||||
</figure>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</section>
|
||||
</section>
|
||||
<section id="obimultiplex" class="level2" data-number="11.2">
|
||||
<h2 data-number="11.2" class="anchored" data-anchor-id="obimultiplex"><span class="header-section-number">11.2</span> <code>obimultiplex</code></h2>
|
||||
<blockquote class="blockquote">
|
||||
<p>Replace the <code>ngsfilter</code> original <em>OBITools</em></p>
|
||||
</blockquote>
|
||||
</section>
|
||||
<section id="obicomplement" class="level2" data-number="11.3">
|
||||
<h2 data-number="11.3" class="anchored" data-anchor-id="obicomplement"><span class="header-section-number">11.3</span> <code>obicomplement</code></h2>
|
||||
</section>
|
||||
<section id="obiclean" class="level2" data-number="11.4">
|
||||
<h2 data-number="11.4" class="anchored" data-anchor-id="obiclean"><span class="header-section-number">11.4</span> <code>obiclean</code></h2>
|
||||
</section>
|
||||
<section id="obiuniq" class="level2" data-number="11.5">
|
||||
<h2 data-number="11.5" class="anchored" data-anchor-id="obiuniq"><span class="header-section-number">11.5</span> <code>obiuniq</code></h2>
|
||||
|
||||
|
||||
<div id="refs" class="references csl-bib-body hanging-indent" role="doc-bibliography" style="display: none">
|
||||
<div id="ref-Lipman1985-hw" class="csl-entry" role="doc-biblioentry">
|
||||
Lipman, D J, and W R Pearson. 1985. <span>“<span class="nocase">Rapid and sensitive protein similarity searches</span>.”</span> <em>Science</em> 227 (4693): 1435–41. <a href="http://www.ncbi.nlm.nih.gov/pubmed/2983426">http://www.ncbi.nlm.nih.gov/pubmed/2983426</a>.
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67ad5e762743fa43802a59dffd91edfba9a6b132
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doc/build/_book/comm_metabarcode_design.html
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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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<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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<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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<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>
|
||||
<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>
|
||||
<p><strong>Selection based on the sequence</strong></p>
|
||||
<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>
|
||||
<dl>
|
||||
<dt><strong>--sequence</strong>|<strong>-s</strong> <em>PATTERN</em></dt>
|
||||
<dd>
|
||||
<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>
|
||||
</dd>
|
||||
<dt><em>Examples:</em></dt>
|
||||
<dd>
|
||||
<p>Selects only the sequence records that contain an <em>EcoRI</em> restriction site.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
<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>
|
||||
<p>: Selects only the sequence records that contain a stretch of at least 10 <code>A</code>.</p>
|
||||
<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 <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mn>1</mn><annotation encoding="application/x-tex">1</annotation></semantics></math>.</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 <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mn>1</mn><annotation encoding="application/x-tex">1</annotation></semantics></math>.</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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<li><a href="#obicount" id="toc-obicount" class="nav-link active" data-scroll-target="#obicount"><span class="toc-section-number">13.1</span> <code>obicount</code></a></li>
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<h2 data-number="13.1" class="anchored" data-anchor-id="obicount"><span class="header-section-number">13.1</span> <code>obicount</code></h2>
|
||||
<p><code>obicount</code> counts the number of sequence records, the sum of the <code>count</code> attributes, and the sum of the length of all the sequences.</p>
|
||||
<p><em>Example:</em></p>
|
||||
<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">obicount</span> seq.fasta </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>Prints the number of sequence records contained in the <code>seq.fasta</code> file and the sum of their <code>count</code> attributes.</p>
|
||||
<p><em>Options specific to the command</em></p>
|
||||
<ul>
|
||||
<li><code>--reads|-r</code> Prints read counts.</li>
|
||||
<li><code>--symbols|-s</code> Prints symbol counts.</li>
|
||||
<li><code>--variants|-v</code> Prints variant counts.</li>
|
||||
</ul>
|
||||
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|
||||
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|
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|
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<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
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<ul>
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<li><a href="#helpful-options" id="toc-helpful-options" class="nav-link active" data-scroll-target="#helpful-options"><span class="toc-section-number">6.1</span> Helpful options</a></li>
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<li><a href="#system-related-options" id="toc-system-related-options" class="nav-link" data-scroll-target="#system-related-options"><span class="toc-section-number">6.2</span> System related options</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></h1>
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<h2 data-number="6.1" class="anchored" data-anchor-id="helpful-options"><span class="header-section-number">6.1</span> Helpful options</h2>
|
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<dl>
|
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<dt><strong>--help</strong>, <strong>-h</strong></dt>
|
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<dd>
|
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<p>Display a friendly help message.</p>
|
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</dd>
|
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<p><strong>--no-progressbar</strong></p>
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<section id="system-related-options" class="level2" data-number="6.2">
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<h2 data-number="6.2" class="anchored" data-anchor-id="system-related-options"><span class="header-section-number">6.2</span> System related options</h2>
|
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<p><strong>Managing parallel execution of tasks</strong></p>
|
||||
<p>A new feature of <em>OBITools</em> V4 is the ability to run multiple tasks in parallel, reading files, calculating on the data, formatting and writing the results. Each of these tasks can itself be parallelized by dividing the data into batches and running the calculation on several batches in parallel. This allows the overall calculation time of an <em>OBITools</em> command to be reduced considerably. The parameters organizing the parallel calculation are determined automatically to use the maximum capacity of your computer. But in some circumstances, it is necessary to override these default settings either to try to optimize the computation on a given machine, or to limit the OBITools to using only a part of the computational capacity. There are two options for doing this.</p>
|
||||
<dl>
|
||||
<dt><strong>--max-cpu</strong></dt>
|
||||
<dd>
|
||||
<p>OBITools V4 are able to run in parallel on all the CPU cores available on the computer. It is sometime required to limit the computation to a smaller number of cores. That option specify the maximum number of cores that the OBITools command can use. This behaviour can also be set up using the <code>OBIMAXCPU</code> environment variable.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
<p><strong>--workers</strong>, <strong>-w</strong></p>
|
||||
<p>If your computer has 8 cores, but you want to limit <em>OBITools</em> to use only two of them you have several solution:</p>
|
||||
<ul>
|
||||
<li><p>If you want to set the limit for a single execution you can use the <strong>–max-cpu</strong> option</p>
|
||||
<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">obiconvert</span> <span class="at">--max-cpu</span> 2 <span class="at">--fasta-output</span> data.fastq <span class="op">></span> data.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>or you can precede the command by setting the environment variable <code>OBIMAXCPU</code></p>
|
||||
<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="va">OBIMAXCPU</span><span class="op">=</span>2 <span class="ex">obiconvert</span> <span class="at">--fasta-output</span> data.fastq <span class="op">></span> data.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div></li>
|
||||
<li><p>If you want to set the limit to your complete session, you have to export <code>OBIMAXCPU</code></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="bu">export</span> <span class="va">OBIMAXCPU</span><span class="op">=</span>2 </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>all the following OBITools commands will be limited to use at max 2 CPU cores.</p></li>
|
||||
<li><p>If all the time you want to impose this limit, you must include the above <code>export</code> command in your <code>.bashrc</code> file.</p></li>
|
||||
</ul>
|
||||
<p><strong>OBITools debuging related options</strong></p>
|
||||
<p><strong>--debug</strong></p>
|
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|
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<li><a href="#variables-usable-in-the-expression" id="toc-variables-usable-in-the-expression" class="nav-link active" data-scroll-target="#variables-usable-in-the-expression"><span class="toc-section-number">7.1</span> Variables usable in the expression</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></h1>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<div class="quarto-title-meta">
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<p>Several OBITools (<em>e.g.</em> obigrep, obiannotate) allow the user to specify some simple expressions to compute values or define predicates. This expressions are parsed and evaluated using the <a href="https://pkg.go.dev/github.com/PaesslerAG/gval" title="Gval (Go eVALuate) for evaluating arbitrary expressions Go-like expressions.">gval</a> go package, which allows for evaluating go-Like expression.</p>
|
||||
<section id="variables-usable-in-the-expression" class="level2" data-number="7.1">
|
||||
<h2 data-number="7.1" class="anchored" data-anchor-id="variables-usable-in-the-expression"><span class="header-section-number">7.1</span> Variables usable in the expression</h2>
|
||||
<ul>
|
||||
<li><code>sequence</code> is the sequence object on which the expression is evaluated.</li>
|
||||
<li><code>annotations</code>is a map object containing every annotations associated to the currently processed sequence.</li>
|
||||
</ul>
|
||||
</section>
|
||||
<section id="function-defined-in-the-language" class="level2" data-number="7.2">
|
||||
<h2 data-number="7.2" class="anchored" data-anchor-id="function-defined-in-the-language"><span class="header-section-number">7.2</span> Function defined in the language</h2>
|
||||
<section id="instrospection-functions" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="instrospection-functions">Instrospection functions</h3>
|
||||
<dl>
|
||||
<dt><strong><code>len(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>It is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like <code>annotations</code>, the number of elements in an array. The reurned value is an <code>int</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>contains(map,key)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Tests if the <code>map</code> contains a value assciated to <code>key</code></p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="cast-functions" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="cast-functions">Cast functions</h3>
|
||||
<dl>
|
||||
<dt><strong><code>int(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Converts if possible the <code>x</code> value to an integer value. The function returns an <code>int</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>numeric(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Converts if possible the <code>x</code> value to a float value. The function returns a <code>float</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>bool(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Converts if possible the <code>x</code> value to a boolean value. The function returns a <code>bool</code>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="string-related-functions" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="string-related-functions">String related functions</h3>
|
||||
<dl>
|
||||
<dt><strong><code>printf(format,...)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Allows to combine several values to build a string. <code>format</code> follows the classical C <code>printf</code> syntax. The function returns a <code>string</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>subspc(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>substitutes every space in the <code>x</code> string by the underscore (<code>_</code>) character. The function returns a <code>string</code>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="condition-function" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="condition-function">Condition function</h3>
|
||||
<dl>
|
||||
<dt><strong><code>ifelse(condition,val1,val2)</code></strong></dt>
|
||||
<dd>
|
||||
<p>The <code>condition</code> value has to be a <code>bool</code> value. If it is <code>true</code> the function returns <code>val1</code>, otherwise, it is returning <code>val2</code>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="sequence-analysis-related-function" class="level3" data-number="7.2.1">
|
||||
<h3 data-number="7.2.1" class="anchored" data-anchor-id="sequence-analysis-related-function"><span class="header-section-number">7.2.1</span> Sequence analysis related function</h3>
|
||||
<dl>
|
||||
<dt><strong><code>composition(sequence)</code></strong></dt>
|
||||
<dd>
|
||||
<p>The nucleotide composition of the sequence is returned as as map indexed by <code>a</code>, <code>c</code>, <code>g</code>, or <code>t</code> and each value is the number of occurrences of that nucleotide. A fifth key <code>others</code> accounts for all others symboles.</p>
|
||||
</dd>
|
||||
<dt><strong><code>gcskew(sequence)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Computes the excess of g compare to c of the sequence, known as the GC skew.</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>S</mi><mi>k</mi><mi>e</mi><msub><mi>w</mi><mrow><mi>G</mi><mi>C</mi></mrow></msub><mo>=</mo><mfrac><mrow><mi>G</mi><mo>−</mo><mi>C</mi></mrow><mrow><mi>G</mi><mo>+</mo><mi>C</mi></mrow></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
Skew_{GC}=\frac{G-C}{G+C}
|
||||
</annotation></semantics></math></p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
</section>
|
||||
<section id="accessing-to-the-sequence-annotations" class="level2" data-number="7.3">
|
||||
<h2 data-number="7.3" class="anchored" data-anchor-id="accessing-to-the-sequence-annotations"><span class="header-section-number">7.3</span> Accessing to the sequence annotations</h2>
|
||||
<p>The <code>annotations</code> variable is a map object containing all the annotations associated to the currently processed sequence. Index of the map are the attribute names. It exists to possibillities to retreive an annotation. It is possible to use the classical <code>[]</code> indexing operator, putting the attribute name quoted by double quotes between them.</p>
|
||||
<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>annotations<span class="op">[</span><span class="st">"direction"</span><span class="op">]</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>The above code retreives the <code>direction</code> annotation. A second notation using the dot (<code>.</code>) is often more convenient.</p>
|
||||
<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>annotations<span class="op">.</span>direction</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>Special attributes of the sequence are accessible only by dedicated methods of the <code>sequence</code> object.</p>
|
||||
<ul>
|
||||
<li>The sequence identifier : <code>Id()</code></li>
|
||||
<li>THe sequence definition : <code>Definition()</code></li>
|
||||
</ul>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>sequence<span class="op">.</span>Id<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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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></span>
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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">BioSequence</a>
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<ul class="collapse">
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<li><a href="#creating-new-instances" id="toc-creating-new-instances" class="nav-link" data-scroll-target="#creating-new-instances">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">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">Accessing to the elements of a sequence</a></li>
|
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<li><a href="#the-annotations-of-a-sequence" id="toc-the-annotations-of-a-sequence" class="nav-link" data-scroll-target="#the-annotations-of-a-sequence">The annotations of a sequence</a></li>
|
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</ul></li>
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<li><a href="#the-sequence-iterator" id="toc-the-sequence-iterator" class="nav-link" data-scroll-target="#the-sequence-iterator">The sequence iterator</a>
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<li><a href="#basic-usage-of-a-sequence-iterator" id="toc-basic-usage-of-a-sequence-iterator" class="nav-link" data-scroll-target="#basic-usage-of-a-sequence-iterator">Basic usage of a sequence iterator</a></li>
|
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<li><a href="#the-pipable-functions" id="toc-the-pipable-functions" class="nav-link" data-scroll-target="#the-pipable-functions">The <code>Pipable</code> functions</a></li>
|
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<li><a href="#the-teeable-functions" id="toc-the-teeable-functions" class="nav-link" data-scroll-target="#the-teeable-functions">The <code>Teeable</code> functions</a></li>
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<h1 class="title d-none d-lg-block">The GO <em>OBITools</em> library</h1>
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||||
<section id="biosequence" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="biosequence">BioSequence</h2>
|
||||
<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>
|
||||
<p>BioSequence is defined in the obiseq module and is included using the code</p>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<section id="creating-new-instances" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="creating-new-instances">Creating new instances</h3>
|
||||
<p>To create new instance, use</p>
|
||||
<ul>
|
||||
<li><code>MakeBioSequence(id string, sequence []byte, definition string) obiseq.BioSequence</code></li>
|
||||
<li><code>NewBioSequence(id string, sequence []byte, definition string) *obiseq.BioSequence</code></li>
|
||||
</ul>
|
||||
<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>
|
||||
<ul>
|
||||
<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>
|
||||
<li><code>sequence</code> is the DNA sequence itself, provided as a <code>byte</code> array (<code>[]byte</code>).</li>
|
||||
<li><code>definition</code> is a <code>string</code>, potentially empty, but usualy containing a sentence explaining what is that sequence.</li>
|
||||
</ul>
|
||||
<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>
|
||||
<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>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
|
||||
<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>
|
||||
<p>When formated as fasta the parameters correspond to the following schema</p>
|
||||
<pre><code>>id definition containing potentially several words
|
||||
sequence</code></pre>
|
||||
</section>
|
||||
<section id="end-of-life-of-a-biosequence-instance" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="end-of-life-of-a-biosequence-instance">End of life of a <code>BioSequence</code> instance</h3>
|
||||
<p>When an instance of <code>BioSequence</code> is no longer in use, it is normally taken over by the GO garbage collector. If you know that an instance will never be used again, you can, if you wish, call the <code>Recycle</code> method on it to store the allocated memory elements in a <code>pool</code> to limit the allocation effort when many sequences are being handled. Once the recycle method has been called on an instance, you must ensure that no other method is called on it.</p>
|
||||
</section>
|
||||
<section id="accessing-to-the-elements-of-a-sequence" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="accessing-to-the-elements-of-a-sequence">Accessing to the elements of a sequence</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="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>
|
||||
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||||
<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>
|
||||
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<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>
|
||||
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
|
||||
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<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">
|
||||
<h4 class="anchored" data-anchor-id="different-ways-for-accessing-an-editing-the-sequence">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">
|
||||
<h4 class="anchored" data-anchor-id="sequence-quality-scores">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>
|
||||
</section>
|
||||
<section id="the-annotations-of-a-sequence" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="the-annotations-of-a-sequence">The annotations of a sequence</h3>
|
||||
<p>A sequence can be annotated with attributes. Each attribute is associated with a value. An attribute is identified by its name. The name of an attribute consists of a character string containing no spaces or blank characters. Values can be of several types.</p>
|
||||
<ul>
|
||||
<li>Scalar types:
|
||||
<ul>
|
||||
<li>integer</li>
|
||||
<li>numeric</li>
|
||||
<li>character</li>
|
||||
<li>boolean</li>
|
||||
</ul></li>
|
||||
<li>Container types:
|
||||
<ul>
|
||||
<li>vector</li>
|
||||
<li>map</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
<p>Vectors can contain any type of scalar. Maps are compulsorily indexed by strings and can contain any scalar type. It is not possible to have nested container type.</p>
|
||||
<p>Annotations are stored in an object of type <code>bioseq.Annotation</code> which is an alias of <code>map[string]interface{}</code>. This map can be retrieved using the <code>Annotations() Annotation</code> method. If no annotation has been defined for this sequence, the method returns an empty map. It is possible to test an instance of <code>BioSequence</code> using its <code>HasAnnotation() bool</code> method to see if it has any annotations associated with it.</p>
|
||||
<ul>
|
||||
<li>GetAttribute(key string) (interface{}, bool)</li>
|
||||
</ul>
|
||||
</section>
|
||||
</section>
|
||||
<section id="the-sequence-iterator" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="the-sequence-iterator">The sequence iterator</h2>
|
||||
<p>The pakage <em>obiter</em> provides an iterator mecanism for manipulating sequences. The main class provided by this package is <code>obiiter.IBioSequence</code>. An <code>IBioSequence</code> iterator provides batch of sequences.</p>
|
||||
<section id="basic-usage-of-a-sequence-iterator" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="basic-usage-of-a-sequence-iterator">Basic usage of a sequence iterator</h3>
|
||||
<p>Many functions, among them functions reading sequences from a text file, return a <code>IBioSequence</code> iterator. The iterator class provides two main methods:</p>
|
||||
<ul>
|
||||
<li><code>Next() bool</code></li>
|
||||
<li><code>Get() obiiter.BioSequenceBatch</code></li>
|
||||
</ul>
|
||||
<p>The <code>Next</code> method moves the iterator to the next value, while the <code>Get</code> method returns the currently pointed value. Using them, it is possible to loop over the data as in the following code chunk.</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"</span></span>
|
||||
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> mydata <span class="op">:=</span> obiformats<span class="op">.</span>ReadFastSeqFromFile<span class="op">(</span><span class="st">"myfile.fasta"</span><span class="op">)</span></span>
|
||||
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a> </span>
|
||||
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a> <span class="cf">for</span> mydata<span class="op">.</span>Next<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> data <span class="op">:=</span> mydata<span class="op">.</span>Get<span class="op">()</span></span>
|
||||
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a> <span class="co">//</span></span>
|
||||
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a> <span class="co">// Whatever you want to do with the data chunk</span></span>
|
||||
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a> <span class="co">//</span></span>
|
||||
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a> <span class="op">}</span></span>
|
||||
<span id="cb6-14"><a href="#cb6-14" 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>
|
||||
<p>An <code>obiseq.BioSequenceBatch</code> instance is a set of sequences stored in an <code>obiseq.BioSequenceSlice</code> and a sequence number. The number of sequences in a batch is not defined. A batch can even contain zero sequences, if for example all sequences initially included in the batch have been filtered out at some stage of their processing.</p>
|
||||
</section>
|
||||
<section id="the-pipable-functions" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="the-pipable-functions">The <code>Pipable</code> functions</h3>
|
||||
<p>A function consuming a <code>obiiter.IBioSequence</code> and returning a <code>obiiter.IBioSequence</code> is of class <code>obiiter.Pipable</code>.</p>
|
||||
</section>
|
||||
<section id="the-teeable-functions" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="the-teeable-functions">The <code>Teeable</code> functions</h3>
|
||||
<p>A function consuming a <code>obiiter.IBioSequence</code> and returning two <code>obiiter.IBioSequence</code> instance is of class <code>obiiter.Teeable</code>.</p>
|
||||
|
||||
|
||||
</section>
|
||||
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<h2 data-number="5.1" class="anchored" data-anchor-id="specifying-output-format"><span class="header-section-number">5.1</span> Specifying output format</h2>
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<p>Only two output sequence formats are supported by OBITools, Fasta and Fastq. Fastq is used when output sequences are associated with quality information. Otherwise, Fasta is the default format. However, it is possible to force the output format by using one of the following two options. Forcing the use of Fasta results in the loss of quality information. Conversely, when the Fastq format is forced with sequences that have no quality data, dummy qualities set to 40 for each nucleotide are added.</p>
|
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|
||||
<li><code>--fasta-output</code> Read data following the ecoPCR output format.</li>
|
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<li><code>--fastq-output</code> Read data following the EMBL flatfile format.</li>
|
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<li><code>--no-order</code> When several input files are provided, indicates that there is no order among them. (default: false). Using such option can increase a lot the processing of the data.</li>
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|
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<p>OBITools extend the <a href="#the-fasta-sequence-format">Fasta</a> and <a href="#the-fastq-sequence-format">Fastq</a> formats by introducing a format for the title lines of these formats allowing to annotate every sequence. While the previous version of OBITools used an <em>ad-hoc</em> format for these annotation, this new version introduce the usage of the standard JSON format to store them.</p>
|
||||
<p>On input, OBITools automatically recognize the format of the annotations, but two options allows to force the parsing following one of them. You should normally not need to use these options.</p>
|
||||
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|
||||
<li><p><code>--input-OBI-header</code> FASTA/FASTQ title line annotations follow OBI format. (default: false)</p></li>
|
||||
<li><p><code>--input-json-header</code> FASTA/FASTQ title line annotations follow json format. (default: false)</p></li>
|
||||
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|
||||
<p>On output, by default annotation are formatted using the new JSON format. For compatibility with previous version of OBITools and with external scripts and software, it is possible to force the usage of the previous OBITools format.</p>
|
||||
<ul>
|
||||
<li><p><code>--output-OBI-header|-O</code> output FASTA/FASTQ title line annotations follow OBI format. (default: false)</p></li>
|
||||
<li><p><code>--output-json-header</code> output FASTA/FASTQ title line annotations follow json format. (default: false)</p></li>
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<div id="ref-Andersen2012-gj" class="csl-entry" role="doc-biblioentry">
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Andersen, Kenneth, Karen Lise Bird, Morten Rasmussen, James Haile,
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Henrik Breuning-Madsen, Kurt H Kjaer, Ludovic Orlando, M Thomas P
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Gilbert, and Eske Willerslev. 2012. <span>“<span class="nocase">Meta-barcoding of <span class="nocase">ë</span>dirt<span class="nocase">ı́</span>DNA from soil reflects vertebrate
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Baldwin, Darren S, Matthew J Colloff, Gavin N Rees, Anthony A Chariton,
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Garth O Watson, Leon N Court, Diana M Hartley, et al. 2013. <span>“<span class="nocase">Impacts of inundation and drought on eukaryote
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biodiversity in semi-arid floodplain soils</span>.”</span> <em>Molecular
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Ecology</em> 22 (6): 1746–58. <a href="https://doi.org/10.1111/mec.12190">https://doi.org/10.1111/mec.12190</a>.
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Boyer, Frédéric, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre
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Taberlet, and Eric Coissac. 2016. <span>“<span class="nocase">obitools:
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<em>Molecular Ecology Resources</em> 16 (1): 176–82. <a href="https://doi.org/10.1111/1755-0998.12428">https://doi.org/10.1111/1755-0998.12428</a>.
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Caporaso, J Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger,
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Frederic D Bushman, Elizabeth K Costello, Noah Fierer, et al. 2010.
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<span>“<span class="nocase">QIIME allows analysis of high-throughput
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Cock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and
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Peter M Rice. 2010. <span>“The Sanger FASTQ File Format for Sequences
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<em>Forest Ecology and Management</em> 261 (4): 821–28. <a href="https://doi.org/10.1016/j.foreco.2010.11.026">https://doi.org/10.1016/j.foreco.2010.11.026</a>.
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