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<h1 class="quarto-secondary-nav-title"><span class="chapter-number">5</span> <span class="chapter-title">Annexes</span></h1>
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<a href="./index.html" class="sidebar-item-text sidebar-link">Preface</a>
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<a href="./intro.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></a>
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<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></a>
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<a href="./library.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
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<a href="./annexes.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">5</span> <span class="chapter-title">Annexes</span></a>
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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">5.0.1</span> Sequence attributes</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">5</span> <span class="chapter-title">Annexes</span></h1>
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<section id="sequence-attributes" class="level3" data-number="5.0.1">
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<h3 data-number="5.0.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">5.0.1</span> Sequence attributes</h3>
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<section id="reserved-sequence-attributes" class="level4" data-number="5.0.1.1">
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<h4 data-number="5.0.1.1" class="anchored" data-anchor-id="reserved-sequence-attributes"><span class="header-section-number">5.0.1.1</span> Reserved sequence attributes</h4>
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<section id="ali_dir" class="level5" data-number="5.0.1.1.1">
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<h5 data-number="5.0.1.1.1" class="anchored" data-anchor-id="ali_dir"><span class="header-section-number">5.0.1.1.1</span> <code>ali_dir</code></h5>
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<section id="type-string" class="level6" data-number="5.0.1.1.1.1">
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<h6 data-number="5.0.1.1.1.1" class="anchored" data-anchor-id="type-string"><span class="header-section-number">5.0.1.1.1.1</span> Type : <code>string</code></h6>
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<p>The attribute can contain 2 string values <code>"left"</code> or <code>"right".</code></p>
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</section>
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<section id="set-by-the-obipairing-tool" class="level6" data-number="5.0.1.1.1.2">
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<h6 data-number="5.0.1.1.1.2" class="anchored" data-anchor-id="set-by-the-obipairing-tool"><span class="header-section-number">5.0.1.1.1.2</span> Set by the <em>obipairing</em> tool</h6>
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<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>
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</section>
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</section>
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<section id="ali_length" class="level5" data-number="5.0.1.1.2">
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<h5 data-number="5.0.1.1.2" class="anchored" data-anchor-id="ali_length"><span class="header-section-number">5.0.1.1.2</span> <code>ali_length</code></h5>
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<section id="set-by-the-obipairing-tool-1" class="level6" data-number="5.0.1.1.2.1">
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<h6 data-number="5.0.1.1.2.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-1"><span class="header-section-number">5.0.1.1.2.1</span> Set by the <em>obipairing</em> tool</h6>
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<p>Length of the aligned parts when merging forward and reverse reads</p>
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</section>
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</section>
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<section id="count-the-number-of-sequence-occurrences" class="level5" data-number="5.0.1.1.3">
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<h5 data-number="5.0.1.1.3" class="anchored" data-anchor-id="count-the-number-of-sequence-occurrences"><span class="header-section-number">5.0.1.1.3</span> <code>count</code> : the number of sequence occurrences</h5>
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<section id="set-by-the-obiuniq-tool" class="level6" data-number="5.0.1.1.3.1">
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<h6 data-number="5.0.1.1.3.1" class="anchored" data-anchor-id="set-by-the-obiuniq-tool"><span class="header-section-number">5.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool</h6>
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<p>The <code>count</code> attribute indicates how-many strictly identical sequences 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>
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</section>
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<section id="getter-method-count" class="level6" data-number="5.0.1.1.3.2">
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<h6 data-number="5.0.1.1.3.2" class="anchored" data-anchor-id="getter-method-count"><span class="header-section-number">5.0.1.1.3.2</span> Getter : method <code>Count()</code></h6>
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<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>
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</section>
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</section>
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<section id="merged_" class="level5" data-number="5.0.1.1.4">
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<h5 data-number="5.0.1.1.4" class="anchored" data-anchor-id="merged_"><span class="header-section-number">5.0.1.1.4</span> <code>merged_*</code></h5>
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<section id="type-mapstringint" class="level6" data-number="5.0.1.1.4.1">
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<h6 data-number="5.0.1.1.4.1" class="anchored" data-anchor-id="type-mapstringint"><span class="header-section-number">5.0.1.1.4.1</span> Type : <code>map[string]int</code></h6>
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</section>
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<section id="set-by-the-obiuniq-tool-1" class="level6" data-number="5.0.1.1.4.2">
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<h6 data-number="5.0.1.1.4.2" class="anchored" data-anchor-id="set-by-the-obiuniq-tool-1"><span class="header-section-number">5.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool</h6>
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<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>
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</section>
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</section>
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<section id="mode" class="level5" data-number="5.0.1.1.5">
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<h5 data-number="5.0.1.1.5" class="anchored" data-anchor-id="mode"><span class="header-section-number">5.0.1.1.5</span> <code>mode</code></h5>
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<section id="set-by-the-obipairing-tool-2" class="level6" data-number="5.0.1.1.5.1">
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<h6 data-number="5.0.1.1.5.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-2"><span class="header-section-number">5.0.1.1.5.1</span> Set by the <em>obipairing</em> tool</h6>
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<p><strong><code>obitag_ref_index</code></strong></p>
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</section>
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<section id="set-by-the-obirefidx-tool." class="level6" data-number="5.0.1.1.5.2">
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<h6 data-number="5.0.1.1.5.2" class="anchored" data-anchor-id="set-by-the-obirefidx-tool."><span class="header-section-number">5.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.</h6>
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<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>
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</section>
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<section id="getter-method-count-1" class="level6" data-number="5.0.1.1.5.3">
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<h6 data-number="5.0.1.1.5.3" class="anchored" data-anchor-id="getter-method-count-1"><span class="header-section-number">5.0.1.1.5.3</span> Getter : method <code>Count()</code></h6>
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</section>
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</section>
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<section id="pairing_mismatches" class="level5" data-number="5.0.1.1.6">
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<h5 data-number="5.0.1.1.6" class="anchored" data-anchor-id="pairing_mismatches"><span class="header-section-number">5.0.1.1.6</span> <code>pairing_mismatches</code></h5>
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<section id="set-by-the-obipairing-tool-3" class="level6" data-number="5.0.1.1.6.1">
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<h6 data-number="5.0.1.1.6.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-3"><span class="header-section-number">5.0.1.1.6.1</span> Set by the <em>obipairing</em> tool</h6>
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</section>
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</section>
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<section id="score" class="level5" data-number="5.0.1.1.7">
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<h5 data-number="5.0.1.1.7" class="anchored" data-anchor-id="score"><span class="header-section-number">5.0.1.1.7</span> <code>score</code></h5>
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<section id="set-by-the-obipairing-tool-4" class="level6" data-number="5.0.1.1.7.1">
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<h6 data-number="5.0.1.1.7.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-4"><span class="header-section-number">5.0.1.1.7.1</span> Set by the <em>obipairing</em> tool</h6>
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</section>
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</section>
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<section id="score_norm" class="level5" data-number="5.0.1.1.8">
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<h5 data-number="5.0.1.1.8" class="anchored" data-anchor-id="score_norm"><span class="header-section-number">5.0.1.1.8</span> <code>score_norm</code></h5>
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<section id="set-by-the-obipairing-tool-5" class="level6" data-number="5.0.1.1.8.1">
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||||||
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<h6 data-number="5.0.1.1.8.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-5"><span class="header-section-number">5.0.1.1.8.1</span> Set by the <em>obipairing</em> tool</h6>
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</section>
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<h1 class="quarto-secondary-nav-title"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></h1>
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|
||||||
|
<ul>
|
||||||
|
<li><a href="#specifying-the-input-files-to-obitools-commands" id="toc-specifying-the-input-files-to-obitools-commands" class="nav-link active" data-scroll-target="#specifying-the-input-files-to-obitools-commands"><span class="toc-section-number">3.1</span> Specifying the input files to <em>OBITools</em> commands</a></li>
|
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|
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|
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<li><a href="#specifying-input-format" id="toc-specifying-input-format" class="nav-link" data-scroll-target="#specifying-input-format"><span class="toc-section-number">3.2.1</span> Specifying input format</a></li>
|
||||||
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<li><a href="#specifying-output-format" id="toc-specifying-output-format" class="nav-link" data-scroll-target="#specifying-output-format"><span class="toc-section-number">3.2.2</span> Specifying output format</a></li>
|
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|
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|
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<li><a href="#obitools-expression-language" id="toc-obitools-expression-language" class="nav-link" data-scroll-target="#obitools-expression-language"><span class="toc-section-number">3.3</span> OBITools expression language</a>
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<li><a href="#variables-usable-in-the-expression" id="toc-variables-usable-in-the-expression" class="nav-link" data-scroll-target="#variables-usable-in-the-expression"><span class="toc-section-number">3.3.1</span> Variables usable in the expression</a></li>
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<li><a href="#function-defined-in-the-language" id="toc-function-defined-in-the-language" class="nav-link" data-scroll-target="#function-defined-in-the-language"><span class="toc-section-number">3.3.2</span> Function defined in the language</a></li>
|
||||||
|
<li><a href="#accessing-to-the-sequence-annotations" id="toc-accessing-to-the-sequence-annotations" class="nav-link" data-scroll-target="#accessing-to-the-sequence-annotations"><span class="toc-section-number">3.3.3</span> Accessing to the sequence annotations</a></li>
|
||||||
|
</ul></li>
|
||||||
|
<li><a href="#metabarcode-design-and-quality-assessment" id="toc-metabarcode-design-and-quality-assessment" class="nav-link" data-scroll-target="#metabarcode-design-and-quality-assessment"><span class="toc-section-number">3.4</span> Metabarcode design and quality assessment</a></li>
|
||||||
|
<li><a href="#file-format-conversions" id="toc-file-format-conversions" class="nav-link" data-scroll-target="#file-format-conversions"><span class="toc-section-number">3.5</span> File format conversions</a></li>
|
||||||
|
<li><a href="#sequence-annotations" id="toc-sequence-annotations" class="nav-link" data-scroll-target="#sequence-annotations"><span class="toc-section-number">3.6</span> Sequence annotations</a></li>
|
||||||
|
<li><a href="#computations-on-sequences" id="toc-computations-on-sequences" class="nav-link" data-scroll-target="#computations-on-sequences"><span class="toc-section-number">3.7</span> Computations on sequences</a>
|
||||||
|
<ul class="collapse">
|
||||||
|
<li><a href="#obipairing" id="toc-obipairing" class="nav-link" data-scroll-target="#obipairing"><span class="toc-section-number">3.7.1</span> <code>obipairing</code></a></li>
|
||||||
|
</ul></li>
|
||||||
|
<li><a href="#sequence-sampling-and-filtering" id="toc-sequence-sampling-and-filtering" class="nav-link" data-scroll-target="#sequence-sampling-and-filtering"><span class="toc-section-number">3.8</span> Sequence sampling and filtering</a>
|
||||||
|
<ul class="collapse">
|
||||||
|
<li><a href="#utilities" id="toc-utilities" class="nav-link" data-scroll-target="#utilities"><span class="toc-section-number">3.8.1</span> Utilities</a></li>
|
||||||
|
</ul></li>
|
||||||
|
</ul>
|
||||||
|
</nav>
|
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<!-- main -->
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<main class="content" id="quarto-document-content">
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<header id="title-block-header" class="quarto-title-block default">
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||||||
|
<div class="quarto-title">
|
||||||
|
<h1 class="title d-none d-lg-block"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></h1>
|
||||||
|
</div>
|
||||||
|
|
||||||
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|
||||||
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|
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<div class="quarto-title-meta">
|
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</div>
|
||||||
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|
||||||
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|
||||||
|
</header>
|
||||||
|
|
||||||
|
<section id="specifying-the-input-files-to-obitools-commands" class="level2" data-number="3.1">
|
||||||
|
<h2 data-number="3.1" class="anchored" data-anchor-id="specifying-the-input-files-to-obitools-commands"><span class="header-section-number">3.1</span> Specifying the input files to <em>OBITools</em> commands</h2>
|
||||||
|
</section>
|
||||||
|
<section id="options-common-to-most-of-the-obitools-commands" class="level2" data-number="3.2">
|
||||||
|
<h2 data-number="3.2" class="anchored" data-anchor-id="options-common-to-most-of-the-obitools-commands"><span class="header-section-number">3.2</span> Options common to most of the <em>OBITools</em> commands</h2>
|
||||||
|
<section id="specifying-input-format" class="level3" data-number="3.2.1">
|
||||||
|
<h3 data-number="3.2.1" class="anchored" data-anchor-id="specifying-input-format"><span class="header-section-number">3.2.1</span> Specifying input format</h3>
|
||||||
|
<p>Five sequence formats are accepted for input files. <a href="#fasta-classical" title="Fasta format description">Fasta</a> and <a href="#fastq-classical" title="Fastq format description">Fastq</a> are the main ones, EMBL and Genbank allow the use of flat files produced by these two international databases. The last one, ecoPCR, is maintained for compatibility with previous <em>OBITools</em> and allows to read <em>ecoPCR</em> outputs as sequence files.</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>--ecopcr</code> : Read data following the <em>ecoPCR</em> output format.</li>
|
||||||
|
<li><code>--embl</code> Read data following the <em>EMBL</em> flatfile format.</li>
|
||||||
|
<li><code>--genbank</code> Read data following the <em>Genbank</em> flatfile format.</li>
|
||||||
|
</ul>
|
||||||
|
<p>Several encoding schemes have been proposed for quality scores in <a href="#fastq-classical" title="Fastq format description">Fastq</a> format. Currently, <em>OBITools</em> considers Sanger encoding as the standard. For reasons of compatibility with older datasets produced with <em>Solexa</em> sequencers, it is possible, by using the following option, to force the use of the corresponding quality encoding scheme when reading these older files.</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>--solexa</code> Decodes quality string according to the Solexa specification. (default: false)</li>
|
||||||
|
</ul>
|
||||||
|
</section>
|
||||||
|
<section id="specifying-output-format" class="level3" data-number="3.2.2">
|
||||||
|
<h3 data-number="3.2.2" class="anchored" data-anchor-id="specifying-output-format"><span class="header-section-number">3.2.2</span> Specifying output format</h3>
|
||||||
|
<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>
|
||||||
|
<ul>
|
||||||
|
<li><code>--fasta-output</code> Read data following the ecoPCR output format.</li>
|
||||||
|
<li><code>--fastq-output</code> Read data following the EMBL flatfile format.</li>
|
||||||
|
</ul>
|
||||||
|
<p>OBITools allows multiple input files to be specified for a single command.</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>--no-order</code> When several input files are provided, indicates that there is no order among them. (default: false)</li>
|
||||||
|
</ul>
|
||||||
|
</section>
|
||||||
|
<section id="format-of-the-annotations-in-fasta-and-fastq-files" class="level3" data-number="3.2.3">
|
||||||
|
<h3 data-number="3.2.3" class="anchored" data-anchor-id="format-of-the-annotations-in-fasta-and-fastq-files"><span class="header-section-number">3.2.3</span> Format of the annotations in Fasta and Fastq files</h3>
|
||||||
|
<p>OBITools extend the <a href="#fasta-classical" title="Fasta format description">Fasta</a> and <a href="#fastq-classical" title="Fastq format description">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>
|
||||||
|
<ul>
|
||||||
|
<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>
|
||||||
|
</ul>
|
||||||
|
<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>
|
||||||
|
</ul>
|
||||||
|
<section id="system-related-options" class="level4" data-number="3.2.3.1">
|
||||||
|
<h4 data-number="3.2.3.1" class="anchored" data-anchor-id="system-related-options"><span class="header-section-number">3.2.3.1</span> System related options</h4>
|
||||||
|
<ul>
|
||||||
|
<li><code>--debug</code> (default: false)</li>
|
||||||
|
<li><code>--help\|-h\|-?</code> (default: false)</li>
|
||||||
|
<li><code>--max-cpu <int></code> Number of parallele threads computing the result (default: 10)</li>
|
||||||
|
<li><code>--workers\|-w <int></code> Number of parallele threads computing the result (default: 9)</li>
|
||||||
|
</ul>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="obitools-expression-language" class="level2" data-number="3.3">
|
||||||
|
<h2 data-number="3.3" class="anchored" data-anchor-id="obitools-expression-language"><span class="header-section-number">3.3</span> OBITools expression language</h2>
|
||||||
|
<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="level3" data-number="3.3.1">
|
||||||
|
<h3 data-number="3.3.1" class="anchored" data-anchor-id="variables-usable-in-the-expression"><span class="header-section-number">3.3.1</span> Variables usable in the expression</h3>
|
||||||
|
<section id="sequence" class="level4" data-number="3.3.1.1">
|
||||||
|
<h4 data-number="3.3.1.1" class="anchored" data-anchor-id="sequence"><span class="header-section-number">3.3.1.1</span> sequence</h4>
|
||||||
|
<p>sequence is the sequence object on which the expression is evaluated</p>
|
||||||
|
</section>
|
||||||
|
<section id="annotation" class="level4" data-number="3.3.1.2">
|
||||||
|
<h4 data-number="3.3.1.2" class="anchored" data-anchor-id="annotation"><span class="header-section-number">3.3.1.2</span> annotation</h4>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="function-defined-in-the-language" class="level3" data-number="3.3.2">
|
||||||
|
<h3 data-number="3.3.2" class="anchored" data-anchor-id="function-defined-in-the-language"><span class="header-section-number">3.3.2</span> Function defined in the language</h3>
|
||||||
|
<section id="len" class="level4" data-number="3.3.2.1">
|
||||||
|
<h4 data-number="3.3.2.1" class="anchored" data-anchor-id="len"><span class="header-section-number">3.3.2.1</span> len</h4>
|
||||||
|
</section>
|
||||||
|
<section id="ismap" class="level4" data-number="3.3.2.2">
|
||||||
|
<h4 data-number="3.3.2.2" class="anchored" data-anchor-id="ismap"><span class="header-section-number">3.3.2.2</span> ismap</h4>
|
||||||
|
</section>
|
||||||
|
<section id="hasattribute" class="level4" data-number="3.3.2.3">
|
||||||
|
<h4 data-number="3.3.2.3" class="anchored" data-anchor-id="hasattribute"><span class="header-section-number">3.3.2.3</span> hasattribute</h4>
|
||||||
|
</section>
|
||||||
|
<section id="min" class="level4" data-number="3.3.2.4">
|
||||||
|
<h4 data-number="3.3.2.4" class="anchored" data-anchor-id="min"><span class="header-section-number">3.3.2.4</span> min</h4>
|
||||||
|
</section>
|
||||||
|
<section id="max" class="level4" data-number="3.3.2.5">
|
||||||
|
<h4 data-number="3.3.2.5" class="anchored" data-anchor-id="max"><span class="header-section-number">3.3.2.5</span> max</h4>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="accessing-to-the-sequence-annotations" class="level3" data-number="3.3.3">
|
||||||
|
<h3 data-number="3.3.3" class="anchored" data-anchor-id="accessing-to-the-sequence-annotations"><span class="header-section-number">3.3.3</span> Accessing to the sequence annotations</h3>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="metabarcode-design-and-quality-assessment" class="level2" data-number="3.4">
|
||||||
|
<h2 data-number="3.4" class="anchored" data-anchor-id="metabarcode-design-and-quality-assessment"><span class="header-section-number">3.4</span> Metabarcode design and quality assessment</h2>
|
||||||
|
<section id="obipcr" class="level4" data-number="3.4.0.1">
|
||||||
|
<h4 data-number="3.4.0.1" class="anchored" data-anchor-id="obipcr"><span class="header-section-number">3.4.0.1</span> <code>obipcr</code></h4>
|
||||||
|
<blockquote class="blockquote">
|
||||||
|
<p>Replace the <code>ecoPCR</code> original <em>OBITools</em></p>
|
||||||
|
</blockquote>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="file-format-conversions" class="level2" data-number="3.5">
|
||||||
|
<h2 data-number="3.5" class="anchored" data-anchor-id="file-format-conversions"><span class="header-section-number">3.5</span> File format conversions</h2>
|
||||||
|
<section id="obiconvert" class="level4" data-number="3.5.0.1">
|
||||||
|
<h4 data-number="3.5.0.1" class="anchored" data-anchor-id="obiconvert"><span class="header-section-number">3.5.0.1</span> <code>obiconvert</code></h4>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="sequence-annotations" class="level2" data-number="3.6">
|
||||||
|
<h2 data-number="3.6" class="anchored" data-anchor-id="sequence-annotations"><span class="header-section-number">3.6</span> Sequence annotations</h2>
|
||||||
|
<section id="obitag" class="level4" data-number="3.6.0.1">
|
||||||
|
<h4 data-number="3.6.0.1" class="anchored" data-anchor-id="obitag"><span class="header-section-number">3.6.0.1</span> <code>obitag</code></h4>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="computations-on-sequences" class="level2" data-number="3.7">
|
||||||
|
<h2 data-number="3.7" class="anchored" data-anchor-id="computations-on-sequences"><span class="header-section-number">3.7</span> Computations on sequences</h2>
|
||||||
|
<section id="obipairing" class="level3" data-number="3.7.1">
|
||||||
|
<h3 data-number="3.7.1" class="anchored" data-anchor-id="obipairing"><span class="header-section-number">3.7.1</span> <code>obipairing</code></h3>
|
||||||
|
<blockquote class="blockquote">
|
||||||
|
<p>Replace the <code>illuminapairedends</code> original <em>OBITools</em></p>
|
||||||
|
</blockquote>
|
||||||
|
<section id="alignment-procedure" class="level4" data-number="3.7.1.1">
|
||||||
|
<h4 data-number="3.7.1.1" class="anchored" data-anchor-id="alignment-procedure"><span class="header-section-number">3.7.1.1</span> Alignment procedure</h4>
|
||||||
|
<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 <span class="math inline">\(\Delta\)</span> 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="level4" data-number="3.7.1.2">
|
||||||
|
<h4 data-number="3.7.1.2" class="anchored" data-anchor-id="the-scoring-system"><span class="header-section-number">3.7.1.2</span> The scoring system</h4>
|
||||||
|
<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 <span class="math inline">\(Q\)</span>, the probability of misreading this base (<span class="math inline">\(P_E\)</span>) is : <span class="math display">\[
|
||||||
|
P_E = 10^{-\frac{Q}{10}}
|
||||||
|
\]</span></p>
|
||||||
|
<p>Thus, when a given nucleotide <span class="math inline">\(X\)</span> is observed with the quality score <span class="math inline">\(Q\)</span>. The probability that <span class="math inline">\(X\)</span> is really an <span class="math inline">\(X\)</span> is :</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
P(X=X) = 1 - P_E
|
||||||
|
\]</span></p>
|
||||||
|
<p>Otherwise, <span class="math inline">\(X\)</span> is actually one of the three other possible nucleotides (<span class="math inline">\(X_{E1}\)</span>, <span class="math inline">\(X_{E2}\)</span> or <span class="math inline">\(X_{E3}\)</span>). If we suppose that the three reading error have the same probability :</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
P(X=X_{E1}) = P(X=X_{E3}) = P(X=X_{E3}) = \frac{P_E}{3}
|
||||||
|
\]</span></p>
|
||||||
|
<p>At each position in an alignment where the two nucleotides <span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_2\)</span> face each other (not a gapped position), the probability of a true match varies depending on whether <span class="math inline">\(X_1=X_2\)</span>, an observed match, or <span class="math inline">\(X_1 \neq X_2\)</span>, an observed mismatch.</p>
|
||||||
|
<p><strong>Probability of a true match when <span class="math inline">\(X_1=X_2\)</span></strong></p>
|
||||||
|
<p>That probability can be divided in two parts. First <span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_2\)</span> have been correctly read. The corresponding probability is :</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
\begin{aligned}
|
||||||
|
P_{TM} &= (1- PE_1)(1-PE_2)\\
|
||||||
|
&=(1 - 10^{-\frac{Q_1}{10} } )(1 - 10^{-\frac{Q_2}{10}} )
|
||||||
|
\end{aligned}
|
||||||
|
\]</span></p>
|
||||||
|
<p>Secondly, a match can occure if the true nucleotides read as <span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_2\)</span> are not <span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_2\)</span> but identical.</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
\begin{aligned}
|
||||||
|
P(X_1==X_{E1}) \cap P(X_2==X_{E1}) &= \frac{P_{E1} P_{E2}}{9} \\
|
||||||
|
P(X_1==X_{Ex}) \cap P(X_2==X_{Ex}) & = \frac{P_{E1} P_{E2}}{3}
|
||||||
|
\end{aligned}
|
||||||
|
\]</span></p>
|
||||||
|
<p>The probability of a true match between <span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_2\)</span> when <span class="math inline">\(X_1 = X_2\)</span> an observed match :</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
\begin{aligned}
|
||||||
|
P(MATCH | X_1 = X_2) = (1- PE_1)(1-PE_2) + \frac{P_{E1} P_{E2}}{3}
|
||||||
|
\end{aligned}
|
||||||
|
\]</span></p>
|
||||||
|
<p><strong>Probability of a true match when <span class="math inline">\(X_1 \neq X_2\)</span></strong></p>
|
||||||
|
<p>That probability can be divided in three parts.</p>
|
||||||
|
<ol type="a">
|
||||||
|
<li><span class="math inline">\(X_1\)</span> has been correctly read and <span class="math inline">\(X_2\)</span> is a sequencing error and is actually equal to <span class="math inline">\(X_1\)</span>. <span class="math display">\[
|
||||||
|
P_a = (1-P_{E1})\frac{P_{E2}}{3}
|
||||||
|
\]</span></li>
|
||||||
|
<li><span class="math inline">\(X_2\)</span> has been correctly read and <span class="math inline">\(X_1\)</span> is a sequencing error and is actually equal to <span class="math inline">\(X_2\)</span>. <span class="math display">\[
|
||||||
|
P_b = (1-P_{E2})\frac{P_{E1}}{3}
|
||||||
|
\]</span></li>
|
||||||
|
<li><span class="math inline">\(X_1\)</span> and <span class="math inline">\(X_2\)</span> corresponds to sequencing error but are actually the same base <span class="math inline">\(X_{Ex}\)</span> <span class="math display">\[
|
||||||
|
P_c = 2\frac{P_{E1} P_{E2}}{9}
|
||||||
|
\]</span></li>
|
||||||
|
</ol>
|
||||||
|
<p>Consequently : <span class="math display">\[
|
||||||
|
\begin{aligned}
|
||||||
|
P(MATCH | X_1 \neq X_2) = (1-P_{E1})\frac{P_{E2}}{3} + (1-P_{E2})\frac{P_{E1}}{3} + 2\frac{P_{E1} P_{E2}}{9}
|
||||||
|
\end{aligned}
|
||||||
|
\]</span></p>
|
||||||
|
<p><strong>Probability of a match under the random model</strong></p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="cell-output-display">
|
||||||
|
<div class="quarto-figure quarto-figure-center">
|
||||||
|
<figure class="figure">
|
||||||
|
<p><img src="commands_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 id="obimultiplex" class="level4" data-number="3.7.1.3">
|
||||||
|
<h4 data-number="3.7.1.3" class="anchored" data-anchor-id="obimultiplex"><span class="header-section-number">3.7.1.3</span> <code>obimultiplex</code></h4>
|
||||||
|
<blockquote class="blockquote">
|
||||||
|
<p>Replace the <code>ngsfilter</code> original <em>OBITools</em></p>
|
||||||
|
</blockquote>
|
||||||
|
</section>
|
||||||
|
<section id="obicomplement" class="level4" data-number="3.7.1.4">
|
||||||
|
<h4 data-number="3.7.1.4" class="anchored" data-anchor-id="obicomplement"><span class="header-section-number">3.7.1.4</span> <code>obicomplement</code></h4>
|
||||||
|
</section>
|
||||||
|
<section id="obiclean" class="level4" data-number="3.7.1.5">
|
||||||
|
<h4 data-number="3.7.1.5" class="anchored" data-anchor-id="obiclean"><span class="header-section-number">3.7.1.5</span> <code>obiclean</code></h4>
|
||||||
|
</section>
|
||||||
|
<section id="obiuniq" class="level4" data-number="3.7.1.6">
|
||||||
|
<h4 data-number="3.7.1.6" class="anchored" data-anchor-id="obiuniq"><span class="header-section-number">3.7.1.6</span> <code>obiuniq</code></h4>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="sequence-sampling-and-filtering" class="level2" data-number="3.8">
|
||||||
|
<h2 data-number="3.8" class="anchored" data-anchor-id="sequence-sampling-and-filtering"><span class="header-section-number">3.8</span> Sequence sampling and filtering</h2>
|
||||||
|
<section id="obigrep" class="level4" data-number="3.8.0.1">
|
||||||
|
<h4 data-number="3.8.0.1" class="anchored" data-anchor-id="obigrep"><span class="header-section-number">3.8.0.1</span> <code>obigrep</code></h4>
|
||||||
|
</section>
|
||||||
|
<section id="utilities" class="level3" data-number="3.8.1">
|
||||||
|
<h3 data-number="3.8.1" class="anchored" data-anchor-id="utilities"><span class="header-section-number">3.8.1</span> Utilities</h3>
|
||||||
|
<section id="obicount" class="level4" data-number="3.8.1.1">
|
||||||
|
<h4 data-number="3.8.1.1" class="anchored" data-anchor-id="obicount"><span class="header-section-number">3.8.1.1</span> <code>obicount</code></h4>
|
||||||
|
</section>
|
||||||
|
<section id="obidistribute" class="level4" data-number="3.8.1.2">
|
||||||
|
<h4 data-number="3.8.1.2" class="anchored" data-anchor-id="obidistribute"><span class="header-section-number">3.8.1.2</span> <code>obidistribute</code></h4>
|
||||||
|
</section>
|
||||||
|
<section id="obifind" class="level4" data-number="3.8.1.3">
|
||||||
|
<h4 data-number="3.8.1.3" class="anchored" data-anchor-id="obifind"><span class="header-section-number">3.8.1.3</span> <code>obifind</code></h4>
|
||||||
|
<blockquote class="blockquote">
|
||||||
|
<p>Replace the <code>ecofind</code> original <em>OBITools.</em></p>
|
||||||
|
</blockquote>
|
||||||
|
|
||||||
|
|
||||||
|
<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>.
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
</section>
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|
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|
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<script id="quarto-html-after-body" type="application/javascript">
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// use id or data attribute instead here
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try { href = new URL(href).hash; } catch {}
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const cites = parentEl.dataset.cites;
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<h1 class="title d-none d-lg-block">OBITools V4</h1>
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<div class="quarto-title-meta-heading">Author</div>
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<p>Eric Coissac </p>
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<div class="quarto-title-meta-heading">Published</div>
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<p class="date">January 17, 2023</p>
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<section id="preface" class="level1 unnumbered">
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<h1 class="unnumbered">Preface</h1>
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<p>The first version of <em>OBITools</em> started to be developed in 2005. This was at the beginning of the DNA metabarcoding story at the Laboratoire d’Ecologie Alpine (LECA) in Grenoble. At that time, with Pierre Taberlet and François Pompanon, we were thinking about the potential of this new methodology under development. PIerre and François developed more the laboratory methods, while I was thinking more about the tools for analysing the sequences produced. Two ideas were behind this development. I wanted something modular, and something easy to extend. To achieve the first goal, I decided to implement obitools as a suite of unix commands mimicking the classic unix commands but dedicated to sequence files. The basic unix commands are very useful for automatically manipulating, parsing and editing text files. They work in flow, line by line on the input text. The result is a new text file that can be used as input for the next command. Such a design makes it possible to quickly develop a text processing pipeline by chaining simple elementary operations. The <em>OBITools</em> are the exact counterpart of these basic Unix commands, but the basic information they process is a sequence (potentially spanning several lines of text), not a single line of text. Most <em>OBITools</em> consume sequence files and produce sequence files. Thus, the principles of chaining and modularity are respected. In order to be able to easily extend the <em>OBITools</em> to keep up with our evolving ideas about processing DNA metabarcoding data, it was decided to develop them using an interpreted language: Python. Python 2, the version available at the time, allowed us to develop the <em>OBITools</em> efficiently. When parts of the algorithms were computationally demanding, they were implemented in C and linked to the Python code. Even though Python is not the most efficient language available, even though computers were not as powerful as they are today, the size of the data we could produce using 454 sequencers or early solexa machines was small enough to be processed in a reasonable time.</p>
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<p>The first public version of obitools was <a href="https://metabarcoding.org/obitools"><em>OBITools2</em></a> <span class="citation" data-cites="Boyer2016-gq">(<a href="references.html#ref-Boyer2016-gq" role="doc-biblioref">Boyer et al. 2016</a>)</span>, this was actually a cleaned up and documented version of <em>OBITools</em> that had been running at LECA for years and was not really distributed except to a few collaborators. This is where <em>OBITools</em> started its public life from then on. The DNA metabarcoding spring schools provided and still provide user training every year. But <em>OBITools2</em> soon suffered from two limitations: it was developed in Python2, which was increasingly abandoned in favour of Python3, and the data size kept increasing with the new illumina machines. Python’s intrinsic slowness coupled with the increasing size of the datasets made OBITools computation times increasingly long. The abandonment of all maintenance of Python2 by its developers also imposed the need for a new version of OBITools.</p>
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<p><a href="https://metabarcoding.org/obitools3"><em>OBITools3</em></a> was the first response to this crisis. Developed and maintained by <a href="https://www.celine-mercier.info">Céline Mercier</a>, <em>OBITools3</em> attempted to address several limitations of <em>OBITools2</em>. It is a complete new code, mainly developed in Python3, with most of the lower layer code written in C for efficiency. OBITools3 has also abandoned text files for binary files for the same reason of efficiency. They have been replaced by a database structure that keeps track of every operation performed on the data.</p>
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<p>Here we present <em>OBITools4</em> which can be seen as a return to the origins of OBITools. While <em>OBITools3</em> offered traceability of analyses, which is in line with the concept of open science, and faster execution, <em>OBITools2</em> was more versatile and not only usable for the analysis of DNA metabarcoding data. <em>OBITools4</em> is the third full implementation of <em>OBITools</em>. The idea behind this new version is to go back to the original design of <em>OBITools</em> which ran on text files containing sequences, like the classic Unix commands, but running at least as fast as <em>OBITools3</em> and taking advantage of the multicore architecture of all modern laptops. For this, the idea of relying on an interpreted language was abandoned. The <em>OBITools4</em> are now fully implemented in the <a href="https://go.dev">GO</a> language with the exception of a few small pieces of specific code already implemented very efficiently in C. <em>OBITools4</em> also implement a new format for the annotations inserted in the header of every sequences. Rather tha relying on a format specific to <em>OBITools</em>, by default <em>OBITools4</em> use the <a href="https://www.json.org">JSON</a> format. This simplifies the writing of parsers in any languages, and thus allows obitools to easiestly interact with other software.</p>
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<div id="ref-Boyer2016-gq" class="csl-entry" role="doc-biblioentry">
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Boyer, Frédéric, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre Taberlet, and Eric Coissac. 2016. <span>“<span class="nocase">obitools: a unix-inspired software package for DNA metabarcoding</span>.”</span> <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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<li><a href="#aims-of-obitools" id="toc-aims-of-obitools" class="nav-link active" data-scroll-target="#aims-of-obitools"><span class="toc-section-number">1.1</span> Aims of <em>OBITools</em></a></li>
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<li><a href="#file-formats-usable-with-obitools" id="toc-file-formats-usable-with-obitools" class="nav-link" data-scroll-target="#file-formats-usable-with-obitools"><span class="toc-section-number">1.2</span> File formats usable with <em>OBITools</em></a>
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<li><a href="#the-sequence-files" id="toc-the-sequence-files" class="nav-link" data-scroll-target="#the-sequence-files"><span class="toc-section-number">1.2.1</span> The sequence files</a></li>
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<li><a href="#the-iupac-code" id="toc-the-iupac-code" class="nav-link" data-scroll-target="#the-iupac-code"><span class="toc-section-number">1.2.2</span> The IUPAC Code</a></li>
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<li><a href="#classical-fasta" id="toc-classical-fasta" class="nav-link" data-scroll-target="#classical-fasta"><span class="toc-section-number">1.2.3</span> The <em>fasta</em> format</a></li>
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<li><a href="#classical-fastq" id="toc-classical-fastq" class="nav-link" data-scroll-target="#classical-fastq"><span class="toc-section-number">1.2.4</span> The <em>fastq</em> sequence format</a></li>
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|
<li><a href="#file-extension" id="toc-file-extension" class="nav-link" data-scroll-target="#file-extension"><span class="toc-section-number">1.3</span> File extension</a></li>
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<li><a href="#see-also" id="toc-see-also" class="nav-link" data-scroll-target="#see-also"><span class="toc-section-number">1.4</span> See also</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></h1>
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<section id="aims-of-obitools" class="level2" data-number="1.1">
|
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<h2 data-number="1.1" class="anchored" data-anchor-id="aims-of-obitools"><span class="header-section-number">1.1</span> Aims of <em>OBITools</em></h2>
|
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</section>
|
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<section id="file-formats-usable-with-obitools" class="level2" data-number="1.2">
|
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<h2 data-number="1.2" class="anchored" data-anchor-id="file-formats-usable-with-obitools"><span class="header-section-number">1.2</span> File formats usable with <em>OBITools</em></h2>
|
||||||
|
<section id="the-sequence-files" class="level3" data-number="1.2.1">
|
||||||
|
<h3 data-number="1.2.1" class="anchored" data-anchor-id="the-sequence-files"><span class="header-section-number">1.2.1</span> The sequence files</h3>
|
||||||
|
<p>Sequences can be stored following various format. OBITools knows some of them. The central formats for sequence files manipulated by OBITools scripts are the <code>fasta</code> and fastq format. OBITools extends the both these formats by specifying a syntax to include in the definition line data qualifying the sequence. All file formats use the <code>IUPAC</code> code for encoding nucleotides.</p>
|
||||||
|
</section>
|
||||||
|
<section id="the-iupac-code" class="level3" data-number="1.2.2">
|
||||||
|
<h3 data-number="1.2.2" class="anchored" data-anchor-id="the-iupac-code"><span class="header-section-number">1.2.2</span> The IUPAC Code</h3>
|
||||||
|
<p>The International Union of Pure and Applied Chemistry (IUPAC_) defined the standard code for representing protein or DNA sequences.</p>
|
||||||
|
<section id="DNA-IUPAC" class="level4" data-number="1.2.2.1">
|
||||||
|
<h4 data-number="1.2.2.1" class="anchored" data-anchor-id="DNA-IUPAC"><span class="header-section-number">1.2.2.1</span> Nucleic IUPAC Code</h4>
|
||||||
|
<table class="table">
|
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<thead>
|
||||||
|
<tr class="header">
|
||||||
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<th><strong>Code</strong></th>
|
||||||
|
<th><strong>Nucleotide</strong></th>
|
||||||
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|
||||||
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</thead>
|
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||||||
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<td>A</td>
|
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<td>Adenine</td>
|
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|
||||||
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<td>C</td>
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<td>Cytosine</td>
|
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||||||
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|
||||||
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<td>G</td>
|
||||||
|
<td>Guanine</td>
|
||||||
|
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|
||||||
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<tr class="even">
|
||||||
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<td>T</td>
|
||||||
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<td>Thymine</td>
|
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|
||||||
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<td>U</td>
|
||||||
|
<td>Uracil</td>
|
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|
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|
||||||
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<tr class="even">
|
||||||
|
<td>R</td>
|
||||||
|
<td>Purine (A or G)</td>
|
||||||
|
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|
||||||
|
<tr class="odd">
|
||||||
|
<td>Y</td>
|
||||||
|
<td>Pyrimidine (C, T, or U)</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>M</td>
|
||||||
|
<td>C or A</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>K</td>
|
||||||
|
<td>T, U, or G</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>W</td>
|
||||||
|
<td>T, U, or A</td>
|
||||||
|
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|
||||||
|
<tr class="odd">
|
||||||
|
<td>S</td>
|
||||||
|
<td>C or G</td>
|
||||||
|
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|
||||||
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<tr class="even">
|
||||||
|
<td>B</td>
|
||||||
|
<td>C, T, U, or G (not A)</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>D</td>
|
||||||
|
<td>A, T, U, or G (not C)</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>H</td>
|
||||||
|
<td>A, T, U, or C (not G)</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>V</td>
|
||||||
|
<td>A, C, or G (not T, not U)</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td>N</td>
|
||||||
|
<td>Any base (A, C, G, T, or U)</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="classical-fasta" class="level3" data-number="1.2.3">
|
||||||
|
<h3 data-number="1.2.3" class="anchored" data-anchor-id="classical-fasta"><span class="header-section-number">1.2.3</span> The <em>fasta</em> format</h3>
|
||||||
|
<p>The <strong>fasta format</strong> is certainly the most widely used sequence file format. This is certainly due to its great simplicity. It was originally created for the Lipman and Pearson <a href="http://www.ncbi.nlm.nih.gov/pubmed/3162770?dopt=Citation">FASTA program</a>. OBITools use in more of the classical :ref:<code>fasta</code> format an :ref:<code>extended version</code> of this format where structured data are included in the title line.</p>
|
||||||
|
<p>In <em>fasta</em> format a sequence is represented by a title line beginning with a <strong><code>></code></strong> character and the sequences by itself following the :doc:<code>iupac</code> code. The sequence is usually split other severals lines of the same length (expect for the last one)</p>
|
||||||
|
<pre><code>>my_sequence this is my pretty sequence
|
||||||
|
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||||
|
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||||
|
AACGACGTTGCAGTACGTTGCAGT</code></pre>
|
||||||
|
<p>This is no special format for the title line excepting that this line should be unique. Usually the first word following the <strong>></strong> character is considered as the sequence identifier. The end of the title line corresponding to a description of the sequence. Several sequences can be concatenated in a same file. The description of the next sequence is just pasted at the end of the record of the previous one</p>
|
||||||
|
<pre><code>>sequence_A this is my first pretty sequence
|
||||||
|
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||||
|
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||||
|
AACGACGTTGCAGTACGTTGCAGT
|
||||||
|
>sequence_B this is my second pretty sequence
|
||||||
|
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||||
|
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||||
|
AACGACGTTGCAGTACGTTGCAGT
|
||||||
|
>sequence_C this is my third pretty sequence
|
||||||
|
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||||
|
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||||
|
AACGACGTTGCAGTACGTTGCAGT</code></pre>
|
||||||
|
</section>
|
||||||
|
<section id="classical-fastq" class="level3" data-number="1.2.4">
|
||||||
|
<h3 data-number="1.2.4" class="anchored" data-anchor-id="classical-fastq"><span class="header-section-number">1.2.4</span> The <em>fastq</em> sequence format<a href="#fn1" class="footnote-ref" id="fnref1" role="doc-noteref"><sup>1</sup></a></h3>
|
||||||
|
<p><strong>fastq format</strong> is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are encoded with a single ASCII character for brevity. It was originally developed at the <code>Wellcome Trust Sanger Institute</code> to bundle a <a href="#classical-fasta">fasta</a> sequence and its quality data, but has recently become the <em>de facto</em> standard for storing the output of high throughput sequencing instruments such as the Illumina Genome Analyzer Illumina <span class="citation" data-cites="cock2010sanger">(<a href="references.html#ref-cock2010sanger" role="doc-biblioref">Cock et al. 2010</a>)</span> .</p>
|
||||||
|
<p>A fastq file normally uses four lines per sequence.</p>
|
||||||
|
<ul>
|
||||||
|
<li>Line 1 begins with a ‘@’ character and is followed by a sequence identifier and an <em>optional</em> description (like a :ref:<code>fasta</code> title line).</li>
|
||||||
|
<li>Line 2 is the raw sequence letters.</li>
|
||||||
|
<li>Line 3 begins with a ‘+’ character and is <em>optionally</em> followed by the same sequence identifier (and any description) again.</li>
|
||||||
|
<li>Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.</li>
|
||||||
|
</ul>
|
||||||
|
<p>A fastq file containing a single sequence might look like this:</p>
|
||||||
|
<pre><code>@SEQ_ID
|
||||||
|
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
|
||||||
|
+
|
||||||
|
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65</code></pre>
|
||||||
|
<p>The character ‘!’ represents the lowest quality while ‘~’ is the highest. Here are the quality value characters in left-to-right increasing order of quality (<code>ASCII</code>):</p>
|
||||||
|
<pre><code>!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~</code></pre>
|
||||||
|
<p>The original Sanger FASTQ files also allowed the sequence and quality strings to be wrapped (split over multiple lines), but this is generally discouraged as it can make parsing complicated due to the unfortunate choice of “@” and “+” as markers (these characters can also occur in the quality string).</p>
|
||||||
|
<section id="variations" class="level4" data-number="1.2.4.1">
|
||||||
|
<h4 data-number="1.2.4.1" class="anchored" data-anchor-id="variations"><span class="header-section-number">1.2.4.1</span> Variations</h4>
|
||||||
|
<section id="quality" class="level5" data-number="1.2.4.1.1">
|
||||||
|
<h5 data-number="1.2.4.1.1" class="anchored" data-anchor-id="quality"><span class="header-section-number">1.2.4.1.1</span> Quality</h5>
|
||||||
|
<p>A quality value <em>Q</em> is an integer mapping of <em>p</em> (i.e., the probability that the corresponding base call is incorrect). Two different equations have been in use. The first is the standard Sanger variant to assess reliability of a base call, otherwise known as Phred quality score:</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
Q_\text{sanger} = -10 \, \log_{10} p
|
||||||
|
\]</span></p>
|
||||||
|
<p>The Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) earlier used a different mapping, encoding the odds <span class="math inline">\(\mathbf{p}/(1-\mathbf{p})\)</span> instead of the probability <span class="math inline">\(\mathbf{p}\)</span>:</p>
|
||||||
|
<p><span class="math display">\[
|
||||||
|
Q_\text{solexa-prior to v.1.3} = -10 \, \log_{10} \frac{p}{1-p}
|
||||||
|
\]</span></p>
|
||||||
|
<p>Although both mappings are asymptotically identical at higher quality values, they differ at lower quality levels (i.e., approximately <span class="math inline">\(\mathbf{p} > 0.05\)</span>, or equivalently, <span class="math inline">\(\mathbf{Q} < 13\)</span>).</p>
|
||||||
|
<p>|Relationship between <em>Q</em> and <em>p</em> using the Sanger (red) and Solexa (black) equations (described above). The vertical dotted line indicates <span class="math inline">\(\mathbf{p}= 0.05\)</span>, or equivalently, <span class="math inline">\(Q = 13\)</span>.|</p>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="encoding" class="level4" data-number="1.2.4.2">
|
||||||
|
<h4 data-number="1.2.4.2" class="anchored" data-anchor-id="encoding"><span class="header-section-number">1.2.4.2</span> Encoding</h4>
|
||||||
|
<ul>
|
||||||
|
<li>Sanger format can encode a Phred quality score from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60, higher scores are possible in assemblies or read maps).</li>
|
||||||
|
<li>Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)</li>
|
||||||
|
<li>Starting with Illumina 1.3 and before Illumina 1.8, the format encoded a Phred quality score from 0 to 62 using ASCII 64 to 126 (although in raw read data Phred scores from 0 to 40 only are expected).</li>
|
||||||
|
<li>Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 “B”.</li>
|
||||||
|
</ul>
|
||||||
|
<p>Sequencing Control Software, Version 2.6, Catalog # SY-960-2601, Part # 15009921 Rev. A, November 2009] <a href="[http://watson.nci.nih.gov/solexa/Using_SCSv2.6_15009921_A.pdf](http://watson.nci.nih.gov/solexa/Using_SCSv2.6_15009921_A.pdf){.uri}" class="uri">[http://watson.nci.nih.gov/solexa/Using_SCSv2.6_15009921_A.pdf\\](http://watson.nci.nih.gov/solexa/Using_SCSv2.6_15009921_A.pdf){.uri}</a> (page 30) states the following: <em>If a read ends with a segment of mostly low quality (Q15 or below), then all of the quality values in the segment are replaced with a value of 2 (encoded as the letter B in Illumina’s text-based encoding of quality scores)… This Q2 indicator does not predict a specific error rate, but rather indicates that a specific final portion of the read should not be used in further analyses.</em> Also, the quality score encoded as “B” letter may occur internally within reads at least as late as pipeline version 1.6, as shown in the following example:</p>
|
||||||
|
<pre><code>@HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1
|
||||||
|
TTAATTGGTAAATAAATCTCCTAATAGCTTAGATNTTACCTTNNNNNNNNNNTAGTTTCTTGAGATTTGTTGGGGGAGACATTTTTGTGATTGCCTTGAT
|
||||||
|
+HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1
|
||||||
|
efcfffffcfeefffcffffffddf`feed]`]_Ba_^__[YBBBBBBBBBBRTT\]][]dddd`ddd^dddadd^BBBBBBBBBBBBBBBBBBBBBBBB</code></pre>
|
||||||
|
<p>An alternative interpretation of this ASCII encoding has been proposed. Also, in Illumina runs using PhiX controls, the character ‘B’ was observed to represent an “unknown quality score”. The error rate of ‘B’ reads was roughly 3 phred scores lower the mean observed score of a given run.</p>
|
||||||
|
<ul>
|
||||||
|
<li>Starting in Illumina 1.8, the quality scores have basically returned to the use of the Sanger format (Phred+33).</li>
|
||||||
|
</ul>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="file-extension" class="level2" data-number="1.3">
|
||||||
|
<h2 data-number="1.3" class="anchored" data-anchor-id="file-extension"><span class="header-section-number">1.3</span> File extension</h2>
|
||||||
|
<p>There is no standard file extension for a FASTQ file, but .fq and .fastq, are commonly used.</p>
|
||||||
|
</section>
|
||||||
|
<section id="see-also" class="level2" data-number="1.4">
|
||||||
|
<h2 data-number="1.4" class="anchored" data-anchor-id="see-also"><span class="header-section-number">1.4</span> See also</h2>
|
||||||
|
<ul>
|
||||||
|
<li>:ref:<code>fasta</code></li>
|
||||||
|
</ul>
|
||||||
|
</section>
|
||||||
|
<section id="references" class="level2" data-number="1.5">
|
||||||
|
<h2 data-number="1.5" class="anchored" data-anchor-id="references"><span class="header-section-number">1.5</span> References</h2>
|
||||||
|
<p>.. [1] Cock et al (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research,</p>
|
||||||
|
<p>.. [2] Illumina Quality Scores, Tobias Mann, Bioinformatics, San Diego, Illumina <code>1</code>__</p>
|
||||||
|
<p>.. |Relationship between <em>Q</em> and <em>p</em> using the Sanger (red) and Solexa (black) equations (described above). The vertical dotted line indicates <em>p</em> = 0.05, or equivalently, <em>Q</em> Å 13.| image:: Probability metrics.png</p>
|
||||||
|
<p>See <a href="http://en.wikipedia.org/wiki/FASTQ_format" class="uri">http://en.wikipedia.org/wiki/FASTQ_format</a></p>
|
||||||
|
|
||||||
|
|
||||||
|
<div id="refs" class="references csl-bib-body hanging-indent" role="doc-bibliography" style="display: none">
|
||||||
|
<div id="ref-cock2010sanger" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Cock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and Peter M Rice. 2010. <span>“The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa/Illumina FASTQ Variants.”</span> <em>Nucleic Acids Research</em> 38 (6): 1767–71.
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
<section id="footnotes" class="footnotes footnotes-end-of-document" role="doc-endnotes">
|
||||||
|
<hr>
|
||||||
|
<ol>
|
||||||
|
<li id="fn1"><p>This article uses material from the Wikipedia article <a href="http://en.wikipedia.org/wiki/FASTQ_format"><code>FASTQ format</code></a> which is released under the <code>Creative Commons Attribution-Share-Alike License 3.0</code><a href="#fnref1" class="footnote-back" role="doc-backlink">↩︎</a></p></li>
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<h2 id="toc-title">Table of contents</h2>
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<li><a href="#biosequence" id="toc-biosequence" class="nav-link active" data-scroll-target="#biosequence"><span class="toc-section-number">4.1</span> BioSequence</a>
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<li><a href="#creating-new-instances" id="toc-creating-new-instances" class="nav-link" data-scroll-target="#creating-new-instances"><span class="toc-section-number">4.1.1</span> Creating new instances</a></li>
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<li><a href="#end-of-life-of-a-biosequence-instance" id="toc-end-of-life-of-a-biosequence-instance" class="nav-link" data-scroll-target="#end-of-life-of-a-biosequence-instance"><span class="toc-section-number">4.1.2</span> End of life of a <code>BioSequence</code> instance</a></li>
|
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<li><a href="#accessing-to-the-elements-of-a-sequence" id="toc-accessing-to-the-elements-of-a-sequence" class="nav-link" data-scroll-target="#accessing-to-the-elements-of-a-sequence"><span class="toc-section-number">4.1.3</span> 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"><span class="toc-section-number">4.1.4</span> The annotations of a sequence</a></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"><span class="toc-section-number">4.2</span> The sequence iterator</a>
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<li><a href="#the-pipable-functions" id="toc-the-pipable-functions" class="nav-link" data-scroll-target="#the-pipable-functions"><span class="toc-section-number">4.2.2</span> 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"><span class="toc-section-number">4.2.3</span> The <code>Teeable</code> functions</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">4</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></h1>
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<section id="biosequence" class="level2" data-number="4.1">
|
||||||
|
<h2 data-number="4.1" class="anchored" data-anchor-id="biosequence"><span class="header-section-number">4.1</span> 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" data-number="4.1.1">
|
||||||
|
<h3 data-number="4.1.1" class="anchored" data-anchor-id="creating-new-instances"><span class="header-section-number">4.1.1</span> 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" data-number="4.1.2">
|
||||||
|
<h3 data-number="4.1.2" class="anchored" data-anchor-id="end-of-life-of-a-biosequence-instance"><span class="header-section-number">4.1.2</span> 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" data-number="4.1.3">
|
||||||
|
<h3 data-number="4.1.3" class="anchored" data-anchor-id="accessing-to-the-elements-of-a-sequence"><span class="header-section-number">4.1.3</span> 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" data-number="4.1.3.1">
|
||||||
|
<h4 data-number="4.1.3.1" class="anchored" data-anchor-id="different-ways-for-accessing-an-editing-the-sequence"><span class="header-section-number">4.1.3.1</span> Different ways for accessing an editing the sequence</h4>
|
||||||
|
<p>If <code>Sequence()</code>and <code>SetSequence(sequence []byte)</code> methods are the basic ones, several other methods exist.</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>String() string</code> return the sequence directly converted to a <code>string</code> instance.</li>
|
||||||
|
<li>The <code>Write</code> method family allows for extending an existing sequence following the buffer protocol.
|
||||||
|
<ul>
|
||||||
|
<li><code>Write(data []byte) (int, error)</code> allows for appending a byte array on 3’ end of the sequence.</li>
|
||||||
|
<li><code>WriteString(data string) (int, error)</code> allows for appending a <code>string</code>.</li>
|
||||||
|
<li><code>WriteByte(data byte) error</code> allows for appending a single <code>byte</code>.</li>
|
||||||
|
</ul></li>
|
||||||
|
</ul>
|
||||||
|
<p>The <code>Clear</code> method empties the sequence buffer.</p>
|
||||||
|
<div class="sourceCode" id="cb5"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||||
|
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||||||
|
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||||||
|
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||||
|
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||||||
|
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewEmptyBiosequence<span class="op">()</span></span>
|
||||||
|
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>WriteString<span class="op">(</span><span class="st">"accc"</span><span class="op">)</span></span>
|
||||||
|
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>WriteByte<span class="op">(</span><span class="dt">byte</span><span class="op">(</span><span class="ch">'c'</span><span class="op">))</span></span>
|
||||||
|
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>String<span class="op">())</span></span>
|
||||||
|
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</section>
|
||||||
|
<section id="sequence-quality-scores" class="level4" data-number="4.1.3.2">
|
||||||
|
<h4 data-number="4.1.3.2" class="anchored" data-anchor-id="sequence-quality-scores"><span class="header-section-number">4.1.3.2</span> Sequence quality scores</h4>
|
||||||
|
<p>Sequence quality scores cannot be initialized at the time of instance creation. You must use dedicated methods to add quality scores to a sequence.</p>
|
||||||
|
<p>To be coherent the length of both the DNA sequence and que quality score sequence must be equal. But assessment of this constraint is realized. It is of the programmer responsability to check that invariant.</p>
|
||||||
|
<p>While accessing to the quality scores relies on the method <code>Quality() []byte</code>, setting the quality need to call one of the following method. They run similarly to their sequence dedicated conterpart.</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>SetQualities(qualities Quality)</code></li>
|
||||||
|
<li><code>WriteQualities(data []byte) (int, error)</code></li>
|
||||||
|
<li><code>WriteByteQualities(data byte) error</code></li>
|
||||||
|
</ul>
|
||||||
|
<p>In a way analogous to the <code>Clear</code> method, <code>ClearQualities()</code> empties the sequence of quality scores.</p>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="the-annotations-of-a-sequence" class="level3" data-number="4.1.4">
|
||||||
|
<h3 data-number="4.1.4" class="anchored" data-anchor-id="the-annotations-of-a-sequence"><span class="header-section-number">4.1.4</span> 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" data-number="4.2">
|
||||||
|
<h2 data-number="4.2" class="anchored" data-anchor-id="the-sequence-iterator"><span class="header-section-number">4.2</span> 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" data-number="4.2.1">
|
||||||
|
<h3 data-number="4.2.1" class="anchored" data-anchor-id="basic-usage-of-a-sequence-iterator"><span class="header-section-number">4.2.1</span> 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" data-number="4.2.2">
|
||||||
|
<h3 data-number="4.2.2" class="anchored" data-anchor-id="the-pipable-functions"><span class="header-section-number">4.2.2</span> 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" data-number="4.2.3">
|
||||||
|
<h3 data-number="4.2.3" class="anchored" data-anchor-id="the-teeable-functions"><span class="header-section-number">4.2.3</span> 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>
|
||||||
|
</section>
|
||||||
|
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|
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></span>
|
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|
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<h1 class="quarto-secondary-nav-title">References</h1>
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|
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|
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|
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|
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|
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<a href="./intro.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></a>
|
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|
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|
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|
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|
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|
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|
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<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></a>
|
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|
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|
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|
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|
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|
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<a href="./library.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
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|
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|
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|
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|
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|
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|
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<a href="./references.html" class="sidebar-item-text sidebar-link active">References</a>
|
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|
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|
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|
||||||
|
<h1 class="title d-none d-lg-block">References</h1>
|
||||||
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
||||||
|
<div id="refs" class="references csl-bib-body hanging-indent" role="doc-bibliography">
|
||||||
|
<div id="ref-Boyer2016-gq" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Boyer, Frédéric, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre
|
||||||
|
Taberlet, and Eric Coissac. 2016. <span>“<span class="nocase">obitools:
|
||||||
|
a unix-inspired software package for DNA metabarcoding</span>.”</span>
|
||||||
|
<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>.
|
||||||
|
</div>
|
||||||
|
<div id="ref-cock2010sanger" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Cock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and
|
||||||
|
Peter M Rice. 2010. <span>“The Sanger FASTQ File Format for Sequences
|
||||||
|
with Quality Scores, and the Solexa/Illumina FASTQ Variants.”</span>
|
||||||
|
<em>Nucleic Acids Research</em> 38 (6): 1767–71.
|
||||||
|
</div>
|
||||||
|
<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>.
|
||||||
|
</div>
|
||||||
|
<div id="ref-Riaz2011-gn" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Riaz, Tiayyba, Wasim Shehzad, Alain Viari, François Pompanon, Pierre
|
||||||
|
Taberlet, and Eric Coissac. 2011. <span>“<span class="nocase">ecoPrimers: inference of new DNA barcode markers from
|
||||||
|
whole genome sequence analysis</span>.”</span> <em>Nucleic Acids
|
||||||
|
Research</em> 39 (21): e145. <a href="https://doi.org/10.1093/nar/gkr732">https://doi.org/10.1093/nar/gkr732</a>.
|
||||||
|
</div>
|
||||||
|
<div id="ref-Seguritan2001-tg" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Seguritan, V, and F Rohwer. 2001. <span>“<span class="nocase">FastGroup:
|
||||||
|
a program to dereplicate libraries of 16S rDNA sequences</span>.”</span>
|
||||||
|
<em>BMC Bioinformatics</em> 2 (October): 9. <a href="https://doi.org/10.1186/1471-2105-2-9">https://doi.org/10.1186/1471-2105-2-9</a>.
|
||||||
|
</div>
|
||||||
|
<div id="ref-Shehzad2012-pn" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Shehzad, Wasim, Tiayyba Riaz, Muhammad A Nawaz, Christian Miquel, Carole
|
||||||
|
Poillot, Safdar A Shah, Francois Pompanon, Eric Coissac, and Pierre
|
||||||
|
Taberlet. 2012. <span>“<span class="nocase">Carnivore diet analysis
|
||||||
|
based on next-generation sequencing: Application to the leopard cat
|
||||||
|
(Prionailurus bengalensis) in Pakistan</span>.”</span> <em>Molecular
|
||||||
|
Ecology</em> 21 (8): 1951–65. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x">https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x</a>.
|
||||||
|
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|
||||||
|
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|
||||||
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|
||||||
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|
||||||
|
|
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|
</main> <!-- /main -->
|
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|
<script id="quarto-html-after-body" type="application/javascript">
|
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cites: cites.split(' ')
|
||||||
|
};
|
||||||
|
} else {
|
||||||
|
return findCites(el.parentElement)
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
return undefined;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
|
||||||
|
for (var i=0; i<bibliorefs.length; i++) {
|
||||||
|
const ref = bibliorefs[i];
|
||||||
|
const citeInfo = findCites(ref);
|
||||||
|
if (citeInfo) {
|
||||||
|
tippyHover(citeInfo.el, function() {
|
||||||
|
var popup = window.document.createElement('div');
|
||||||
|
citeInfo.cites.forEach(function(cite) {
|
||||||
|
var citeDiv = window.document.createElement('div');
|
||||||
|
citeDiv.classList.add('hanging-indent');
|
||||||
|
citeDiv.classList.add('csl-entry');
|
||||||
|
var biblioDiv = window.document.getElementById('ref-' + cite);
|
||||||
|
if (biblioDiv) {
|
||||||
|
citeDiv.innerHTML = biblioDiv.innerHTML;
|
||||||
|
}
|
||||||
|
popup.appendChild(citeDiv);
|
||||||
|
});
|
||||||
|
return popup.innerHTML;
|
||||||
|
});
|
||||||
|
}
|
||||||
|
}
|
||||||
|
});
|
||||||
|
</script>
|
||||||
|
<nav class="page-navigation">
|
||||||
|
<div class="nav-page nav-page-previous">
|
||||||
|
<a href="./annexes.html" class="pagination-link">
|
||||||
|
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">5</span> <span class="chapter-title">Annexes</span></span>
|
||||||
|
</a>
|
||||||
|
</div>
|
||||||
|
<div class="nav-page nav-page-next">
|
||||||
|
</div>
|
||||||
|
</nav>
|
||||||
|
</div> <!-- /content -->
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
</body></html>
|
||||||
142
public/search.json
Normal file
142
public/search.json
Normal file
File diff suppressed because one or more lines are too long
1704
public/site_libs/bootstrap/bootstrap-icons.css
vendored
Normal file
1704
public/site_libs/bootstrap/bootstrap-icons.css
vendored
Normal file
File diff suppressed because it is too large
Load Diff
BIN
public/site_libs/bootstrap/bootstrap-icons.woff
Normal file
BIN
public/site_libs/bootstrap/bootstrap-icons.woff
Normal file
Binary file not shown.
10
public/site_libs/bootstrap/bootstrap.min.css
vendored
Normal file
10
public/site_libs/bootstrap/bootstrap.min.css
vendored
Normal file
File diff suppressed because one or more lines are too long
7
public/site_libs/bootstrap/bootstrap.min.js
vendored
Normal file
7
public/site_libs/bootstrap/bootstrap.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
7
public/site_libs/clipboard/clipboard.min.js
vendored
Normal file
7
public/site_libs/clipboard/clipboard.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
9
public/site_libs/quarto-html/anchor.min.js
vendored
Normal file
9
public/site_libs/quarto-html/anchor.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
6
public/site_libs/quarto-html/popper.min.js
vendored
Normal file
6
public/site_libs/quarto-html/popper.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
171
public/site_libs/quarto-html/quarto-syntax-highlighting.css
Normal file
171
public/site_libs/quarto-html/quarto-syntax-highlighting.css
Normal file
@ -0,0 +1,171 @@
|
|||||||
|
/* quarto syntax highlight colors */
|
||||||
|
:root {
|
||||||
|
--quarto-hl-ot-color: #003B4F;
|
||||||
|
--quarto-hl-at-color: #657422;
|
||||||
|
--quarto-hl-ss-color: #20794D;
|
||||||
|
--quarto-hl-an-color: #5E5E5E;
|
||||||
|
--quarto-hl-fu-color: #4758AB;
|
||||||
|
--quarto-hl-st-color: #20794D;
|
||||||
|
--quarto-hl-cf-color: #003B4F;
|
||||||
|
--quarto-hl-op-color: #5E5E5E;
|
||||||
|
--quarto-hl-er-color: #AD0000;
|
||||||
|
--quarto-hl-bn-color: #AD0000;
|
||||||
|
--quarto-hl-al-color: #AD0000;
|
||||||
|
--quarto-hl-va-color: #111111;
|
||||||
|
--quarto-hl-bu-color: inherit;
|
||||||
|
--quarto-hl-ex-color: inherit;
|
||||||
|
--quarto-hl-pp-color: #AD0000;
|
||||||
|
--quarto-hl-in-color: #5E5E5E;
|
||||||
|
--quarto-hl-vs-color: #20794D;
|
||||||
|
--quarto-hl-wa-color: #5E5E5E;
|
||||||
|
--quarto-hl-do-color: #5E5E5E;
|
||||||
|
--quarto-hl-im-color: #00769E;
|
||||||
|
--quarto-hl-ch-color: #20794D;
|
||||||
|
--quarto-hl-dt-color: #AD0000;
|
||||||
|
--quarto-hl-fl-color: #AD0000;
|
||||||
|
--quarto-hl-co-color: #5E5E5E;
|
||||||
|
--quarto-hl-cv-color: #5E5E5E;
|
||||||
|
--quarto-hl-cn-color: #8f5902;
|
||||||
|
--quarto-hl-sc-color: #5E5E5E;
|
||||||
|
--quarto-hl-dv-color: #AD0000;
|
||||||
|
--quarto-hl-kw-color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* other quarto variables */
|
||||||
|
:root {
|
||||||
|
--quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
|
||||||
|
}
|
||||||
|
|
||||||
|
pre > code.sourceCode > span {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
code.sourceCode > span {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
div.sourceCode,
|
||||||
|
div.sourceCode pre.sourceCode {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.ot {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.at {
|
||||||
|
color: #657422;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.ss {
|
||||||
|
color: #20794D;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.an {
|
||||||
|
color: #5E5E5E;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.fu {
|
||||||
|
color: #4758AB;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.st {
|
||||||
|
color: #20794D;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.cf {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.op {
|
||||||
|
color: #5E5E5E;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.er {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.bn {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.al {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.va {
|
||||||
|
color: #111111;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.pp {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.in {
|
||||||
|
color: #5E5E5E;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.vs {
|
||||||
|
color: #20794D;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.wa {
|
||||||
|
color: #5E5E5E;
|
||||||
|
font-style: italic;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.do {
|
||||||
|
color: #5E5E5E;
|
||||||
|
font-style: italic;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.im {
|
||||||
|
color: #00769E;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.ch {
|
||||||
|
color: #20794D;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.dt {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.fl {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.co {
|
||||||
|
color: #5E5E5E;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.cv {
|
||||||
|
color: #5E5E5E;
|
||||||
|
font-style: italic;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.cn {
|
||||||
|
color: #8f5902;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.sc {
|
||||||
|
color: #5E5E5E;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.dv {
|
||||||
|
color: #AD0000;
|
||||||
|
}
|
||||||
|
|
||||||
|
code span.kw {
|
||||||
|
color: #003B4F;
|
||||||
|
}
|
||||||
|
|
||||||
|
.prevent-inlining {
|
||||||
|
content: "</";
|
||||||
|
}
|
||||||
|
|
||||||
|
/*# sourceMappingURL=debc5d5d77c3f9108843748ff7464032.css.map */
|
||||||
770
public/site_libs/quarto-html/quarto.js
Normal file
770
public/site_libs/quarto-html/quarto.js
Normal file
@ -0,0 +1,770 @@
|
|||||||
|
const sectionChanged = new CustomEvent("quarto-sectionChanged", {
|
||||||
|
detail: {},
|
||||||
|
bubbles: true,
|
||||||
|
cancelable: false,
|
||||||
|
composed: false,
|
||||||
|
});
|
||||||
|
|
||||||
|
window.document.addEventListener("DOMContentLoaded", function (_event) {
|
||||||
|
const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
|
||||||
|
const sidebarEl = window.document.getElementById("quarto-sidebar");
|
||||||
|
const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
|
||||||
|
const marginSidebarEl = window.document.getElementById(
|
||||||
|
"quarto-margin-sidebar"
|
||||||
|
);
|
||||||
|
// function to determine whether the element has a previous sibling that is active
|
||||||
|
const prevSiblingIsActiveLink = (el) => {
|
||||||
|
const sibling = el.previousElementSibling;
|
||||||
|
if (sibling && sibling.tagName === "A") {
|
||||||
|
return sibling.classList.contains("active");
|
||||||
|
} else {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
// fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior)
|
||||||
|
function fireSlideEnter(e) {
|
||||||
|
const event = window.document.createEvent("Event");
|
||||||
|
event.initEvent("slideenter", true, true);
|
||||||
|
window.document.dispatchEvent(event);
|
||||||
|
}
|
||||||
|
const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
|
||||||
|
tabs.forEach((tab) => {
|
||||||
|
tab.addEventListener("shown.bs.tab", fireSlideEnter);
|
||||||
|
});
|
||||||
|
|
||||||
|
// fire slideEnter for tabby tab activations (for htmlwidget resize behavior)
|
||||||
|
document.addEventListener("tabby", fireSlideEnter, false);
|
||||||
|
|
||||||
|
// Track scrolling and mark TOC links as active
|
||||||
|
// get table of contents and sidebar (bail if we don't have at least one)
|
||||||
|
const tocLinks = tocEl
|
||||||
|
? [...tocEl.querySelectorAll("a[data-scroll-target]")]
|
||||||
|
: [];
|
||||||
|
const makeActive = (link) => tocLinks[link].classList.add("active");
|
||||||
|
const removeActive = (link) => tocLinks[link].classList.remove("active");
|
||||||
|
const removeAllActive = () =>
|
||||||
|
[...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
|
||||||
|
|
||||||
|
// activate the anchor for a section associated with this TOC entry
|
||||||
|
tocLinks.forEach((link) => {
|
||||||
|
link.addEventListener("click", () => {
|
||||||
|
if (link.href.indexOf("#") !== -1) {
|
||||||
|
const anchor = link.href.split("#")[1];
|
||||||
|
const heading = window.document.querySelector(
|
||||||
|
`[data-anchor-id=${anchor}]`
|
||||||
|
);
|
||||||
|
if (heading) {
|
||||||
|
// Add the class
|
||||||
|
heading.classList.add("reveal-anchorjs-link");
|
||||||
|
|
||||||
|
// function to show the anchor
|
||||||
|
const handleMouseout = () => {
|
||||||
|
heading.classList.remove("reveal-anchorjs-link");
|
||||||
|
heading.removeEventListener("mouseout", handleMouseout);
|
||||||
|
};
|
||||||
|
|
||||||
|
// add a function to clear the anchor when the user mouses out of it
|
||||||
|
heading.addEventListener("mouseout", handleMouseout);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
});
|
||||||
|
});
|
||||||
|
|
||||||
|
const sections = tocLinks.map((link) => {
|
||||||
|
const target = link.getAttribute("data-scroll-target");
|
||||||
|
if (target.startsWith("#")) {
|
||||||
|
return window.document.getElementById(decodeURI(`${target.slice(1)}`));
|
||||||
|
} else {
|
||||||
|
return window.document.querySelector(decodeURI(`${target}`));
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
const sectionMargin = 200;
|
||||||
|
let currentActive = 0;
|
||||||
|
// track whether we've initialized state the first time
|
||||||
|
let init = false;
|
||||||
|
|
||||||
|
const updateActiveLink = () => {
|
||||||
|
// The index from bottom to top (e.g. reversed list)
|
||||||
|
let sectionIndex = -1;
|
||||||
|
if (
|
||||||
|
window.innerHeight + window.pageYOffset >=
|
||||||
|
window.document.body.offsetHeight
|
||||||
|
) {
|
||||||
|
sectionIndex = 0;
|
||||||
|
} else {
|
||||||
|
sectionIndex = [...sections].reverse().findIndex((section) => {
|
||||||
|
if (section) {
|
||||||
|
return window.pageYOffset >= section.offsetTop - sectionMargin;
|
||||||
|
} else {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
if (sectionIndex > -1) {
|
||||||
|
const current = sections.length - sectionIndex - 1;
|
||||||
|
if (current !== currentActive) {
|
||||||
|
removeAllActive();
|
||||||
|
currentActive = current;
|
||||||
|
makeActive(current);
|
||||||
|
if (init) {
|
||||||
|
window.dispatchEvent(sectionChanged);
|
||||||
|
}
|
||||||
|
init = true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
const inHiddenRegion = (top, bottom, hiddenRegions) => {
|
||||||
|
for (const region of hiddenRegions) {
|
||||||
|
if (top <= region.bottom && bottom >= region.top) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return false;
|
||||||
|
};
|
||||||
|
|
||||||
|
const categorySelector = "header.quarto-title-block .quarto-category";
|
||||||
|
const activateCategories = (href) => {
|
||||||
|
// Find any categories
|
||||||
|
// Surround them with a link pointing back to:
|
||||||
|
// #category=Authoring
|
||||||
|
try {
|
||||||
|
const categoryEls = window.document.querySelectorAll(categorySelector);
|
||||||
|
for (const categoryEl of categoryEls) {
|
||||||
|
const categoryText = categoryEl.textContent;
|
||||||
|
if (categoryText) {
|
||||||
|
const link = `${href}#category=${encodeURIComponent(categoryText)}`;
|
||||||
|
const linkEl = window.document.createElement("a");
|
||||||
|
linkEl.setAttribute("href", link);
|
||||||
|
for (const child of categoryEl.childNodes) {
|
||||||
|
linkEl.append(child);
|
||||||
|
}
|
||||||
|
categoryEl.appendChild(linkEl);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} catch {
|
||||||
|
// Ignore errors
|
||||||
|
}
|
||||||
|
};
|
||||||
|
function hasTitleCategories() {
|
||||||
|
return window.document.querySelector(categorySelector) !== null;
|
||||||
|
}
|
||||||
|
|
||||||
|
function offsetRelativeUrl(url) {
|
||||||
|
const offset = getMeta("quarto:offset");
|
||||||
|
return offset ? offset + url : url;
|
||||||
|
}
|
||||||
|
|
||||||
|
function offsetAbsoluteUrl(url) {
|
||||||
|
const offset = getMeta("quarto:offset");
|
||||||
|
const baseUrl = new URL(offset, window.location);
|
||||||
|
|
||||||
|
const projRelativeUrl = url.replace(baseUrl, "");
|
||||||
|
if (projRelativeUrl.startsWith("/")) {
|
||||||
|
return projRelativeUrl;
|
||||||
|
} else {
|
||||||
|
return "/" + projRelativeUrl;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// read a meta tag value
|
||||||
|
function getMeta(metaName) {
|
||||||
|
const metas = window.document.getElementsByTagName("meta");
|
||||||
|
for (let i = 0; i < metas.length; i++) {
|
||||||
|
if (metas[i].getAttribute("name") === metaName) {
|
||||||
|
return metas[i].getAttribute("content");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return "";
|
||||||
|
}
|
||||||
|
|
||||||
|
async function findAndActivateCategories() {
|
||||||
|
const currentPagePath = offsetAbsoluteUrl(window.location.href);
|
||||||
|
const response = await fetch(offsetRelativeUrl("listings.json"));
|
||||||
|
if (response.status == 200) {
|
||||||
|
return response.json().then(function (listingPaths) {
|
||||||
|
const listingHrefs = [];
|
||||||
|
for (const listingPath of listingPaths) {
|
||||||
|
const pathWithoutLeadingSlash = listingPath.listing.substring(1);
|
||||||
|
for (const item of listingPath.items) {
|
||||||
|
if (
|
||||||
|
item === currentPagePath ||
|
||||||
|
item === currentPagePath + "index.html"
|
||||||
|
) {
|
||||||
|
// Resolve this path against the offset to be sure
|
||||||
|
// we already are using the correct path to the listing
|
||||||
|
// (this adjusts the listing urls to be rooted against
|
||||||
|
// whatever root the page is actually running against)
|
||||||
|
const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
|
||||||
|
const baseUrl = window.location;
|
||||||
|
const resolvedPath = new URL(relative, baseUrl);
|
||||||
|
listingHrefs.push(resolvedPath.pathname);
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// Look up the tree for a nearby linting and use that if we find one
|
||||||
|
const nearestListing = findNearestParentListing(
|
||||||
|
offsetAbsoluteUrl(window.location.pathname),
|
||||||
|
listingHrefs
|
||||||
|
);
|
||||||
|
if (nearestListing) {
|
||||||
|
activateCategories(nearestListing);
|
||||||
|
} else {
|
||||||
|
// See if the referrer is a listing page for this item
|
||||||
|
const referredRelativePath = offsetAbsoluteUrl(document.referrer);
|
||||||
|
const referrerListing = listingHrefs.find((listingHref) => {
|
||||||
|
const isListingReferrer =
|
||||||
|
listingHref === referredRelativePath ||
|
||||||
|
listingHref === referredRelativePath + "index.html";
|
||||||
|
return isListingReferrer;
|
||||||
|
});
|
||||||
|
|
||||||
|
if (referrerListing) {
|
||||||
|
// Try to use the referrer if possible
|
||||||
|
activateCategories(referrerListing);
|
||||||
|
} else if (listingHrefs.length > 0) {
|
||||||
|
// Otherwise, just fall back to the first listing
|
||||||
|
activateCategories(listingHrefs[0]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (hasTitleCategories()) {
|
||||||
|
findAndActivateCategories();
|
||||||
|
}
|
||||||
|
|
||||||
|
const findNearestParentListing = (href, listingHrefs) => {
|
||||||
|
if (!href || !listingHrefs) {
|
||||||
|
return undefined;
|
||||||
|
}
|
||||||
|
// Look up the tree for a nearby linting and use that if we find one
|
||||||
|
const relativeParts = href.substring(1).split("/");
|
||||||
|
while (relativeParts.length > 0) {
|
||||||
|
const path = relativeParts.join("/");
|
||||||
|
for (const listingHref of listingHrefs) {
|
||||||
|
if (listingHref.startsWith(path)) {
|
||||||
|
return listingHref;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
relativeParts.pop();
|
||||||
|
}
|
||||||
|
|
||||||
|
return undefined;
|
||||||
|
};
|
||||||
|
|
||||||
|
const manageSidebarVisiblity = (el, placeholderDescriptor) => {
|
||||||
|
let isVisible = true;
|
||||||
|
|
||||||
|
return (hiddenRegions) => {
|
||||||
|
if (el === null) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Find the last element of the TOC
|
||||||
|
const lastChildEl = el.lastElementChild;
|
||||||
|
|
||||||
|
if (lastChildEl) {
|
||||||
|
// Find the top and bottom o the element that is being managed
|
||||||
|
const elTop = el.offsetTop;
|
||||||
|
const elBottom =
|
||||||
|
elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
|
||||||
|
|
||||||
|
// Converts the sidebar to a menu
|
||||||
|
const convertToMenu = () => {
|
||||||
|
for (const child of el.children) {
|
||||||
|
child.style.opacity = 0;
|
||||||
|
child.style.overflow = "hidden";
|
||||||
|
}
|
||||||
|
|
||||||
|
const toggleContainer = window.document.createElement("div");
|
||||||
|
toggleContainer.style.width = "100%";
|
||||||
|
toggleContainer.classList.add("zindex-over-content");
|
||||||
|
toggleContainer.classList.add("quarto-sidebar-toggle");
|
||||||
|
toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
|
||||||
|
toggleContainer.id = placeholderDescriptor.id;
|
||||||
|
toggleContainer.style.position = "fixed";
|
||||||
|
|
||||||
|
const toggleIcon = window.document.createElement("i");
|
||||||
|
toggleIcon.classList.add("quarto-sidebar-toggle-icon");
|
||||||
|
toggleIcon.classList.add("bi");
|
||||||
|
toggleIcon.classList.add("bi-caret-down-fill");
|
||||||
|
|
||||||
|
const toggleTitle = window.document.createElement("div");
|
||||||
|
const titleEl = window.document.body.querySelector(
|
||||||
|
placeholderDescriptor.titleSelector
|
||||||
|
);
|
||||||
|
if (titleEl) {
|
||||||
|
toggleTitle.append(titleEl.innerText, toggleIcon);
|
||||||
|
}
|
||||||
|
toggleTitle.classList.add("zindex-over-content");
|
||||||
|
toggleTitle.classList.add("quarto-sidebar-toggle-title");
|
||||||
|
toggleContainer.append(toggleTitle);
|
||||||
|
|
||||||
|
const toggleContents = window.document.createElement("div");
|
||||||
|
toggleContents.classList = el.classList;
|
||||||
|
toggleContents.classList.add("zindex-over-content");
|
||||||
|
toggleContents.classList.add("quarto-sidebar-toggle-contents");
|
||||||
|
for (const child of el.children) {
|
||||||
|
if (child.id === "toc-title") {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
const clone = child.cloneNode(true);
|
||||||
|
clone.style.opacity = 1;
|
||||||
|
clone.style.display = null;
|
||||||
|
toggleContents.append(clone);
|
||||||
|
}
|
||||||
|
toggleContents.style.height = "0px";
|
||||||
|
toggleContainer.append(toggleContents);
|
||||||
|
el.parentElement.prepend(toggleContainer);
|
||||||
|
|
||||||
|
// Process clicks
|
||||||
|
let tocShowing = false;
|
||||||
|
// Allow the caller to control whether this is dismissed
|
||||||
|
// when it is clicked (e.g. sidebar navigation supports
|
||||||
|
// opening and closing the nav tree, so don't dismiss on click)
|
||||||
|
const clickEl = placeholderDescriptor.dismissOnClick
|
||||||
|
? toggleContainer
|
||||||
|
: toggleTitle;
|
||||||
|
|
||||||
|
const closeToggle = () => {
|
||||||
|
if (tocShowing) {
|
||||||
|
toggleContainer.classList.remove("expanded");
|
||||||
|
toggleContents.style.height = "0px";
|
||||||
|
tocShowing = false;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
const positionToggle = () => {
|
||||||
|
// position the element (top left of parent, same width as parent)
|
||||||
|
const elRect = el.getBoundingClientRect();
|
||||||
|
toggleContainer.style.left = `${elRect.left}px`;
|
||||||
|
toggleContainer.style.top = `${elRect.top}px`;
|
||||||
|
toggleContainer.style.width = `${elRect.width}px`;
|
||||||
|
};
|
||||||
|
|
||||||
|
// Get rid of any expanded toggle if the user scrolls
|
||||||
|
window.document.addEventListener(
|
||||||
|
"scroll",
|
||||||
|
throttle(() => {
|
||||||
|
closeToggle();
|
||||||
|
}, 50)
|
||||||
|
);
|
||||||
|
|
||||||
|
// Handle positioning of the toggle
|
||||||
|
window.addEventListener(
|
||||||
|
"resize",
|
||||||
|
throttle(() => {
|
||||||
|
positionToggle();
|
||||||
|
}, 50)
|
||||||
|
);
|
||||||
|
positionToggle();
|
||||||
|
|
||||||
|
// Process the click
|
||||||
|
clickEl.onclick = () => {
|
||||||
|
if (!tocShowing) {
|
||||||
|
toggleContainer.classList.add("expanded");
|
||||||
|
toggleContents.style.height = null;
|
||||||
|
tocShowing = true;
|
||||||
|
} else {
|
||||||
|
closeToggle();
|
||||||
|
}
|
||||||
|
};
|
||||||
|
};
|
||||||
|
|
||||||
|
// Converts a sidebar from a menu back to a sidebar
|
||||||
|
const convertToSidebar = () => {
|
||||||
|
for (const child of el.children) {
|
||||||
|
child.style.opacity = 1;
|
||||||
|
child.style.overflow = null;
|
||||||
|
}
|
||||||
|
|
||||||
|
const placeholderEl = window.document.getElementById(
|
||||||
|
placeholderDescriptor.id
|
||||||
|
);
|
||||||
|
if (placeholderEl) {
|
||||||
|
placeholderEl.remove();
|
||||||
|
}
|
||||||
|
|
||||||
|
el.classList.remove("rollup");
|
||||||
|
};
|
||||||
|
|
||||||
|
if (isReaderMode()) {
|
||||||
|
convertToMenu();
|
||||||
|
isVisible = false;
|
||||||
|
} else {
|
||||||
|
if (!isVisible) {
|
||||||
|
// If the element is current not visible reveal if there are
|
||||||
|
// no conflicts with overlay regions
|
||||||
|
if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
|
||||||
|
convertToSidebar();
|
||||||
|
isVisible = true;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
// If the element is visible, hide it if it conflicts with overlay regions
|
||||||
|
// and insert a placeholder toggle (or if we're in reader mode)
|
||||||
|
if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
|
||||||
|
convertToMenu();
|
||||||
|
isVisible = false;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
};
|
||||||
|
};
|
||||||
|
|
||||||
|
// Find any conflicting margin elements and add margins to the
|
||||||
|
// top to prevent overlap
|
||||||
|
const marginChildren = window.document.querySelectorAll(
|
||||||
|
".column-margin.column-container > * "
|
||||||
|
);
|
||||||
|
|
||||||
|
nexttick(() => {
|
||||||
|
let lastBottom = 0;
|
||||||
|
for (const marginChild of marginChildren) {
|
||||||
|
const top = marginChild.getBoundingClientRect().top + window.scrollY;
|
||||||
|
if (top < lastBottom) {
|
||||||
|
const margin = lastBottom - top;
|
||||||
|
marginChild.style.marginTop = `${margin}px`;
|
||||||
|
}
|
||||||
|
const styles = window.getComputedStyle(marginChild);
|
||||||
|
const marginTop = parseFloat(styles["marginTop"]);
|
||||||
|
|
||||||
|
lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
// Manage the visibility of the toc and the sidebar
|
||||||
|
const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
|
||||||
|
id: "quarto-toc-toggle",
|
||||||
|
titleSelector: "#toc-title",
|
||||||
|
dismissOnClick: true,
|
||||||
|
});
|
||||||
|
const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
|
||||||
|
id: "quarto-sidebarnav-toggle",
|
||||||
|
titleSelector: ".title",
|
||||||
|
dismissOnClick: false,
|
||||||
|
});
|
||||||
|
let tocLeftScrollVisibility;
|
||||||
|
if (leftTocEl) {
|
||||||
|
tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
|
||||||
|
id: "quarto-lefttoc-toggle",
|
||||||
|
titleSelector: "#toc-title",
|
||||||
|
dismissOnClick: true,
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
// Find the first element that uses formatting in special columns
|
||||||
|
const conflictingEls = window.document.body.querySelectorAll(
|
||||||
|
'[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
|
||||||
|
);
|
||||||
|
|
||||||
|
// Filter all the possibly conflicting elements into ones
|
||||||
|
// the do conflict on the left or ride side
|
||||||
|
const arrConflictingEls = Array.from(conflictingEls);
|
||||||
|
const leftSideConflictEls = arrConflictingEls.filter((el) => {
|
||||||
|
if (el.tagName === "ASIDE") {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
return Array.from(el.classList).find((className) => {
|
||||||
|
return (
|
||||||
|
className !== "column-body" &&
|
||||||
|
className.startsWith("column-") &&
|
||||||
|
!className.endsWith("right") &&
|
||||||
|
!className.endsWith("container") &&
|
||||||
|
className !== "column-margin"
|
||||||
|
);
|
||||||
|
});
|
||||||
|
});
|
||||||
|
const rightSideConflictEls = arrConflictingEls.filter((el) => {
|
||||||
|
if (el.tagName === "ASIDE") {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
const hasMarginCaption = Array.from(el.classList).find((className) => {
|
||||||
|
return className == "margin-caption";
|
||||||
|
});
|
||||||
|
if (hasMarginCaption) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
return Array.from(el.classList).find((className) => {
|
||||||
|
return (
|
||||||
|
className !== "column-body" &&
|
||||||
|
!className.endsWith("container") &&
|
||||||
|
className.startsWith("column-") &&
|
||||||
|
!className.endsWith("left")
|
||||||
|
);
|
||||||
|
});
|
||||||
|
});
|
||||||
|
|
||||||
|
const kOverlapPaddingSize = 10;
|
||||||
|
function toRegions(els) {
|
||||||
|
return els.map((el) => {
|
||||||
|
const top =
|
||||||
|
el.getBoundingClientRect().top +
|
||||||
|
document.documentElement.scrollTop -
|
||||||
|
kOverlapPaddingSize;
|
||||||
|
return {
|
||||||
|
top,
|
||||||
|
bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
|
||||||
|
};
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
const hideOverlappedSidebars = () => {
|
||||||
|
marginScrollVisibility(toRegions(rightSideConflictEls));
|
||||||
|
sidebarScrollVisiblity(toRegions(leftSideConflictEls));
|
||||||
|
if (tocLeftScrollVisibility) {
|
||||||
|
tocLeftScrollVisibility(toRegions(leftSideConflictEls));
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
window.quartoToggleReader = () => {
|
||||||
|
// Applies a slow class (or removes it)
|
||||||
|
// to update the transition speed
|
||||||
|
const slowTransition = (slow) => {
|
||||||
|
const manageTransition = (id, slow) => {
|
||||||
|
const el = document.getElementById(id);
|
||||||
|
if (el) {
|
||||||
|
if (slow) {
|
||||||
|
el.classList.add("slow");
|
||||||
|
} else {
|
||||||
|
el.classList.remove("slow");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
manageTransition("TOC", slow);
|
||||||
|
manageTransition("quarto-sidebar", slow);
|
||||||
|
};
|
||||||
|
|
||||||
|
const readerMode = !isReaderMode();
|
||||||
|
setReaderModeValue(readerMode);
|
||||||
|
|
||||||
|
// If we're entering reader mode, slow the transition
|
||||||
|
if (readerMode) {
|
||||||
|
slowTransition(readerMode);
|
||||||
|
}
|
||||||
|
highlightReaderToggle(readerMode);
|
||||||
|
hideOverlappedSidebars();
|
||||||
|
|
||||||
|
// If we're exiting reader mode, restore the non-slow transition
|
||||||
|
if (!readerMode) {
|
||||||
|
slowTransition(!readerMode);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
const highlightReaderToggle = (readerMode) => {
|
||||||
|
const els = document.querySelectorAll(".quarto-reader-toggle");
|
||||||
|
if (els) {
|
||||||
|
els.forEach((el) => {
|
||||||
|
if (readerMode) {
|
||||||
|
el.classList.add("reader");
|
||||||
|
} else {
|
||||||
|
el.classList.remove("reader");
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
const setReaderModeValue = (val) => {
|
||||||
|
if (window.location.protocol !== "file:") {
|
||||||
|
window.localStorage.setItem("quarto-reader-mode", val);
|
||||||
|
} else {
|
||||||
|
localReaderMode = val;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
const isReaderMode = () => {
|
||||||
|
if (window.location.protocol !== "file:") {
|
||||||
|
return window.localStorage.getItem("quarto-reader-mode") === "true";
|
||||||
|
} else {
|
||||||
|
return localReaderMode;
|
||||||
|
}
|
||||||
|
};
|
||||||
|
let localReaderMode = null;
|
||||||
|
|
||||||
|
// Walk the TOC and collapse/expand nodes
|
||||||
|
// Nodes are expanded if:
|
||||||
|
// - they are top level
|
||||||
|
// - they have children that are 'active' links
|
||||||
|
// - they are directly below an link that is 'active'
|
||||||
|
const walk = (el, depth) => {
|
||||||
|
// Tick depth when we enter a UL
|
||||||
|
if (el.tagName === "UL") {
|
||||||
|
depth = depth + 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// It this is active link
|
||||||
|
let isActiveNode = false;
|
||||||
|
if (el.tagName === "A" && el.classList.contains("active")) {
|
||||||
|
isActiveNode = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
// See if there is an active child to this element
|
||||||
|
let hasActiveChild = false;
|
||||||
|
for (child of el.children) {
|
||||||
|
hasActiveChild = walk(child, depth) || hasActiveChild;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Process the collapse state if this is an UL
|
||||||
|
if (el.tagName === "UL") {
|
||||||
|
if (depth === 1 || hasActiveChild || prevSiblingIsActiveLink(el)) {
|
||||||
|
el.classList.remove("collapse");
|
||||||
|
} else {
|
||||||
|
el.classList.add("collapse");
|
||||||
|
}
|
||||||
|
|
||||||
|
// untick depth when we leave a UL
|
||||||
|
depth = depth - 1;
|
||||||
|
}
|
||||||
|
return hasActiveChild || isActiveNode;
|
||||||
|
};
|
||||||
|
|
||||||
|
// walk the TOC and expand / collapse any items that should be shown
|
||||||
|
|
||||||
|
if (tocEl) {
|
||||||
|
walk(tocEl, 0);
|
||||||
|
updateActiveLink();
|
||||||
|
}
|
||||||
|
|
||||||
|
// Throttle the scroll event and walk peridiocally
|
||||||
|
window.document.addEventListener(
|
||||||
|
"scroll",
|
||||||
|
throttle(() => {
|
||||||
|
if (tocEl) {
|
||||||
|
updateActiveLink();
|
||||||
|
walk(tocEl, 0);
|
||||||
|
}
|
||||||
|
if (!isReaderMode()) {
|
||||||
|
hideOverlappedSidebars();
|
||||||
|
}
|
||||||
|
}, 5)
|
||||||
|
);
|
||||||
|
window.addEventListener(
|
||||||
|
"resize",
|
||||||
|
throttle(() => {
|
||||||
|
if (!isReaderMode()) {
|
||||||
|
hideOverlappedSidebars();
|
||||||
|
}
|
||||||
|
}, 10)
|
||||||
|
);
|
||||||
|
hideOverlappedSidebars();
|
||||||
|
highlightReaderToggle(isReaderMode());
|
||||||
|
});
|
||||||
|
|
||||||
|
// grouped tabsets
|
||||||
|
window.addEventListener("pageshow", (_event) => {
|
||||||
|
function getTabSettings() {
|
||||||
|
const data = localStorage.getItem("quarto-persistent-tabsets-data");
|
||||||
|
if (!data) {
|
||||||
|
localStorage.setItem("quarto-persistent-tabsets-data", "{}");
|
||||||
|
return {};
|
||||||
|
}
|
||||||
|
if (data) {
|
||||||
|
return JSON.parse(data);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
function setTabSettings(data) {
|
||||||
|
localStorage.setItem(
|
||||||
|
"quarto-persistent-tabsets-data",
|
||||||
|
JSON.stringify(data)
|
||||||
|
);
|
||||||
|
}
|
||||||
|
|
||||||
|
function setTabState(groupName, groupValue) {
|
||||||
|
const data = getTabSettings();
|
||||||
|
data[groupName] = groupValue;
|
||||||
|
setTabSettings(data);
|
||||||
|
}
|
||||||
|
|
||||||
|
function toggleTab(tab, active) {
|
||||||
|
const tabPanelId = tab.getAttribute("aria-controls");
|
||||||
|
const tabPanel = document.getElementById(tabPanelId);
|
||||||
|
if (active) {
|
||||||
|
tab.classList.add("active");
|
||||||
|
tabPanel.classList.add("active");
|
||||||
|
} else {
|
||||||
|
tab.classList.remove("active");
|
||||||
|
tabPanel.classList.remove("active");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
function toggleAll(selectedGroup, selectorsToSync) {
|
||||||
|
for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
|
||||||
|
const active = selectedGroup === thisGroup;
|
||||||
|
for (const tab of tabs) {
|
||||||
|
toggleTab(tab, active);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
function findSelectorsToSyncByLanguage() {
|
||||||
|
const result = {};
|
||||||
|
const tabs = Array.from(
|
||||||
|
document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
|
||||||
|
);
|
||||||
|
for (const item of tabs) {
|
||||||
|
const div = item.parentElement.parentElement.parentElement;
|
||||||
|
const group = div.getAttribute("data-group");
|
||||||
|
if (!result[group]) {
|
||||||
|
result[group] = {};
|
||||||
|
}
|
||||||
|
const selectorsToSync = result[group];
|
||||||
|
const value = item.innerHTML;
|
||||||
|
if (!selectorsToSync[value]) {
|
||||||
|
selectorsToSync[value] = [];
|
||||||
|
}
|
||||||
|
selectorsToSync[value].push(item);
|
||||||
|
}
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
function setupSelectorSync() {
|
||||||
|
const selectorsToSync = findSelectorsToSyncByLanguage();
|
||||||
|
Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
|
||||||
|
Object.entries(tabSetsByValue).forEach(([value, items]) => {
|
||||||
|
items.forEach((item) => {
|
||||||
|
item.addEventListener("click", (_event) => {
|
||||||
|
setTabState(group, value);
|
||||||
|
toggleAll(value, selectorsToSync[group]);
|
||||||
|
});
|
||||||
|
});
|
||||||
|
});
|
||||||
|
});
|
||||||
|
return selectorsToSync;
|
||||||
|
}
|
||||||
|
|
||||||
|
const selectorsToSync = setupSelectorSync();
|
||||||
|
for (const [group, selectedName] of Object.entries(getTabSettings())) {
|
||||||
|
const selectors = selectorsToSync[group];
|
||||||
|
// it's possible that stale state gives us empty selections, so we explicitly check here.
|
||||||
|
if (selectors) {
|
||||||
|
toggleAll(selectedName, selectors);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
function throttle(func, wait) {
|
||||||
|
let waiting = false;
|
||||||
|
return function () {
|
||||||
|
if (!waiting) {
|
||||||
|
func.apply(this, arguments);
|
||||||
|
waiting = true;
|
||||||
|
setTimeout(function () {
|
||||||
|
waiting = false;
|
||||||
|
}, wait);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
function nexttick(func) {
|
||||||
|
return setTimeout(func, 0);
|
||||||
|
}
|
||||||
1
public/site_libs/quarto-html/tippy.css
Normal file
1
public/site_libs/quarto-html/tippy.css
Normal file
@ -0,0 +1 @@
|
|||||||
|
.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
|
||||||
2
public/site_libs/quarto-html/tippy.umd.min.js
vendored
Normal file
2
public/site_libs/quarto-html/tippy.umd.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
7
public/site_libs/quarto-nav/headroom.min.js
vendored
Normal file
7
public/site_libs/quarto-nav/headroom.min.js
vendored
Normal file
@ -0,0 +1,7 @@
|
|||||||
|
/*!
|
||||||
|
* headroom.js v0.12.0 - Give your page some headroom. Hide your header until you need it
|
||||||
|
* Copyright (c) 2020 Nick Williams - http://wicky.nillia.ms/headroom.js
|
||||||
|
* License: MIT
|
||||||
|
*/
|
||||||
|
|
||||||
|
!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?module.exports=n():"function"==typeof define&&define.amd?define(n):(t=t||self).Headroom=n()}(this,function(){"use strict";function t(){return"undefined"!=typeof window}function d(t){return function(t){return t&&t.document&&function(t){return 9===t.nodeType}(t.document)}(t)?function(t){var n=t.document,o=n.body,s=n.documentElement;return{scrollHeight:function(){return Math.max(o.scrollHeight,s.scrollHeight,o.offsetHeight,s.offsetHeight,o.clientHeight,s.clientHeight)},height:function(){return t.innerHeight||s.clientHeight||o.clientHeight},scrollY:function(){return void 0!==t.pageYOffset?t.pageYOffset:(s||o.parentNode||o).scrollTop}}}(t):function(t){return{scrollHeight:function(){return Math.max(t.scrollHeight,t.offsetHeight,t.clientHeight)},height:function(){return Math.max(t.offsetHeight,t.clientHeight)},scrollY:function(){return t.scrollTop}}}(t)}function n(t,s,e){var n,o=function(){var n=!1;try{var t={get passive(){n=!0}};window.addEventListener("test",t,t),window.removeEventListener("test",t,t)}catch(t){n=!1}return n}(),i=!1,r=d(t),l=r.scrollY(),a={};function c(){var t=Math.round(r.scrollY()),n=r.height(),o=r.scrollHeight();a.scrollY=t,a.lastScrollY=l,a.direction=l<t?"down":"up",a.distance=Math.abs(t-l),a.isOutOfBounds=t<0||o<t+n,a.top=t<=s.offset[a.direction],a.bottom=o<=t+n,a.toleranceExceeded=a.distance>s.tolerance[a.direction],e(a),l=t,i=!1}function h(){i||(i=!0,n=requestAnimationFrame(c))}var u=!!o&&{passive:!0,capture:!1};return t.addEventListener("scroll",h,u),c(),{destroy:function(){cancelAnimationFrame(n),t.removeEventListener("scroll",h,u)}}}function o(t){return t===Object(t)?t:{down:t,up:t}}function s(t,n){n=n||{},Object.assign(this,s.options,n),this.classes=Object.assign({},s.options.classes,n.classes),this.elem=t,this.tolerance=o(this.tolerance),this.offset=o(this.offset),this.initialised=!1,this.frozen=!1}return s.prototype={constructor:s,init:function(){return s.cutsTheMustard&&!this.initialised&&(this.addClass("initial"),this.initialised=!0,setTimeout(function(t){t.scrollTracker=n(t.scroller,{offset:t.offset,tolerance:t.tolerance},t.update.bind(t))},100,this)),this},destroy:function(){this.initialised=!1,Object.keys(this.classes).forEach(this.removeClass,this),this.scrollTracker.destroy()},unpin:function(){!this.hasClass("pinned")&&this.hasClass("unpinned")||(this.addClass("unpinned"),this.removeClass("pinned"),this.onUnpin&&this.onUnpin.call(this))},pin:function(){this.hasClass("unpinned")&&(this.addClass("pinned"),this.removeClass("unpinned"),this.onPin&&this.onPin.call(this))},freeze:function(){this.frozen=!0,this.addClass("frozen")},unfreeze:function(){this.frozen=!1,this.removeClass("frozen")},top:function(){this.hasClass("top")||(this.addClass("top"),this.removeClass("notTop"),this.onTop&&this.onTop.call(this))},notTop:function(){this.hasClass("notTop")||(this.addClass("notTop"),this.removeClass("top"),this.onNotTop&&this.onNotTop.call(this))},bottom:function(){this.hasClass("bottom")||(this.addClass("bottom"),this.removeClass("notBottom"),this.onBottom&&this.onBottom.call(this))},notBottom:function(){this.hasClass("notBottom")||(this.addClass("notBottom"),this.removeClass("bottom"),this.onNotBottom&&this.onNotBottom.call(this))},shouldUnpin:function(t){return"down"===t.direction&&!t.top&&t.toleranceExceeded},shouldPin:function(t){return"up"===t.direction&&t.toleranceExceeded||t.top},addClass:function(t){this.elem.classList.add.apply(this.elem.classList,this.classes[t].split(" "))},removeClass:function(t){this.elem.classList.remove.apply(this.elem.classList,this.classes[t].split(" "))},hasClass:function(t){return this.classes[t].split(" ").every(function(t){return this.classList.contains(t)},this.elem)},update:function(t){t.isOutOfBounds||!0!==this.frozen&&(t.top?this.top():this.notTop(),t.bottom?this.bottom():this.notBottom(),this.shouldUnpin(t)?this.unpin():this.shouldPin(t)&&this.pin())}},s.options={tolerance:{up:0,down:0},offset:0,scroller:t()?window:null,classes:{frozen:"headroom--frozen",pinned:"headroom--pinned",unpinned:"headroom--unpinned",top:"headroom--top",notTop:"headroom--not-top",bottom:"headroom--bottom",notBottom:"headroom--not-bottom",initial:"headroom"}},s.cutsTheMustard=!!(t()&&function(){}.bind&&"classList"in document.documentElement&&Object.assign&&Object.keys&&requestAnimationFrame),s});
|
||||||
221
public/site_libs/quarto-nav/quarto-nav.js
Normal file
221
public/site_libs/quarto-nav/quarto-nav.js
Normal file
@ -0,0 +1,221 @@
|
|||||||
|
const headroomChanged = new CustomEvent("quarto-hrChanged", {
|
||||||
|
detail: {},
|
||||||
|
bubbles: true,
|
||||||
|
cancelable: false,
|
||||||
|
composed: false,
|
||||||
|
});
|
||||||
|
|
||||||
|
window.document.addEventListener("DOMContentLoaded", function () {
|
||||||
|
let init = false;
|
||||||
|
|
||||||
|
function throttle(func, wait) {
|
||||||
|
var timeout;
|
||||||
|
return function () {
|
||||||
|
const context = this;
|
||||||
|
const args = arguments;
|
||||||
|
const later = function () {
|
||||||
|
clearTimeout(timeout);
|
||||||
|
timeout = null;
|
||||||
|
func.apply(context, args);
|
||||||
|
};
|
||||||
|
|
||||||
|
if (!timeout) {
|
||||||
|
timeout = setTimeout(later, wait);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
function headerOffset() {
|
||||||
|
// Set an offset if there is are fixed top navbar
|
||||||
|
const headerEl = window.document.querySelector("header.fixed-top");
|
||||||
|
if (headerEl) {
|
||||||
|
return headerEl.clientHeight;
|
||||||
|
} else {
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
function footerOffset() {
|
||||||
|
const footerEl = window.document.querySelector("footer.footer");
|
||||||
|
if (footerEl) {
|
||||||
|
return footerEl.clientHeight;
|
||||||
|
} else {
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
function updateDocumentOffsetWithoutAnimation() {
|
||||||
|
updateDocumentOffset(false);
|
||||||
|
}
|
||||||
|
|
||||||
|
function updateDocumentOffset(animated) {
|
||||||
|
// set body offset
|
||||||
|
const topOffset = headerOffset();
|
||||||
|
const bodyOffset = topOffset + footerOffset();
|
||||||
|
const bodyEl = window.document.body;
|
||||||
|
bodyEl.setAttribute("data-bs-offset", topOffset);
|
||||||
|
bodyEl.style.paddingTop = topOffset + "px";
|
||||||
|
|
||||||
|
// deal with sidebar offsets
|
||||||
|
const sidebars = window.document.querySelectorAll(
|
||||||
|
".sidebar, .headroom-target"
|
||||||
|
);
|
||||||
|
sidebars.forEach((sidebar) => {
|
||||||
|
if (!animated) {
|
||||||
|
sidebar.classList.add("notransition");
|
||||||
|
// Remove the no transition class after the animation has time to complete
|
||||||
|
setTimeout(function () {
|
||||||
|
sidebar.classList.remove("notransition");
|
||||||
|
}, 201);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (window.Headroom && sidebar.classList.contains("sidebar-unpinned")) {
|
||||||
|
sidebar.style.top = "0";
|
||||||
|
sidebar.style.maxHeight = "100vh";
|
||||||
|
} else {
|
||||||
|
sidebar.style.top = topOffset + "px";
|
||||||
|
sidebar.style.maxHeight = "calc(100vh - " + topOffset + "px)";
|
||||||
|
}
|
||||||
|
});
|
||||||
|
|
||||||
|
// allow space for footer
|
||||||
|
const mainContainer = window.document.querySelector(".quarto-container");
|
||||||
|
if (mainContainer) {
|
||||||
|
mainContainer.style.minHeight = "calc(100vh - " + bodyOffset + "px)";
|
||||||
|
}
|
||||||
|
|
||||||
|
// link offset
|
||||||
|
let linkStyle = window.document.querySelector("#quarto-target-style");
|
||||||
|
if (!linkStyle) {
|
||||||
|
linkStyle = window.document.createElement("style");
|
||||||
|
window.document.head.appendChild(linkStyle);
|
||||||
|
}
|
||||||
|
while (linkStyle.firstChild) {
|
||||||
|
linkStyle.removeChild(linkStyle.firstChild);
|
||||||
|
}
|
||||||
|
if (topOffset > 0) {
|
||||||
|
linkStyle.appendChild(
|
||||||
|
window.document.createTextNode(`
|
||||||
|
section:target::before {
|
||||||
|
content: "";
|
||||||
|
display: block;
|
||||||
|
height: ${topOffset}px;
|
||||||
|
margin: -${topOffset}px 0 0;
|
||||||
|
}`)
|
||||||
|
);
|
||||||
|
}
|
||||||
|
if (init) {
|
||||||
|
window.dispatchEvent(headroomChanged);
|
||||||
|
}
|
||||||
|
init = true;
|
||||||
|
}
|
||||||
|
|
||||||
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<script src="site_libs/quarto-nav/quarto-nav.js"></script>
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<script src="site_libs/quarto-search/quarto-search.js"></script>
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|
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|
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|
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<div id="quarto-search-results"></div>
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<header id="quarto-header" class="headroom fixed-top">
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|
||||||
|
<div class="container-fluid d-flex justify-content-between">
|
||||||
|
<h1 class="quarto-secondary-nav-title"><span class="chapter-number">2</span> <span class="chapter-title">OBITools V4 Tutorial</span></h1>
|
||||||
|
<button type="button" class="quarto-btn-toggle btn" aria-label="Show secondary navigation">
|
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|
||||||
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<nav id="quarto-sidebar" class="sidebar collapse sidebar-navigation floating overflow-auto">
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|
<div class="pt-lg-2 mt-2 text-left sidebar-header">
|
||||||
|
<div class="sidebar-title mb-0 py-0">
|
||||||
|
<a href="./">OBITools V4</a>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
<div class="mt-2 flex-shrink-0 align-items-center">
|
||||||
|
<div class="sidebar-search">
|
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|
<div id="quarto-search" class="" title="Search"></div>
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|
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|
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|
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|
<div class="sidebar-menu-container">
|
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|
<ul class="list-unstyled mt-1">
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./index.html" class="sidebar-item-text sidebar-link">Preface</a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./intro.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./tutorial.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">2</span> <span class="chapter-title">OBITools V4 Tutorial</span></a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./library.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./annexes.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Annexes</span></a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
<li class="sidebar-item">
|
||||||
|
<div class="sidebar-item-container">
|
||||||
|
<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
|
||||||
|
</div>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</div>
|
||||||
|
</nav>
|
||||||
|
<!-- margin-sidebar -->
|
||||||
|
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
|
||||||
|
<nav id="TOC" role="doc-toc" class="toc-active">
|
||||||
|
<h2 id="toc-title">Table of contents</h2>
|
||||||
|
|
||||||
|
<ul>
|
||||||
|
<li><a href="#wolves-diet-based-on-dna-metabarcoding" id="toc-wolves-diet-based-on-dna-metabarcoding" class="nav-link active" data-scroll-target="#wolves-diet-based-on-dna-metabarcoding"><span class="toc-section-number">2.1</span> Wolves’ diet based on DNA metabarcoding</a></li>
|
||||||
|
<li><a href="#step-by-step-analysis" id="toc-step-by-step-analysis" class="nav-link" data-scroll-target="#step-by-step-analysis"><span class="toc-section-number">2.2</span> Step by step analysis</a>
|
||||||
|
<ul class="collapse">
|
||||||
|
<li><a href="#recover-full-sequence-reads-from-forward-and-reverse-partial-reads" id="toc-recover-full-sequence-reads-from-forward-and-reverse-partial-reads" class="nav-link" data-scroll-target="#recover-full-sequence-reads-from-forward-and-reverse-partial-reads"><span class="toc-section-number">2.2.1</span> Recover full sequence reads from forward and reverse partial reads</a></li>
|
||||||
|
<li><a href="#remove-unaligned-sequence-records" id="toc-remove-unaligned-sequence-records" class="nav-link" data-scroll-target="#remove-unaligned-sequence-records"><span class="toc-section-number">2.2.2</span> Remove unaligned sequence records</a></li>
|
||||||
|
<li><a href="#assign-each-sequence-record-to-the-corresponding-samplemarker-combination" id="toc-assign-each-sequence-record-to-the-corresponding-samplemarker-combination" class="nav-link" data-scroll-target="#assign-each-sequence-record-to-the-corresponding-samplemarker-combination"><span class="toc-section-number">2.2.3</span> Assign each sequence record to the corresponding sample/marker combination</a></li>
|
||||||
|
<li><a href="#dereplicate-reads-into-uniq-sequences" id="toc-dereplicate-reads-into-uniq-sequences" class="nav-link" data-scroll-target="#dereplicate-reads-into-uniq-sequences"><span class="toc-section-number">2.2.4</span> Dereplicate reads into uniq sequences</a></li>
|
||||||
|
<li><a href="#denoise-the-sequence-dataset" id="toc-denoise-the-sequence-dataset" class="nav-link" data-scroll-target="#denoise-the-sequence-dataset"><span class="toc-section-number">2.2.5</span> Denoise the sequence dataset</a></li>
|
||||||
|
<li><a href="#taxonomic-assignment-of-sequences" id="toc-taxonomic-assignment-of-sequences" class="nav-link" data-scroll-target="#taxonomic-assignment-of-sequences"><span class="toc-section-number">2.2.6</span> Taxonomic assignment of sequences</a></li>
|
||||||
|
<li><a href="#assign-each-sequence-to-a-taxon" id="toc-assign-each-sequence-to-a-taxon" class="nav-link" data-scroll-target="#assign-each-sequence-to-a-taxon"><span class="toc-section-number">2.2.7</span> Assign each sequence to a taxon</a></li>
|
||||||
|
<li><a href="#generate-the-final-result-table" id="toc-generate-the-final-result-table" class="nav-link" data-scroll-target="#generate-the-final-result-table"><span class="toc-section-number">2.2.8</span> Generate the final result table</a></li>
|
||||||
|
<li><a href="#looking-at-the-data-in-r" id="toc-looking-at-the-data-in-r" class="nav-link" data-scroll-target="#looking-at-the-data-in-r"><span class="toc-section-number">2.2.9</span> Looking at the data in R</a></li>
|
||||||
|
</ul></li>
|
||||||
|
</ul>
|
||||||
|
</nav>
|
||||||
|
</div>
|
||||||
|
<!-- main -->
|
||||||
|
<main class="content" id="quarto-document-content">
|
||||||
|
|
||||||
|
<header id="title-block-header" class="quarto-title-block default">
|
||||||
|
<div class="quarto-title">
|
||||||
|
<h1 class="title d-none d-lg-block"><span class="chapter-number">2</span> <span class="chapter-title">OBITools V4 Tutorial</span></h1>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<div class="quarto-title-meta">
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
</div>
|
||||||
|
|
||||||
|
|
||||||
|
</header>
|
||||||
|
|
||||||
|
<p>Here is a short tutorial on how to analyze DNA metabarcoding data produced on Illumina sequencers using:</p>
|
||||||
|
<ul>
|
||||||
|
<li>the OBITools</li>
|
||||||
|
<li>some basic Unix commands</li>
|
||||||
|
</ul>
|
||||||
|
<section id="wolves-diet-based-on-dna-metabarcoding" class="level2" data-number="2.1">
|
||||||
|
<h2 data-number="2.1" class="anchored" data-anchor-id="wolves-diet-based-on-dna-metabarcoding"><span class="header-section-number">2.1</span> Wolves’ diet based on DNA metabarcoding</h2>
|
||||||
|
<p>The data used in this tutorial correspond to the analysis of four wolf scats, using the protocol published in <span class="citation" data-cites="Shehzad2012-pn">Shehzad et al. (<a href="references.html#ref-Shehzad2012-pn" role="doc-biblioref">2012</a>)</span> for assessing carnivore diet. After extracting DNA from the faeces, the DNA amplifications were carried out using the primers <code>TTAGATACCCCACTATGC</code> and <code>TAGAACAGGCTCCTCTAG</code> amplifiying the <em>12S-V5</em> region <span class="citation" data-cites="Riaz2011-gn">(<a href="references.html#ref-Riaz2011-gn" role="doc-biblioref">Riaz et al. 2011</a>)</span>, together with a wolf blocking oligonucleotide.</p>
|
||||||
|
<p>The complete data set can be downloaded here: <a href="wolf_diet.tgz">the tutorial dataset</a></p>
|
||||||
|
<p>Once the data file is downloaded, using a UNIX terminal unarchive the data from the <code>tgz</code> file.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" 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="fu">tar</span> zxvf wolf_diet.tgz</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>That command create a new directory named <code>wolf_data</code> containing every required data files:</p>
|
||||||
|
<ul>
|
||||||
|
<li><p><code>fastq <fastq></code> files resulting of aGA IIx (Illumina) paired-end (2 x 108 bp) sequencing assay of DNA extracted and amplified from four wolf faeces:</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>wolf_F.fastq</code></li>
|
||||||
|
<li><code>wolf_R.fastq</code></li>
|
||||||
|
</ul></li>
|
||||||
|
<li><p>the file describing the primers and tags used for all samples sequenced:</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>wolf_diet_ngsfilter.txt</code> The tags correspond to short and specific sequences added on the 5' end of each primer to distinguish the different samples</li>
|
||||||
|
</ul></li>
|
||||||
|
<li><p>the file containing the reference database in a fasta format:</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>db_v05_r117.fasta</code> This reference database has been extracted from the release 117 of EMBL using <code>obipcr</code></li>
|
||||||
|
</ul></li>
|
||||||
|
</ul>
|
||||||
|
<div class="cell">
|
||||||
|
|
||||||
|
</div>
|
||||||
|
<p>To not mix raw data and processed data a new directory called <code>results</code> is created.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" 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="fu">mkdir</span> results</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
<section id="step-by-step-analysis" class="level2" data-number="2.2">
|
||||||
|
<h2 data-number="2.2" class="anchored" data-anchor-id="step-by-step-analysis"><span class="header-section-number">2.2</span> Step by step analysis</h2>
|
||||||
|
<section id="recover-full-sequence-reads-from-forward-and-reverse-partial-reads" class="level3" data-number="2.2.1">
|
||||||
|
<h3 data-number="2.2.1" class="anchored" data-anchor-id="recover-full-sequence-reads-from-forward-and-reverse-partial-reads"><span class="header-section-number">2.2.1</span> Recover full sequence reads from forward and reverse partial reads</h3>
|
||||||
|
<p>When using the result of a paired-end sequencing assay with supposedly overlapping forward and reverse reads, the first step is to recover the assembled sequence.</p>
|
||||||
|
<p>The forward and reverse reads of the same fragment are <em>at the same line position</em> in the two fastq files obtained after sequencing. Based on these two files, the assembly of the forward and reverse reads is done with the <code>obipairing</code> utility that aligns the two reads and returns the reconstructed sequence.</p>
|
||||||
|
<p>In our case, the command is:</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" 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">obipairing</span> <span class="at">--min-identity</span><span class="op">=</span>0.8 <span class="dt">\</span></span>
|
||||||
|
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="at">--min-overlap</span><span class="op">=</span>10 <span class="dt">\</span></span>
|
||||||
|
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> <span class="at">-F</span> wolf_data/wolf_F.fastq <span class="dt">\</span></span>
|
||||||
|
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a> <span class="at">-R</span> wolf_data/wolf_R.fastq <span class="dt">\</span></span>
|
||||||
|
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.fastq </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The <code>--min-identity</code> and <code>--min-overlap</code> options allow discarding sequences with low alignment quality. If after the aligment, the overlaping parts of the reads is shorter than 10 base pairs or the similarity over this aligned region is below 80% of identity, in the output file, the forward and reverse reads are not aligned but concatenated, and the value of the <code>mode</code> attribute in the sequence header is set to <code>joined</code> instead of <code>alignment</code>.</p>
|
||||||
|
</section>
|
||||||
|
<section id="remove-unaligned-sequence-records" class="level3" data-number="2.2.2">
|
||||||
|
<h3 data-number="2.2.2" class="anchored" data-anchor-id="remove-unaligned-sequence-records"><span class="header-section-number">2.2.2</span> Remove unaligned sequence records</h3>
|
||||||
|
<p>Unaligned sequences (:py<code class="interpreted-text" role="mod">mode=joined</code>) cannot be used. The following command allows removing them from the dataset:</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" 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">-p</span> <span class="st">'annotations.mode != "join"'</span> <span class="dt">\</span></span>
|
||||||
|
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> results/wolf.fastq <span class="op">></span> results/wolf.ali.fastq</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The <code>-p</code> requires a go like expression. <code>annotations.mode != "join"</code> means that if the value of the <code>mode</code> annotation of a sequence is different from <code>join</code>, the corresponding sequence record will be kept.</p>
|
||||||
|
<p>The first sequence record of <code>wolf.ali.fastq</code> can be obtained using the following command line:</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">head</span> <span class="at">-n</span> 4 results/wolf.ali.fastq</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The folling piece of code appears on thew window of tour terminal.</p>
|
||||||
|
<pre><code>@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":62,"(T:34)->(G:18)":48},"score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46}
|
||||||
|
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
||||||
|
+
|
||||||
|
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC</code></pre>
|
||||||
|
</section>
|
||||||
|
<section id="assign-each-sequence-record-to-the-corresponding-samplemarker-combination" class="level3" data-number="2.2.3">
|
||||||
|
<h3 data-number="2.2.3" class="anchored" data-anchor-id="assign-each-sequence-record-to-the-corresponding-samplemarker-combination"><span class="header-section-number">2.2.3</span> Assign each sequence record to the corresponding sample/marker combination</h3>
|
||||||
|
<p>Each sequence record is assigned to its corresponding sample and marker using the data provided in a text file (here <code>wolf_diet_ngsfilter.txt</code>). This text file contains one line per sample, with the name of the experiment (several experiments can be included in the same file), the name of the tags (for example: <code>aattaac</code> if the same tag has been used on each extremity of the PCR products, or <code>aattaac:gaagtag</code> if the tags were different), the sequence of the forward primer, the sequence of the reverse primer, the letter <code>T</code> or <code>F</code> for sample identification using the forward primer and tag only or using both primers and both tags, respectively (see <code>obimultiplex</code> for details).</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obimultiplex</span> <span class="at">-t</span> wolf_data/wolf_diet_ngsfilter.txt <span class="dt">\</span></span>
|
||||||
|
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="at">-u</span> results/unidentified.fastq <span class="dt">\</span></span>
|
||||||
|
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> results/wolf.ali.fastq <span class="dt">\</span></span>
|
||||||
|
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.fastq</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>This command creates two files:</p>
|
||||||
|
<ul>
|
||||||
|
<li><code>unidentified.fastq</code> containing all the sequence records that were not assigned to a sample/marker combination</li>
|
||||||
|
<li><code>wolf.ali.assigned.fastq</code> containing all the sequence records that were properly assigned to a sample/marker combination</li>
|
||||||
|
</ul>
|
||||||
|
<p>Note that each sequence record of the <code>wolf.ali.assigned.fastq</code> file contains only the barcode sequence as the sequences of primers and tags are removed by the <code>obimultiplex</code> program. Information concerning the experiment, sample, primers and tags is added as attributes in the sequence header.</p>
|
||||||
|
<p>For instance, the first sequence record of <code>wolf.ali.assigned.fastq</code> is:</p>
|
||||||
|
<pre><code>@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1_sub[28..127] {"ali_dir":"left","ali_length":62,"direction":"direct","experiment":"wolf_diet","forward_match":"ttagataccccactatgc","forward_mismatches":0,"forward_primer":"ttagataccccactatgc","forward_tag":"gcctcct","mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":35,"(T:34)->(G:18)":21},"reverse_match":"tagaacaggctcctctag","reverse_mismatches":0,"reverse_primer":"tagaacaggctcctctag","reverse_tag":"gcctcct","sample":"29a_F260619","score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
+
|
||||||
|
CCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC</code></pre>
|
||||||
|
</section>
|
||||||
|
<section id="dereplicate-reads-into-uniq-sequences" class="level3" data-number="2.2.4">
|
||||||
|
<h3 data-number="2.2.4" class="anchored" data-anchor-id="dereplicate-reads-into-uniq-sequences"><span class="header-section-number">2.2.4</span> Dereplicate reads into uniq sequences</h3>
|
||||||
|
<p>The same DNA molecule can be sequenced several times. In order to reduce both file size and computations time, and to get easier interpretable results, it is convenient to work with unique <em>sequences</em> instead of <em>reads</em>. To <em>dereplicate</em> such <em>reads</em> into unique <em>sequences</em>, we use the <code>obiuniq</code> command.</p>
|
||||||
|
<table class="table">
|
||||||
|
<colgroup>
|
||||||
|
<col style="width: 86%">
|
||||||
|
</colgroup>
|
||||||
|
<tbody>
|
||||||
|
<tr class="odd">
|
||||||
|
<td>Definition: Dereplicate reads into unique sequences</td>
|
||||||
|
</tr>
|
||||||
|
<tr class="even">
|
||||||
|
<td><ol type="1">
|
||||||
|
<li>compare all the reads in a data set to each other</li>
|
||||||
|
<li>group strictly identical reads together</li>
|
||||||
|
<li>output the sequence for each group and its count in the original dataset (in this way, all duplicated reads are removed)</li>
|
||||||
|
</ol>
|
||||||
|
<p>Definition adapted from <span class="citation" data-cites="Seguritan2001-tg">Seguritan and Rohwer (<a href="references.html#ref-Seguritan2001-tg" role="doc-biblioref">2001</a>)</span></p></td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
<p>For dereplication, we use the <code>obiuniq</code> command with the <code>-m sample</code>. The <code>-m sample</code> option is used to keep the information of the samples of origin for each uniquesequence.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obiuniq</span> <span class="at">-m</span> sample <span class="dt">\</span></span>
|
||||||
|
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> results/wolf.ali.assigned.fastq <span class="dt">\</span></span>
|
||||||
|
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.uniq.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>Note that <code>obiuniq</code> returns a fasta file.</p>
|
||||||
|
<p>The first sequence record of <code>wolf.ali.assigned.uniq.fasta</code> is:</p>
|
||||||
|
<pre><code>>HELIUM_000100422_612GNAAXX:7:93:6991:1942#0/1_sub[28..126] {"ali_dir":"left","ali_length":63,"count":1,"direction":"reverse","experiment":"wolf_diet","forward_match":"ttagataccccactatgc","forward_mismatches":0,"forward_primer":"ttagataccccactatgc","forward_tag":"gaatatc","merged_sample":{"26a_F040644":1},"mode":"alignment","pairing_mismatches":{"(A:10)->(G:34)":76,"(C:06)->(A:34)":58},"reverse_match":"tagaacaggctcctctag","reverse_mismatches":0,"reverse_primer":"tagaacaggctcctctag","reverse_tag":"gaatatc","score":730,"score_norm":0.968,"seq_a_single":45,"seq_ab_match":61,"seq_b_single":45}
|
||||||
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagaactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttatatccct</code></pre>
|
||||||
|
<p>The run of <code>obiuniq</code> has added two key=values entries in the header of the fasta sequence:</p>
|
||||||
|
<ul>
|
||||||
|
<li><code class="interpreted-text" role="mod">"merged_sample":{"29a_F260619":1}</code>: this sequence have been found once in a single sample called <strong>29a_F260619</strong></li>
|
||||||
|
<li><code>"count":1</code> : the total count for this sequence is <span class="math inline">\(1\)</span></li>
|
||||||
|
</ul>
|
||||||
|
<p>To keep only these two attributes, we can use the <code>obiannotate</code> command:</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obiannotate</span> <span class="at">-k</span> count <span class="at">-k</span> merged_sample <span class="dt">\</span></span>
|
||||||
|
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> results/wolf.ali.assigned.uniq.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.simple.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The first five sequence records of <code>wolf.ali.assigned.simple.fasta</code> become:</p>
|
||||||
|
<pre><code>>HELIUM_000100422_612GNAAXX:7:26:18930:11105#0/1_sub[28..127] {"count":1,"merged_sample":{"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaatwattcgcyagagtactacmggcaat
|
||||||
|
agctyaaarctcamagrwcttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:58:5711:11399#0/1_sub[28..127] {"count":1,"merged_sample":{"29a_F260619":1}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtwctaccgssaat
|
||||||
|
agcttaaaactcaaaggactgggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:100:15836:9304#0/1_sub[28..127] {"count":1,"merged_sample":{"29a_F260619":1}}
|
||||||
|
ttagccctaaacatagataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:55:13242:9085#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4}}
|
||||||
|
ttagccctaaacataaacattcaataaacaagagtgttcgccagagtactactagcaaca
|
||||||
|
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||||
|
>HELIUM_000100422_612GNAAXX:7:86:8429:13723#0/1_sub[28..127] {"count":7,"merged_sample":{"15a_F730814":5,"29a_F260619":2}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggactcggcggtgctttataccctt</code></pre>
|
||||||
|
</section>
|
||||||
|
<section id="denoise-the-sequence-dataset" class="level3" data-number="2.2.5">
|
||||||
|
<h3 data-number="2.2.5" class="anchored" data-anchor-id="denoise-the-sequence-dataset"><span class="header-section-number">2.2.5</span> Denoise the sequence dataset</h3>
|
||||||
|
<p>To have a set of sequences assigned to their corresponding samples does not mean that all sequences are <em>biologically</em> meaningful i.e. some of these sequences can contains PCR and/or sequencing errors, or chimeras.</p>
|
||||||
|
<section id="tag-the-sequences-for-pcr-errors-sequence-variants" class="level4 unnumbered">
|
||||||
|
<h4 class="unnumbered anchored" data-anchor-id="tag-the-sequences-for-pcr-errors-sequence-variants">Tag the sequences for PCR errors (sequence variants)</h4>
|
||||||
|
<p>The <code>obiclean</code> program tags sequence variants as potential error generated during PCR amplification. We ask it to keep the <span class="title-ref">head</span> sequences (<code>-H</code> option) that are sequences which are not variants of another sequence with a count greater than 5% of their own count (<code>-r 0.05</code> option).</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obiclean</span> <span class="at">-s</span> sample <span class="at">-r</span> 0.05 <span class="at">-H</span> <span class="dt">\</span></span>
|
||||||
|
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> results/wolf.ali.assigned.simple.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.simple.clean.fasta </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>One of the sequence records of <code>wolf.ali.assigned.simple.clean.fasta</code> is:</p>
|
||||||
|
<pre><code>>HELIUM_000100422_612GNAAXX:7:66:4039:8016#0/1_sub[28..127] {"count":17,"merged_sample":{"13a_F730603":17},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obi
|
||||||
|
clean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":25}}
|
||||||
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||||
|
agcccaaaactcaaaggacttggcggtgcttcacaccctt</code></pre>
|
||||||
|
<p>To remove such sequences as much as possible, we first discard rare sequences and then rsequence variants that likely correspond to artifacts.</p>
|
||||||
|
</section>
|
||||||
|
<section id="get-some-statistics-about-sequence-counts" class="level4 unnumbered">
|
||||||
|
<h4 class="unnumbered anchored" data-anchor-id="get-some-statistics-about-sequence-counts">Get some statistics about sequence counts</h4>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb15"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obicount</span> results/wolf.ali.assigned.simple.clean.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output cell-output-stdout">
|
||||||
|
<pre><code>time="2023-02-02T23:07:30+01:00" level=info msg="Appending results/wolf.ali.assigned.simple.clean.fasta file\n"
|
||||||
|
2749 36409 273387</code></pre>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
<p>The dataset contains <span class="math inline">\(4313\)</span> sequences variant corresponding to 42452 sequence reads. Most of the variants occur only a single time in the complete dataset and are usualy named <em>singletons</em></p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-p</span> <span class="st">'sequence.Count() == 1'</span> results/wolf.ali.assigned.simple.clean.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a> <span class="kw">|</span> <span class="ex">obicount</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output cell-output-stdout">
|
||||||
|
<pre><code>time="2023-02-02T23:07:30+01:00" level=info msg="Reading sequences from stdin in guessed\n"
|
||||||
|
time="2023-02-02T23:07:30+01:00" level=info msg="Appending results/wolf.ali.assigned.simple.clean.fasta file\n"
|
||||||
|
time="2023-02-02T23:07:30+01:00" level=info msg="On output use JSON headers"
|
||||||
|
2309 2309 229912</code></pre>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
<p>In that dataset sigletons corresponds to <span class="math inline">\(3511\)</span> variants.</p>
|
||||||
|
<p>Using <em>R</em> and the <code>ROBIFastread</code> package able to read headers of the fasta files produced by <em>OBITools</em>, we can get more complete statistics on the distribution of occurrencies.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ROBIFastread)</span>
|
||||||
|
<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
|
||||||
|
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a>seqs <span class="ot"><-</span> <span class="fu">read_obifasta</span>(<span class="st">"results/wolf.ali.assigned.simple.clean.fasta"</span>,<span class="at">keys=</span><span class="st">"count"</span>)</span>
|
||||||
|
<span id="cb19-5"><a href="#cb19-5" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb19-6"><a href="#cb19-6" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> seqs, <span class="at">mapping=</span><span class="fu">aes</span>(<span class="at">x =</span> count)) <span class="sc">+</span></span>
|
||||||
|
<span id="cb19-7"><a href="#cb19-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_histogram</span>(<span class="at">bins=</span><span class="dv">100</span>) <span class="sc">+</span></span>
|
||||||
|
<span id="cb19-8"><a href="#cb19-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_sqrt</span>() <span class="sc">+</span></span>
|
||||||
|
<span id="cb19-9"><a href="#cb19-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_sqrt</span>() <span class="sc">+</span></span>
|
||||||
|
<span id="cb19-10"><a href="#cb19-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_vline</span>(<span class="at">xintercept =</span> <span class="dv">10</span>, <span class="at">col=</span><span class="st">"red"</span>, <span class="at">lty=</span><span class="dv">2</span>) <span class="sc">+</span></span>
|
||||||
|
<span id="cb19-11"><a href="#cb19-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"number of occurrencies of a variant"</span>) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output-display">
|
||||||
|
<p><img src="tutorial_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid" width="672"></p>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
<p>In a similar way it is also possible to plot the distribution of the sequence length.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> seqs, <span class="at">mapping=</span><span class="fu">aes</span>(<span class="at">x =</span> <span class="fu">nchar</span>(sequence))) <span class="sc">+</span></span>
|
||||||
|
<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_histogram</span>() <span class="sc">+</span></span>
|
||||||
|
<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_y_log10</span>() <span class="sc">+</span></span>
|
||||||
|
<span id="cb20-4"><a href="#cb20-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_vline</span>(<span class="at">xintercept =</span> <span class="dv">80</span>, <span class="at">col=</span><span class="st">"red"</span>, <span class="at">lty=</span><span class="dv">2</span>) <span class="sc">+</span></span>
|
||||||
|
<span id="cb20-5"><a href="#cb20-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">xlab</span>(<span class="st">"sequence lengths in base pair"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output-display">
|
||||||
|
<p><img src="tutorial_files/figure-html/unnamed-chunk-10-1.png" class="img-fluid" width="672"></p>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
<section id="keep-only-the-sequences-having-a-count-greater-or-equal-to-10-and-a-length-shorter-than-80-bp" class="level4 unnumbered">
|
||||||
|
<h4 class="unnumbered anchored" data-anchor-id="keep-only-the-sequences-having-a-count-greater-or-equal-to-10-and-a-length-shorter-than-80-bp">Keep only the sequences having a count greater or equal to 10 and a length shorter than 80 bp</h4>
|
||||||
|
<p>Based on the previous observation, we set the cut-off for keeping sequences for further analysis to a count of 10. To do this, we use the <code class="interpreted-text" role="doc">obigrep <scripts/obigrep></code> command. The <code>-p 'count>=10'</code> option means that the <code>python</code> expression :py<code class="interpreted-text" role="mod">count>=10</code> must be evaluated to :py<code class="interpreted-text" role="mod">True</code> for each sequence to be kept. Based on previous knowledge we also remove sequences with a length shorter than 80 bp (option -l) as we know that the amplified 12S-V5 barcode for vertebrates must have a length around 100bp.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb21"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-l</span> 80 <span class="at">-p</span> <span class="st">'sequence.Count() >= 10'</span> results/wolf.ali.assigned.simple.clean.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.simple.clean.c10.l80.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The first sequence record of <code>results/wolf.ali.assigned.simple.clean.c10.l80.fasta</code> is:</p>
|
||||||
|
<pre><code>>HELIUM_000100422_612GNAAXX:7:22:2603:18023#0/1_sub[28..127] {"count":12182,"merged_sample":{"15a_F730814":7559,"29a_F260619":4623},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":9165,"29a_F260619":6275}}
|
||||||
|
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||||
|
agcttaaaactcaaaggacttggcggtgctttataccctt</code></pre>
|
||||||
|
<p>At that time in the data cleanning we have conserved :</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb23"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obicount</span> results/wolf.ali.assigned.simple.clean.c10.l80.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output cell-output-stdout">
|
||||||
|
<pre><code>time="2023-02-02T23:07:31+01:00" level=info msg="Appending results/wolf.ali.assigned.simple.clean.c10.l80.fasta file\n"
|
||||||
|
26 31337 2585</code></pre>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="taxonomic-assignment-of-sequences" class="level3" data-number="2.2.6">
|
||||||
|
<h3 data-number="2.2.6" class="anchored" data-anchor-id="taxonomic-assignment-of-sequences"><span class="header-section-number">2.2.6</span> Taxonomic assignment of sequences</h3>
|
||||||
|
<p>Once denoising has been done, the next step in diet analysis is to assign the barcodes to the corresponding species in order to get the complete list of species associated to each sample.</p>
|
||||||
|
<p>Taxonomic assignment of sequences requires a reference database compiling all possible species to be identified in the sample. Assignment is then done based on sequence comparison between sample sequences and reference sequences.</p>
|
||||||
|
<section id="download-the-taxonomy" class="level4 unnumbered">
|
||||||
|
<h4 class="unnumbered anchored" data-anchor-id="download-the-taxonomy">Download the taxonomy</h4>
|
||||||
|
<p>It is always possible to download the complete taxonomy from NCBI using the following commands.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> TAXO</span>
|
||||||
|
<span id="cb25-2"><a href="#cb25-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> TAXO</span>
|
||||||
|
<span id="cb25-3"><a href="#cb25-3" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz <span class="dt">\</span></span>
|
||||||
|
<span id="cb25-4"><a href="#cb25-4" aria-hidden="true" tabindex="-1"></a> <span class="kw">|</span> <span class="fu">tar</span> <span class="at">-zxvf</span> <span class="at">-</span></span>
|
||||||
|
<span id="cb25-5"><a href="#cb25-5" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ..</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>For people have a low speed internet connection, a copy of the <code>taxdump.tar.gz</code> file is provided in the wolf_data directory. The NCBI taxonomy is dayly updated, but the one provided here is ok for running this tutorial.</p>
|
||||||
|
<p>To build the TAXO directory from the provided <code>taxdump.tar.gz</code>, you need to execute the following commands</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb26"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> TAXO</span>
|
||||||
|
<span id="cb26-2"><a href="#cb26-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> TAXO</span>
|
||||||
|
<span id="cb26-3"><a href="#cb26-3" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> zxvf wolf_data/taxdump.tar.gz </span>
|
||||||
|
<span id="cb26-4"><a href="#cb26-4" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ..</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
<section id="build-a-reference-database" class="level4 unnumbered">
|
||||||
|
<h4 class="unnumbered anchored" data-anchor-id="build-a-reference-database">Build a reference database</h4>
|
||||||
|
<p>One way to build the reference database is to use the <code>obipcr</code> program to simulate a PCR and extract all sequences from a general purpose DNA database such as genbank or EMBL that can be amplified <em>in silico</em> by the two primers (here <strong>TTAGATACCCCACTATGC</strong> and <strong>TAGAACAGGCTCCTCTAG</strong>) used for PCR amplification.</p>
|
||||||
|
<p>The two steps to build this reference database would then be</p>
|
||||||
|
<ol type="1">
|
||||||
|
<li><p>Today, the easiest database to download is <em>Genbank</em>. But this will take you more than a day and occupy more than half a terabyte on your hard drive. In the <code>wolf_data</code> directory, a shell script called <code>download_gb.sh</code> is provided to perform this task. It requires that the programs <code>wget2</code> and <code>curl</code> are available on your computer.</p></li>
|
||||||
|
<li><p>Use <code>obipcr</code> to simulate amplification and build a reference database based on the putatively amplified barcodes and their recorded taxonomic information.</p></li>
|
||||||
|
</ol>
|
||||||
|
<p>As these steps can take a long time (about a day for the download and an hour for the PCR), we already provide the reference database produced by the following commands so you can skip its construction. Note that as the Genbank and taxonomic database evolve frequently, if you run the following commands you may get different results.</p>
|
||||||
|
<section id="download-the-sequences" class="level5 unnumbered">
|
||||||
|
<h5 class="unnumbered anchored" data-anchor-id="download-the-sequences">Download the sequences</h5>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> genbank</span>
|
||||||
|
<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> genbank</span>
|
||||||
|
<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a><span class="ex">../wolf_data/install_gb.sh</span></span>
|
||||||
|
<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ..</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>DO NOT RUN THIS COMMAND EXCEPT IF YOU ARE REALLY CONSIENT OF THE TIME AND DISK SPACE REQUIRED.</p>
|
||||||
|
</section>
|
||||||
|
<section id="use-obipcr-to-simulate-an-in-silico-pcr" class="level5 unnumbered">
|
||||||
|
<h5 class="unnumbered anchored" data-anchor-id="use-obipcr-to-simulate-an-in-silico-pcr">Use obipcr to simulate an in silico` PCR</h5>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb28"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obipcr</span> <span class="at">-t</span> TAXO <span class="at">-e</span> 3 <span class="at">-l</span> 50 <span class="at">-L</span> 150 <span class="dt">\ </span></span>
|
||||||
|
<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a> <span class="ex">--forward</span> TTAGATACCCCACTATGC <span class="dt">\</span></span>
|
||||||
|
<span id="cb28-3"><a href="#cb28-3" aria-hidden="true" tabindex="-1"></a> <span class="at">--reverse</span> TAGAACAGGCTCCTCTAG <span class="dt">\</span></span>
|
||||||
|
<span id="cb28-4"><a href="#cb28-4" aria-hidden="true" tabindex="-1"></a> <span class="at">--no-order</span> <span class="dt">\</span></span>
|
||||||
|
<span id="cb28-5"><a href="#cb28-5" aria-hidden="true" tabindex="-1"></a> genbank/Release-251/gb<span class="pp">*</span>.seq.gz</span>
|
||||||
|
<span id="cb28-6"><a href="#cb28-6" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/v05.pcr.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>Note that the primers must be in the same order both in <code>wolf_diet_ngsfilter.txt</code> and in the <code>obipcr</code> command. The part of the path indicating the <em>Genbank</em> release can change. Please check in your genbank directory the exact name of your release.</p>
|
||||||
|
</section>
|
||||||
|
<section id="clean-the-database" class="level5 unnumbered">
|
||||||
|
<h5 class="unnumbered anchored" data-anchor-id="clean-the-database">Clean the database</h5>
|
||||||
|
<ol type="1">
|
||||||
|
<li>filter sequences so that they have a good taxonomic description at the species, genus, and family levels (<code>obigrep</code> command command below).</li>
|
||||||
|
<li>remove redundant sequences (<code>obiuniq</code> command below).</li>
|
||||||
|
<li>ensure that the dereplicated sequences have a taxid at the family level (<code>obigrep</code> command below).</li>
|
||||||
|
<li>ensure that sequences each have a unique identification (<code>obiannotate</code> command below)</li>
|
||||||
|
</ol>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb29"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-t</span> TAXO <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-2"><a href="#cb29-2" aria-hidden="true" tabindex="-1"></a> <span class="at">--require-rank</span> species <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-3"><a href="#cb29-3" aria-hidden="true" tabindex="-1"></a> <span class="at">--require-rank</span> genus <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-4"><a href="#cb29-4" aria-hidden="true" tabindex="-1"></a> <span class="at">--require-rank</span> family <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-5"><a href="#cb29-5" aria-hidden="true" tabindex="-1"></a> results/v05.ecopcr <span class="op">></span> results/v05_clean.fasta</span>
|
||||||
|
<span id="cb29-6"><a href="#cb29-6" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb29-7"><a href="#cb29-7" aria-hidden="true" tabindex="-1"></a><span class="ex">obiuniq</span> <span class="at">-c</span> taxid <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-8"><a href="#cb29-8" aria-hidden="true" tabindex="-1"></a> results/v05_clean.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-9"><a href="#cb29-9" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/v05_clean_uniq.fasta</span>
|
||||||
|
<span id="cb29-10"><a href="#cb29-10" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb29-11"><a href="#cb29-11" aria-hidden="true" tabindex="-1"></a><span class="ex">obirefidx</span> <span class="at">-t</span> TAXO results/v05_clean_uniq.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb29-12"><a href="#cb29-12" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/v05_clean_uniq.indexed.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<div class="warning">
|
||||||
|
<div class="title">
|
||||||
|
<p>Warning</p>
|
||||||
|
</div>
|
||||||
|
<p>From now on, for the sake of clarity, the following commands will use the filenames of the files provided with the tutorial. If you decided to run the last steps and use the files you have produced, you'll have to use <code>results/v05_clean_uniq.indexed.fasta</code> instead of <code>wolf_data/db_v05_r117.indexed.fasta</code>.</p>
|
||||||
|
</div>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
</section>
|
||||||
|
<section id="assign-each-sequence-to-a-taxon" class="level3" data-number="2.2.7">
|
||||||
|
<h3 data-number="2.2.7" class="anchored" data-anchor-id="assign-each-sequence-to-a-taxon"><span class="header-section-number">2.2.7</span> Assign each sequence to a taxon</h3>
|
||||||
|
<p>Once the reference database is built, taxonomic assignment can be carried out using the <code>obitag</code> command.</p>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb30"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obitag</span> <span class="at">-t</span> TAXO <span class="at">-R</span> wolf_data/db_v05_r117.indexed.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb30-2"><a href="#cb30-2" aria-hidden="true" tabindex="-1"></a> results/wolf.ali.assigned.simple.clean.c10.l80.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb30-3"><a href="#cb30-3" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.simple.clean.c10.l80.taxo.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The <code>obitag</code> adds several attributes in the sequence record header, among them:</p>
|
||||||
|
<ul>
|
||||||
|
<li>obitag_bestmatch=ACCESSION where ACCESSION is the id of hte sequence in the reference database that best aligns to the query sequence;</li>
|
||||||
|
<li>obitag_bestid=FLOAT where FLOAT*100 is the percentage of identity between the best match sequence and the query sequence;</li>
|
||||||
|
<li>taxid=TAXID where TAXID is the final assignation of the sequence by <code>obitag</code></li>
|
||||||
|
<li>scientific_name=NAME where NAME is the scientific name of the assigned taxid.</li>
|
||||||
|
</ul>
|
||||||
|
<p>The first sequence record of <code>wolf.ali.assigned.simple.clean.c10.l80.taxo.fasta</code> is:</p>
|
||||||
|
<div class="sourceCode" id="cb31"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="op">></span>HELIUM_000100422_612GNAAXX:7:81:18704:12346#0/1_sub[28..126] <span class="dt">{</span><span class="st">"count"</span><span class="dt">:88</span><span class="op">,</span><span class="st">"merged_sample"</span><span class="dt">:{</span><span class="st">"26a_F040644"</span><span class="dt">:88}</span><span class="op">,</span><span class="st">"obiclean_head"</span><span class="dt">:true</span><span class="op">,</span><span class="st">"obiclean_headcount"</span><span class="dt">:1</span><span class="op">,</span><span class="st">"obiclean_internalcount"</span><span class="dt">:0</span><span class="op">,</span><span class="st">"obiclean_samplecount"</span><span class="dt">:1</span><span class="op">,</span><span class="st">"obiclean_singletoncount"</span><span class="dt">:0</span><span class="op">,</span><span class="st">"obiclean_status"</span><span class="dt">:{</span><span class="st">"26a_F040644"</span><span class="dt">:</span><span class="st">"h"</span><span class="dt">}</span><span class="op">,</span><span class="st">"obiclean_weight"</span><span class="dt">:{</span><span class="st">"26a_F040644"</span><span class="dt">:208}</span><span class="op">,</span><span class="st">"obitag_bestid"</span><span class="dt">:0.9207920792079208</span><span class="op">,</span><span class="st">"obitag_bestmatch"</span><span class="dt">:</span><span class="st">"AY769263"</span><span class="op">,</span><span class="st">"obitag_difference"</span><span class="dt">:8</span><span class="op">,</span><span class="st">"obitag_match_count"</span><span class="dt">:1</span><span class="op">,</span><span class="st">"obitag_rank"</span><span class="dt">:</span><span class="st">"clade"</span><span class="op">,</span><span class="st">"scientific_name"</span><span class="dt">:</span><span class="st">"Boreoeutheria"</span><span class="op">,</span><span class="st">"taxid"</span><span class="dt">:1437010}</span></span>
|
||||||
|
<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a><span class="ex">ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata</span></span>
|
||||||
|
<span id="cb31-3"><a href="#cb31-3" aria-hidden="true" tabindex="-1"></a><span class="ex">gcttaaaactcaaaggacttggcggtgctttatatccct</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</section>
|
||||||
|
<section id="generate-the-final-result-table" class="level3" data-number="2.2.8">
|
||||||
|
<h3 data-number="2.2.8" class="anchored" data-anchor-id="generate-the-final-result-table"><span class="header-section-number">2.2.8</span> Generate the final result table</h3>
|
||||||
|
<p>Some unuseful attributes can be removed at this stage.</p>
|
||||||
|
<ul>
|
||||||
|
<li>obiclean_head</li>
|
||||||
|
<li>obiclean_headcount</li>
|
||||||
|
<li>obiclean_internalcount</li>
|
||||||
|
<li>obiclean_samplecount</li>
|
||||||
|
<li>obiclean_singletoncount</li>
|
||||||
|
</ul>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb32"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb32-1"><a href="#cb32-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obiannotate</span> <span class="at">--delete-tag</span><span class="op">=</span>obiclean_head <span class="dt">\</span></span>
|
||||||
|
<span id="cb32-2"><a href="#cb32-2" aria-hidden="true" tabindex="-1"></a> <span class="at">--delete-tag</span><span class="op">=</span>obiclean_headcount <span class="dt">\</span></span>
|
||||||
|
<span id="cb32-3"><a href="#cb32-3" aria-hidden="true" tabindex="-1"></a> <span class="at">--delete-tag</span><span class="op">=</span>obiclean_internalcount <span class="dt">\</span></span>
|
||||||
|
<span id="cb32-4"><a href="#cb32-4" aria-hidden="true" tabindex="-1"></a> <span class="at">--delete-tag</span><span class="op">=</span>obiclean_samplecount <span class="dt">\</span></span>
|
||||||
|
<span id="cb32-5"><a href="#cb32-5" aria-hidden="true" tabindex="-1"></a> <span class="at">--delete-tag</span><span class="op">=</span>obiclean_singletoncount <span class="dt">\</span></span>
|
||||||
|
<span id="cb32-6"><a href="#cb32-6" aria-hidden="true" tabindex="-1"></a> results/wolf.ali.assigned.simple.clean.c10.l80.taxo.fasta <span class="dt">\</span></span>
|
||||||
|
<span id="cb32-7"><a href="#cb32-7" aria-hidden="true" tabindex="-1"></a> <span class="op">></span> results/wolf.ali.assigned.simple.clean.c10.l80.taxo.ann.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
</div>
|
||||||
|
<p>The first sequence record of <code>wolf.ali.assigned.simple.c10.l80.clean.taxo.ann.fasta</code> is then:</p>
|
||||||
|
<pre><code>>HELIUM_000100422_612GNAAXX:7:84:16335:5083#0/1_sub[28..126] {"count":96,"merged_sample":{"26a_F040644":11,"29a_F260619":85},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":14,"29a_F260619":110},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_difference":4,"obitag_match_count":1,"obitag_rank":"subspecies","scientific_name":"Canis lupus familiaris","taxid":9615}
|
||||||
|
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||||
|
gattaaacctcaaaggacttggcagtgctttatacccct</code></pre>
|
||||||
|
</section>
|
||||||
|
<section id="looking-at-the-data-in-r" class="level3" data-number="2.2.9">
|
||||||
|
<h3 data-number="2.2.9" class="anchored" data-anchor-id="looking-at-the-data-in-r"><span class="header-section-number">2.2.9</span> Looking at the data in R</h3>
|
||||||
|
<div class="cell">
|
||||||
|
<div class="sourceCode cell-code" id="cb34"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ROBIFastread)</span>
|
||||||
|
<span id="cb34-2"><a href="#cb34-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(vegan)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output cell-output-stderr">
|
||||||
|
<pre><code>Le chargement a nécessité le package : permute</code></pre>
|
||||||
|
</div>
|
||||||
|
<div class="cell-output cell-output-stderr">
|
||||||
|
<pre><code>Le chargement a nécessité le package : lattice</code></pre>
|
||||||
|
</div>
|
||||||
|
<div class="cell-output cell-output-stderr">
|
||||||
|
<pre><code>This is vegan 2.6-4</code></pre>
|
||||||
|
</div>
|
||||||
|
<div class="sourceCode cell-code" id="cb38"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb38-1"><a href="#cb38-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(magrittr)</span>
|
||||||
|
<span id="cb38-2"><a href="#cb38-2" aria-hidden="true" tabindex="-1"></a> </span>
|
||||||
|
<span id="cb38-3"><a href="#cb38-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb38-4"><a href="#cb38-4" aria-hidden="true" tabindex="-1"></a>diet_data <span class="ot"><-</span> <span class="fu">read_obifasta</span>(<span class="st">"results/wolf.ali.assigned.simple.clean.c10.l80.taxo.fasta"</span>) </span>
|
||||||
|
<span id="cb38-5"><a href="#cb38-5" aria-hidden="true" tabindex="-1"></a>diet_data <span class="sc">%<>%</span> <span class="fu">extract_features</span>(<span class="st">"obitag_bestmatch"</span>,<span class="st">"obitag_rank"</span>,<span class="st">"scientific_name"</span>,<span class="st">'taxid'</span>)</span>
|
||||||
|
<span id="cb38-6"><a href="#cb38-6" aria-hidden="true" tabindex="-1"></a></span>
|
||||||
|
<span id="cb38-7"><a href="#cb38-7" aria-hidden="true" tabindex="-1"></a>diet_tab <span class="ot"><-</span> <span class="fu">extract_readcount</span>(diet_data,<span class="at">key=</span><span class="st">"obiclean_weight"</span>)</span>
|
||||||
|
<span id="cb38-8"><a href="#cb38-8" aria-hidden="true" tabindex="-1"></a>diet_tab</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||||
|
<div class="cell-output cell-output-stdout">
|
||||||
|
<pre><code>4 x 26 sparse Matrix of class "dgCMatrix"</code></pre>
|
||||||
|
</div>
|
||||||
|
<div class="cell-output cell-output-stderr">
|
||||||
|
<pre><code> [[ suppressing 26 column names 'HELIUM_000100422_612GNAAXX:7:30:17945:19531#0/1_sub[28..126]', 'HELIUM_000100422_612GNAAXX:7:94:16908:11285#0/1_sub[28..127]', 'HELIUM_000100422_612GNAAXX:7:100:4828:3492#0/1_sub[28..127]' ... ]]</code></pre>
|
||||||
|
</div>
|
||||||
|
<div class="cell-output cell-output-stdout">
|
||||||
|
<pre><code>
|
||||||
|
26a_F040644 43 . . . . 88 . 52 208 15 31 . . 14 481 72 17 . .
|
||||||
|
13a_F730603 . 8409 22 1 . . . . . . . 20 . . 19 . . 15 .
|
||||||
|
29a_F260619 . . . 13 353 . 391 . . . . . 6275 . 1 . . . 44
|
||||||
|
15a_F730814 . . . . . . . . . . . . 9165 . 5 . . . .
|
||||||
|
|
||||||
|
26a_F040644 12830 14 . . 18 . .
|
||||||
|
13a_F730603 . . . 9 . . 25
|
||||||
|
29a_F260619 . 110 16 . . 25 .
|
||||||
|
15a_F730814 . . . 4 . . .</code></pre>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
<dl>
|
||||||
|
<dt>This file contains 26 sequences. You can deduce the diet of each sample:</dt>
|
||||||
|
<dd>
|
||||||
|
<ul>
|
||||||
|
<li>13a_F730603: Cervus elaphus</li>
|
||||||
|
<li>15a_F730814: Capreolus capreolus</li>
|
||||||
|
<li>26a_F040644: Marmota sp. (according to the location, it is Marmota marmota)</li>
|
||||||
|
<li>29a_F260619: Capreolus capreolus</li>
|
||||||
|
</ul>
|
||||||
|
</dd>
|
||||||
|
</dl>
|
||||||
|
<p>Note that we also obtained a few wolf sequences although a wolf-blocking oligonucleotide was used.</p>
|
||||||
|
|
||||||
|
|
||||||
|
<div id="refs" class="references csl-bib-body hanging-indent" role="doc-bibliography" style="display: none">
|
||||||
|
<div id="ref-Riaz2011-gn" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Riaz, Tiayyba, Wasim Shehzad, Alain Viari, François Pompanon, Pierre Taberlet, and Eric Coissac. 2011. <span>“<span class="nocase">ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis</span>.”</span> <em>Nucleic Acids Research</em> 39 (21): e145. <a href="https://doi.org/10.1093/nar/gkr732">https://doi.org/10.1093/nar/gkr732</a>.
|
||||||
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</div>
|
||||||
|
<div id="ref-Seguritan2001-tg" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Seguritan, V, and F Rohwer. 2001. <span>“<span class="nocase">FastGroup: a program to dereplicate libraries of 16S rDNA sequences</span>.”</span> <em>BMC Bioinformatics</em> 2 (October): 9. <a href="https://doi.org/10.1186/1471-2105-2-9">https://doi.org/10.1186/1471-2105-2-9</a>.
|
||||||
|
</div>
|
||||||
|
<div id="ref-Shehzad2012-pn" class="csl-entry" role="doc-biblioentry">
|
||||||
|
Shehzad, Wasim, Tiayyba Riaz, Muhammad A Nawaz, Christian Miquel, Carole Poillot, Safdar A Shah, Francois Pompanon, Eric Coissac, and Pierre Taberlet. 2012. <span>“<span class="nocase">Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan</span>.”</span> <em>Molecular Ecology</em> 21 (8): 1951–65. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x">https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x</a>.
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||||||
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const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
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try { href = new URL(href).hash; } catch {}
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const citeInfo = findCites(ref);
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tippyHover(citeInfo.el, function() {
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></span>
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<span class="nav-page-text"><span class="chapter-number">3</span> <span class="chapter-title">The <em>OBITools V4</em> commands</span></span> <i class="bi bi-arrow-right-short"></i>
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</body></html>
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Reference in New Issue
Block a user