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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">A.1</span> Sequence attributes</a></li>
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<h1 class="title d-none d-lg-block">Appendix A — Annexes</h1>
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<h2 data-number="A.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">A.1</span> Sequence attributes</h2>
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<p><strong>ali_dir (<code>string</code>)</strong></p>
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<ul>
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<li>Set by the <em>obipairing</em> tool</li>
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<li>The attribute can contain 2 string values <code>left</code> or <code>right</code>.</li>
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</ul>
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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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<p><strong>ali_length (<code>int</code>)</strong></p>
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<ul>
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<li>Set by the <em>obipairing</em> tool</li>
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</ul>
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<p>Length of the aligned parts when merging forward and reverse reads</p>
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<p><strong>count (<code>int</code>)</strong></p>
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<ul>
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<li>Set by the <em>obiuniq</em> tool</li>
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<li>Getter : method <code>Count()</code></li>
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<li>Setter : method <code>SetCount(int)</code></li>
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</ul>
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<p>The <code>count</code> attribute indicates how-many strictly identical reads have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.</p>
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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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<p><strong>merged_* (<code>map[string]int</code>)</strong></p>
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<ul>
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<li>Set by the <em>obiuniq</em> tool</li>
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</ul>
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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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<p><strong>mode (<code>string</code>)</strong></p>
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<ul>
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<li>Set by the <em>obipairing</em> tool</li>
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<li>The attribute can contain 2 string values <code>join</code> or <code>alignment</code>.</li>
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</ul>
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<p><strong>obitag_ref_index (<code>map[string]string</code>)</strong></p>
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<ul>
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<li>Set by the <em>obirefidx</em> tool.</li>
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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>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode json code-with-copy"><code class="sourceCode json"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">{</span><span class="dt">"0"</span><span class="fu">:</span><span class="st">"9606@Homo sapiens@species"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="dt">"2"</span><span class="fu">:</span><span class="st">"207598@Homininae@subfamily"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="dt">"3"</span><span class="fu">:</span><span class="st">"9604@Hominidae@family"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="dt">"8"</span><span class="fu">:</span><span class="st">"314295@Hominoidea@superfamily"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="dt">"10"</span><span class="fu">:</span><span class="st">"9526@Catarrhini@parvorder"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="dt">"12"</span><span class="fu">:</span><span class="st">"1437010@Boreoeutheria@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="dt">"16"</span><span class="fu">:</span><span class="st">"9347@Eutheria@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="dt">"17"</span><span class="fu">:</span><span class="st">"40674@Mammalia@class"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="dt">"22"</span><span class="fu">:</span><span class="st">"117571@Euteleostomi@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="dt">"25"</span><span class="fu">:</span><span class="st">"7776@Gnathostomata@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> <span class="dt">"29"</span><span class="fu">:</span><span class="st">"33213@Bilateria@clade"</span><span class="fu">,</span></span>
|
||||
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="dt">"30"</span><span class="fu">:</span><span class="st">"6072@Eumetazoa@clade"</span><span class="fu">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p><strong>pairing_mismatches (<code>map[string]string</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_a_single (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_ab_match (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_b_single (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>score (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>score_norm (<code>float</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
<li>The value ranges between 0 and 1.</li>
|
||||
</ul>
|
||||
<p>Score of the alignment between forward and reverse reads expressed as a fraction of identity.</p>
|
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<h1 class="quarto-secondary-nav-title"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></h1>
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<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./common_options.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./expressions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_metabarcode_design.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span> <span class="chapter-title">Metabarcode design and quality assessment</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_reformat.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span> <span class="chapter-title">File format conversions</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_computation.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_utilities.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></a>
|
||||
</div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="sidebar-item sidebar-item-section">
|
||||
<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
|
||||
</li>
|
||||
<li class="sidebar-item sidebar-item-section">
|
||||
<div class="sidebar-item-container">
|
||||
<a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">Appendices</a>
|
||||
<a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">
|
||||
<i class="bi bi-chevron-right ms-2"></i>
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||||
</a>
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<ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./annexes.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">A</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>
|
||||
</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="#obipairing" id="toc-obipairing" class="nav-link active" data-scroll-target="#obipairing"><span class="toc-section-number">11.1</span> <code>obipairing</code></a>
|
||||
<ul class="collapse">
|
||||
<li><a href="#alignment-procedure" id="toc-alignment-procedure" class="nav-link" data-scroll-target="#alignment-procedure">Alignment procedure</a></li>
|
||||
<li><a href="#the-scoring-system" id="toc-the-scoring-system" class="nav-link" data-scroll-target="#the-scoring-system">The scoring system</a></li>
|
||||
</ul></li>
|
||||
<li><a href="#obimultiplex" id="toc-obimultiplex" class="nav-link" data-scroll-target="#obimultiplex"><span class="toc-section-number">11.2</span> <code>obimultiplex</code></a></li>
|
||||
<li><a href="#obicomplement" id="toc-obicomplement" class="nav-link" data-scroll-target="#obicomplement"><span class="toc-section-number">11.3</span> <code>obicomplement</code></a></li>
|
||||
<li><a href="#obiclean" id="toc-obiclean" class="nav-link" data-scroll-target="#obiclean"><span class="toc-section-number">11.4</span> <code>obiclean</code></a></li>
|
||||
<li><a href="#obiuniq" id="toc-obiuniq" class="nav-link" data-scroll-target="#obiuniq"><span class="toc-section-number">11.5</span> <code>obiuniq</code></a></li>
|
||||
</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">11</span> <span class="chapter-title">Computations on sequences</span></h1>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<div class="quarto-title-meta">
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<section id="obipairing" class="level2" data-number="11.1">
|
||||
<h2 data-number="11.1" class="anchored" data-anchor-id="obipairing"><span class="header-section-number">11.1</span> <code>obipairing</code></h2>
|
||||
<blockquote class="blockquote">
|
||||
<p>Replace the <code>illuminapairedends</code> original <em>OBITools</em></p>
|
||||
</blockquote>
|
||||
<section id="alignment-procedure" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="alignment-procedure">Alignment procedure</h3>
|
||||
<p><code>obipairing</code> is introducing a new alignment algorithm compared to the <code>illuminapairedend</code> command of the <code>OBITools V2</code>. Nethertheless this new algorithm has been design to produce the same results than the previous, except in very few cases.</p>
|
||||
<p>The new algorithm is a two-step procedure. First, a FASTN-type algorithm <span class="citation" data-cites="Lipman1985-hw">(<a href="references.html#ref-Lipman1985-hw" role="doc-biblioref">Lipman and Pearson 1985</a>)</span> identifies the best offset between the two matched readings. This identifies the region of overlap.</p>
|
||||
<p>In the second step, the matching regions of the two reads are extracted along with a flanking sequence of <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>Δ</mi><annotation encoding="application/x-tex">\Delta</annotation></semantics></math> base pairs. The two subsequences are then aligned using a “one side free end-gap” dynamic programming algorithm. This latter step is only called if at least one mismatch is detected by the FASTP step.</p>
|
||||
<p>Unless the similarity between the two reads at their overlap region is very low, the addition of the flanking regions in the second step of the alignment ensures the same alignment as if the dynamic programming alignment was performed on the full reads.</p>
|
||||
</section>
|
||||
<section id="the-scoring-system" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="the-scoring-system">The scoring system</h3>
|
||||
<p>In the dynamic programming step, the match and mismatch scores take into account the quality scores of the two aligned nucleotides. By taking these into account, the probability of a true match can be calculated for each aligned base pair.</p>
|
||||
<p>If we consider a nucleotide read with a quality score <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>Q</mi><annotation encoding="application/x-tex">Q</annotation></semantics></math>, the probability of misreading this base (<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>P</mi><mi>E</mi></msub><annotation encoding="application/x-tex">P_E</annotation></semantics></math>) is : <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>E</mi></msub><mo>=</mo><msup><mn>10</mn><mrow><mo>−</mo><mfrac><mi>Q</mi><mn>10</mn></mfrac></mrow></msup></mrow><annotation encoding="application/x-tex">
|
||||
P_E = 10^{-\frac{Q}{10}}
|
||||
</annotation></semantics></math></p>
|
||||
<p>Thus, when a given nucleotide <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is observed with the quality score <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>Q</mi><annotation encoding="application/x-tex">Q</annotation></semantics></math>. The probability that <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is really an <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><mi>X</mi><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mi>E</mi></msub></mrow><annotation encoding="application/x-tex">
|
||||
P(X=X) = 1 - P_E
|
||||
</annotation></semantics></math></p>
|
||||
<p>Otherwise, <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>X</mi><annotation encoding="application/x-tex">X</annotation></semantics></math> is actually one of the three other possible nucleotides (<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><annotation encoding="application/x-tex">X_{E1}</annotation></semantics></math>, <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><annotation encoding="application/x-tex">X_{E2}</annotation></semantics></math> or <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mn>3</mn></mrow></msub><annotation encoding="application/x-tex">X_{E3}</annotation></semantics></math>). If we suppose that the three reading error have the same probability :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>3</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>X</mi><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>3</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mfrac><msub><mi>P</mi><mi>E</mi></msub><mn>3</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P(X=X_{E1}) = P(X=X_{E3}) = P(X=X_{E3}) = \frac{P_E}{3}
|
||||
</annotation></semantics></math></p>
|
||||
<p>At each position in an alignment where the two nucleotides <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> face each other (not a gapped position), the probability of a true match varies depending on whether <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1=X_2</annotation></semantics></math>, an observed match, or <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>≠</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1 \neq X_2</annotation></semantics></math>, an observed mismatch.</p>
|
||||
<p><strong>Probability of a true match when <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1=X_2</annotation></semantics></math></strong></p>
|
||||
<p>That probability can be divided in two parts. First <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> have been correctly read. The corresponding probability is :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><msub><mi>P</mi><mrow><mi>T</mi><mi>M</mi></mrow></msub></mtd><mtd columnalign="left"><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>1</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr><mtr><mtd columnalign="right"></mtd><mtd columnalign="left"><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msup><mn>10</mn><mrow><mo>−</mo><mfrac><msub><mi>Q</mi><mn>1</mn></msub><mn>10</mn></mfrac></mrow></msup><mo stretchy="true" form="postfix">)</mo></mrow><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msup><mn>10</mn><mrow><mo>−</mo><mfrac><msub><mi>Q</mi><mn>2</mn></msub><mn>10</mn></mfrac></mrow></msup><mo stretchy="true" form="postfix">)</mo></mrow></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P_{TM} &= (1- PE_1)(1-PE_2)\\
|
||||
&=(1 - 10^{-\frac{Q_1}{10} } )(1 - 10^{-\frac{Q_2}{10}} )
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p>Secondly, a match can occure if the true nucleotides read as <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> are not <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> but identical.</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>∩</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>2</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd><mtd columnalign="left"><mo>=</mo><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>9</mn></mfrac></mtd></mtr><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mi>x</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>∩</mo><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>X</mi><mn>2</mn></msub><mo>=</mo><mo>=</mo><msub><mi>X</mi><mrow><mi>E</mi><mi>x</mi></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow></mtd><mtd columnalign="left"><mo>=</mo><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>3</mn></mfrac></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P(X_1==X_{E1}) \cap P(X_2==X_{E1}) &= \frac{P_{E1} P_{E2}}{9} \\
|
||||
P(X_1==X_{Ex}) \cap P(X_2==X_{Ex}) & = \frac{P_{E1} P_{E2}}{3}
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p>The probability of a true match between <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> when <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1 = X_2</annotation></semantics></math> an observed match :</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>M</mi><mi>A</mi><mi>T</mi><mi>C</mi><mi>H</mi><mo stretchy="false" form="prefix">|</mo><msub><mi>X</mi><mn>1</mn></msub><mo>=</mo><msub><mi>X</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>1</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><mi>P</mi><msub><mi>E</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>3</mn></mfrac></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P(MATCH | X_1 = X_2) = (1- PE_1)(1-PE_2) + \frac{P_{E1} P_{E2}}{3}
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p><strong>Probability of a true match when <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>X</mi><mn>1</mn></msub><mo>≠</mo><msub><mi>X</mi><mn>2</mn></msub></mrow><annotation encoding="application/x-tex">X_1 \neq X_2</annotation></semantics></math></strong></p>
|
||||
<p>That probability can be divided in three parts.</p>
|
||||
<ol type="a">
|
||||
<li><math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> has been correctly read and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> is a sequencing error and is actually equal to <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math>. <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>a</mi></msub><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mn>3</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P_a = (1-P_{E1})\frac{P_{E2}}{3}
|
||||
</annotation></semantics></math></li>
|
||||
<li><math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> has been correctly read and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> is a sequencing error and is actually equal to <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math>. <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>b</mi></msub><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mn>3</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P_b = (1-P_{E2})\frac{P_{E1}}{3}
|
||||
</annotation></semantics></math></li>
|
||||
<li><math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>1</mn></msub><annotation encoding="application/x-tex">X_1</annotation></semantics></math> and <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mn>2</mn></msub><annotation encoding="application/x-tex">X_2</annotation></semantics></math> corresponds to sequencing error but are actually the same base <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>X</mi><mrow><mi>E</mi><mi>x</mi></mrow></msub><annotation encoding="application/x-tex">X_{Ex}</annotation></semantics></math> <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>P</mi><mi>c</mi></msub><mo>=</mo><mn>2</mn><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>9</mn></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
P_c = 2\frac{P_{E1} P_{E2}}{9}
|
||||
</annotation></semantics></math></li>
|
||||
</ol>
|
||||
<p>Consequently : <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mtable><mtr><mtd columnalign="right"><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>M</mi><mi>A</mi><mi>T</mi><mi>C</mi><mi>H</mi><mo stretchy="false" form="prefix">|</mo><msub><mi>X</mi><mn>1</mn></msub><mo>≠</mo><msub><mi>X</mi><mn>2</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mn>3</mn></mfrac><mo>+</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>−</mo><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub><mo stretchy="true" form="postfix">)</mo></mrow><mfrac><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><mn>3</mn></mfrac><mo>+</mo><mn>2</mn><mfrac><mrow><msub><mi>P</mi><mrow><mi>E</mi><mn>1</mn></mrow></msub><msub><mi>P</mi><mrow><mi>E</mi><mn>2</mn></mrow></msub></mrow><mn>9</mn></mfrac></mtd></mtr></mtable><annotation encoding="application/x-tex">
|
||||
\begin{aligned}
|
||||
P(MATCH | X_1 \neq X_2) = (1-P_{E1})\frac{P_{E2}}{3} + (1-P_{E2})\frac{P_{E1}}{3} + 2\frac{P_{E1} P_{E2}}{9}
|
||||
\end{aligned}
|
||||
</annotation></semantics></math></p>
|
||||
<p><strong>Probability of a match under the random model</strong></p>
|
||||
<p>The second considered model is a pure random model where every base is equiprobable, hence having a probability of occurrence of a nucleotide equals <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mn>0.25</mn><annotation encoding="application/x-tex">0.25</annotation></semantics></math>. Under that hypothesis</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mrow><mo stretchy="true" form="prefix">(</mo><mi>M</mi><mi>A</mi><mi>T</mi><mi>C</mi><mi>H</mi><mo stretchy="false" form="prefix">|</mo><mtext mathvariant="normal">Random model</mtext><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>0.25</mn></mrow><annotation encoding="application/x-tex">
|
||||
P(MATCH | \text{Random model}) = 0.25
|
||||
</annotation></semantics></math></p>
|
||||
<p><strong>The score is a log ration of likelyhood</strong></p>
|
||||
<p>Score is define as the logarithm of the ratio between the likelyhood of the observations considering the sequencer error model over tha likelyhood u</p>
|
||||
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|
||||
<p></p><figcaption class="figure-caption">Evolution of the match and mismatch scores when the quality of base is 20 while the second range from 10 to 40.</figcaption><p></p>
|
||||
</figure>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</section>
|
||||
</section>
|
||||
<section id="obimultiplex" class="level2" data-number="11.2">
|
||||
<h2 data-number="11.2" class="anchored" data-anchor-id="obimultiplex"><span class="header-section-number">11.2</span> <code>obimultiplex</code></h2>
|
||||
<blockquote class="blockquote">
|
||||
<p>Replace the <code>ngsfilter</code> original <em>OBITools</em></p>
|
||||
</blockquote>
|
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</section>
|
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<section id="obicomplement" class="level2" data-number="11.3">
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<h2 data-number="11.3" class="anchored" data-anchor-id="obicomplement"><span class="header-section-number">11.3</span> <code>obicomplement</code></h2>
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<h2 data-number="11.4" class="anchored" data-anchor-id="obiclean"><span class="header-section-number">11.4</span> <code>obiclean</code></h2>
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<h2 data-number="11.5" class="anchored" data-anchor-id="obiuniq"><span class="header-section-number">11.5</span> <code>obiuniq</code></h2>
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<div id="ref-Lipman1985-hw" class="csl-entry" role="doc-biblioentry">
|
||||
Lipman, D J, and W R Pearson. 1985. <span>“<span class="nocase">Rapid and sensitive protein similarity searches</span>.”</span> <em>Science</em> 227 (4693): 1435–41. <a href="http://www.ncbi.nlm.nih.gov/pubmed/2983426">http://www.ncbi.nlm.nih.gov/pubmed/2983426</a>.
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<li><a href="#obigrep-filters-sequence-files-according-to-numerous-conditions" id="toc-obigrep-filters-sequence-files-according-to-numerous-conditions" class="nav-link active" data-scroll-target="#obigrep-filters-sequence-files-according-to-numerous-conditions"><span class="toc-section-number">12.1</span> <code>obigrep</code> – filters sequence files according to numerous conditions</a>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></h1>
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<h2 data-number="12.1" class="anchored" data-anchor-id="obigrep-filters-sequence-files-according-to-numerous-conditions"><span class="header-section-number">12.1</span> <code>obigrep</code> – filters sequence files according to numerous conditions</h2>
|
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<p>The <code>obigrep</code> command is somewhat analogous to the standard Unix <code>grep</code> command. It selects a subset of sequence records from a sequence file. A sequence record is a complex object consisting of an identifier, a set of attributes (a key, defined by its name, associated with a value), a definition, and the sequence itself. Instead of working text line by text line like the standard Unix tool, <code>obigrep</code> selection is done sequence record by sequence record. A large number of options allow you to refine the selection on any element of the sequence. <code>obigrep</code> allows you to specify multiple conditions simultaneously (which take on the value <code>TRUE</code> or <code>FALSE</code>) and only those sequence records which meet all conditions (all conditions are <code>TRUE</code>) are selected. <code>obigrep</code> is able to work on two paired read files. The selection criteria apply to one or the other of the readings in each pair depending on the mode chosen (<strong>--paired-mode</strong> option). In all cases the selection is applied in the same way to both files, thus maintaining their consistency.</p>
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<h4 data-number="12.1.1.1" class="anchored" data-anchor-id="selecting-sequences-based-on-their-caracteristics"><span class="header-section-number">12.1.1.1</span> Selecting sequences based on their caracteristics</h4>
|
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<p>Sequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.</p>
|
||||
<p><strong>Selection based on the sequence</strong></p>
|
||||
<p>Sequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (<em>e.g</em> <code>AACCTT</code>). But the usage of regular patterns allows for looking for more complex pattern. As example, <code>A[TG]C+G</code> matches a <code>A</code>, followed by a <code>T</code> or a <code>G</code>, then one or several <code>C</code> and endly a <code>G</code>.</p>
|
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<dl>
|
||||
<dt><strong>--sequence</strong>|<strong>-s</strong> <em>PATTERN</em></dt>
|
||||
<dd>
|
||||
<p>Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available <a href="https://yourbasic.org/golang/regexp-cheat-sheet/#cheat-sheet">here</a>.</p>
|
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|
||||
<dt><em>Examples:</em></dt>
|
||||
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|
||||
<p>Selects only the sequence records that contain an <em>EcoRI</em> restriction site.</p>
|
||||
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||||
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'GAATTC'</span> seq1.fasta <span class="op">></span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>: Selects only the sequence records that contain a stretch of at least 10 <code>A</code>.</p>
|
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<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'A{10,}'</span> seq1.fasta <span class="op">></span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
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<p>: Selects only the sequence records that do not contain ambiguous nucleotides.</p>
|
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<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-s</span> <span class="st">'^[ACGT]+$'</span> seq1.fasta <span class="op">></span> seq2.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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|
||||
<dt><strong>--min-count</strong> | <strong>-c</strong> <em>COUNT</em></dt>
|
||||
<dd>
|
||||
<p>only sequences reprensenting at least <em>COUNT</em> reads will be selected. That option rely on the <code>count</code> attribute. If the <code>count</code> attribute is not defined for a sequence record, it is assumed equal to <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mn>1</mn><annotation encoding="application/x-tex">1</annotation></semantics></math>.</p>
|
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</dd>
|
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<dt><strong>--max-count</strong> | <strong>-C</strong> <em>COUNT</em></dt>
|
||||
<dd>
|
||||
<p>only sequences reprensenting no more than <em>COUNT</em> reads will be selected. That option rely on the <code>count</code> attribute. If the <code>count</code> attribute is not defined for a sequence record, it is assumed equal to <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mn>1</mn><annotation encoding="application/x-tex">1</annotation></semantics></math>.</p>
|
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</dd>
|
||||
<dt><em>Examples</em></dt>
|
||||
<dd>
|
||||
<p>Selecting sequence records representing at least five reads in the dataset.</p>
|
||||
</dd>
|
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</dl>
|
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<div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obigrep</span> <span class="at">-c</span> 5 data_SPER01.fasta <span class="op">></span> data_norare_SPER01.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<li><a href="#obicount" id="toc-obicount" class="nav-link active" data-scroll-target="#obicount"><span class="toc-section-number">13.1</span> <code>obicount</code></a></li>
|
||||
<li><a href="#obidistribute" id="toc-obidistribute" class="nav-link" data-scroll-target="#obidistribute"><span class="toc-section-number">13.2</span> <code>obidistribute</code></a></li>
|
||||
<li><a href="#obifind" id="toc-obifind" class="nav-link" data-scroll-target="#obifind"><span class="toc-section-number">13.3</span> <code>obifind</code></a></li>
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|
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<h2 data-number="13.1" class="anchored" data-anchor-id="obicount"><span class="header-section-number">13.1</span> <code>obicount</code></h2>
|
||||
<p><code>obicount</code> counts the number of sequence records, the sum of the <code>count</code> attributes, and the sum of the length of all the sequences.</p>
|
||||
<p><em>Example:</em></p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obicount</span> seq.fasta </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>Prints the number of sequence records contained in the <code>seq.fasta</code> file and the sum of their <code>count</code> attributes.</p>
|
||||
<p><em>Options specific to the command</em></p>
|
||||
<ul>
|
||||
<li><code>--reads|-r</code> Prints read counts.</li>
|
||||
<li><code>--symbols|-s</code> Prints symbol counts.</li>
|
||||
<li><code>--variants|-v</code> Prints variant counts.</li>
|
||||
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|
||||
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|
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<a href="./tutorial.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">OBITools V4 Tutorial</span></a>
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<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
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<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
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<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
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<li><a href="#helpful-options" id="toc-helpful-options" class="nav-link active" data-scroll-target="#helpful-options"><span class="toc-section-number">6.1</span> Helpful options</a></li>
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<li><a href="#system-related-options" id="toc-system-related-options" class="nav-link" data-scroll-target="#system-related-options"><span class="toc-section-number">6.2</span> System related options</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></h1>
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|
||||
<dl>
|
||||
<dt><strong>--help</strong>, <strong>-h</strong></dt>
|
||||
<dd>
|
||||
<p>Display a friendly help message.</p>
|
||||
</dd>
|
||||
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|
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<p><strong>--no-progressbar</strong></p>
|
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|
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<section id="system-related-options" class="level2" data-number="6.2">
|
||||
<h2 data-number="6.2" class="anchored" data-anchor-id="system-related-options"><span class="header-section-number">6.2</span> System related options</h2>
|
||||
<p><strong>Managing parallel execution of tasks</strong></p>
|
||||
<p>A new feature of <em>OBITools</em> V4 is the ability to run multiple tasks in parallel, reading files, calculating on the data, formatting and writing the results. Each of these tasks can itself be parallelized by dividing the data into batches and running the calculation on several batches in parallel. This allows the overall calculation time of an <em>OBITools</em> command to be reduced considerably. The parameters organizing the parallel calculation are determined automatically to use the maximum capacity of your computer. But in some circumstances, it is necessary to override these default settings either to try to optimize the computation on a given machine, or to limit the OBITools to using only a part of the computational capacity. There are two options for doing this.</p>
|
||||
<dl>
|
||||
<dt><strong>--max-cpu</strong></dt>
|
||||
<dd>
|
||||
<p>OBITools V4 are able to run in parallel on all the CPU cores available on the computer. It is sometime required to limit the computation to a smaller number of cores. That option specify the maximum number of cores that the OBITools command can use. This behaviour can also be set up using the <code>OBIMAXCPU</code> environment variable.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
<p><strong>--workers</strong>, <strong>-w</strong></p>
|
||||
<p>If your computer has 8 cores, but you want to limit <em>OBITools</em> to use only two of them you have several solution:</p>
|
||||
<ul>
|
||||
<li><p>If you want to set the limit for a single execution you can use the <strong>–max-cpu</strong> option</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obiconvert</span> <span class="at">--max-cpu</span> 2 <span class="at">--fasta-output</span> data.fastq <span class="op">></span> data.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>or you can precede the command by setting the environment variable <code>OBIMAXCPU</code></p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="va">OBIMAXCPU</span><span class="op">=</span>2 <span class="ex">obiconvert</span> <span class="at">--fasta-output</span> data.fastq <span class="op">></span> data.fasta</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div></li>
|
||||
<li><p>If you want to set the limit to your complete session, you have to export <code>OBIMAXCPU</code></p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="bu">export</span> <span class="va">OBIMAXCPU</span><span class="op">=</span>2 </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>all the following OBITools commands will be limited to use at max 2 CPU cores.</p></li>
|
||||
<li><p>If all the time you want to impose this limit, you must include the above <code>export</code> command in your <code>.bashrc</code> file.</p></li>
|
||||
</ul>
|
||||
<p><strong>OBITools debuging related options</strong></p>
|
||||
<p><strong>--debug</strong></p>
|
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></span>
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<li><a href="#variables-usable-in-the-expression" id="toc-variables-usable-in-the-expression" class="nav-link active" data-scroll-target="#variables-usable-in-the-expression"><span class="toc-section-number">7.1</span> Variables usable in the expression</a></li>
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<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">7.2</span> Function defined in the language</a>
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<li><a href="#string-related-functions" id="toc-string-related-functions" class="nav-link" data-scroll-target="#string-related-functions">String related functions</a></li>
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<li><a href="#sequence-analysis-related-function" id="toc-sequence-analysis-related-function" class="nav-link" data-scroll-target="#sequence-analysis-related-function"><span class="toc-section-number">7.2.1</span> Sequence analysis related function</a></li>
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<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">7.3</span> Accessing to the sequence annotations</a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></h1>
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||||
<p>Several OBITools (<em>e.g.</em> obigrep, obiannotate) allow the user to specify some simple expressions to compute values or define predicates. This expressions are parsed and evaluated using the <a href="https://pkg.go.dev/github.com/PaesslerAG/gval" title="Gval (Go eVALuate) for evaluating arbitrary expressions Go-like expressions.">gval</a> go package, which allows for evaluating go-Like expression.</p>
|
||||
<section id="variables-usable-in-the-expression" class="level2" data-number="7.1">
|
||||
<h2 data-number="7.1" class="anchored" data-anchor-id="variables-usable-in-the-expression"><span class="header-section-number">7.1</span> Variables usable in the expression</h2>
|
||||
<ul>
|
||||
<li><code>sequence</code> is the sequence object on which the expression is evaluated.</li>
|
||||
<li><code>annotations</code>is a map object containing every annotations associated to the currently processed sequence.</li>
|
||||
</ul>
|
||||
</section>
|
||||
<section id="function-defined-in-the-language" class="level2" data-number="7.2">
|
||||
<h2 data-number="7.2" class="anchored" data-anchor-id="function-defined-in-the-language"><span class="header-section-number">7.2</span> Function defined in the language</h2>
|
||||
<section id="instrospection-functions" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="instrospection-functions">Instrospection functions</h3>
|
||||
<dl>
|
||||
<dt><strong><code>len(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>It is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like <code>annotations</code>, the number of elements in an array. The reurned value is an <code>int</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>contains(map,key)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Tests if the <code>map</code> contains a value assciated to <code>key</code></p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="cast-functions" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="cast-functions">Cast functions</h3>
|
||||
<dl>
|
||||
<dt><strong><code>int(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Converts if possible the <code>x</code> value to an integer value. The function returns an <code>int</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>numeric(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Converts if possible the <code>x</code> value to a float value. The function returns a <code>float</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>bool(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Converts if possible the <code>x</code> value to a boolean value. The function returns a <code>bool</code>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="string-related-functions" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="string-related-functions">String related functions</h3>
|
||||
<dl>
|
||||
<dt><strong><code>printf(format,...)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Allows to combine several values to build a string. <code>format</code> follows the classical C <code>printf</code> syntax. The function returns a <code>string</code>.</p>
|
||||
</dd>
|
||||
<dt><strong><code>subspc(x)</code></strong></dt>
|
||||
<dd>
|
||||
<p>substitutes every space in the <code>x</code> string by the underscore (<code>_</code>) character. The function returns a <code>string</code>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="condition-function" class="level3 unnumbered">
|
||||
<h3 class="unnumbered anchored" data-anchor-id="condition-function">Condition function</h3>
|
||||
<dl>
|
||||
<dt><strong><code>ifelse(condition,val1,val2)</code></strong></dt>
|
||||
<dd>
|
||||
<p>The <code>condition</code> value has to be a <code>bool</code> value. If it is <code>true</code> the function returns <code>val1</code>, otherwise, it is returning <code>val2</code>.</p>
|
||||
</dd>
|
||||
</dl>
|
||||
</section>
|
||||
<section id="sequence-analysis-related-function" class="level3" data-number="7.2.1">
|
||||
<h3 data-number="7.2.1" class="anchored" data-anchor-id="sequence-analysis-related-function"><span class="header-section-number">7.2.1</span> Sequence analysis related function</h3>
|
||||
<dl>
|
||||
<dt><strong><code>composition(sequence)</code></strong></dt>
|
||||
<dd>
|
||||
<p>The nucleotide composition of the sequence is returned as as map indexed by <code>a</code>, <code>c</code>, <code>g</code>, or <code>t</code> and each value is the number of occurrences of that nucleotide. A fifth key <code>others</code> accounts for all others symboles.</p>
|
||||
</dd>
|
||||
<dt><strong><code>gcskew(sequence)</code></strong></dt>
|
||||
<dd>
|
||||
<p>Computes the excess of g compare to c of the sequence, known as the GC skew.</p>
|
||||
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>S</mi><mi>k</mi><mi>e</mi><msub><mi>w</mi><mrow><mi>G</mi><mi>C</mi></mrow></msub><mo>=</mo><mfrac><mrow><mi>G</mi><mo>−</mo><mi>C</mi></mrow><mrow><mi>G</mi><mo>+</mo><mi>C</mi></mrow></mfrac></mrow><annotation encoding="application/x-tex">
|
||||
Skew_{GC}=\frac{G-C}{G+C}
|
||||
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|
||||
</dd>
|
||||
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|
||||
</section>
|
||||
</section>
|
||||
<section id="accessing-to-the-sequence-annotations" class="level2" data-number="7.3">
|
||||
<h2 data-number="7.3" class="anchored" data-anchor-id="accessing-to-the-sequence-annotations"><span class="header-section-number">7.3</span> Accessing to the sequence annotations</h2>
|
||||
<p>The <code>annotations</code> variable is a map object containing all the annotations associated to the currently processed sequence. Index of the map are the attribute names. It exists to possibillities to retreive an annotation. It is possible to use the classical <code>[]</code> indexing operator, putting the attribute name quoted by double quotes between them.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>annotations<span class="op">[</span><span class="st">"direction"</span><span class="op">]</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>The above code retreives the <code>direction</code> annotation. A second notation using the dot (<code>.</code>) is often more convenient.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>annotations<span class="op">.</span>direction</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>Special attributes of the sequence are accessible only by dedicated methods of the <code>sequence</code> object.</p>
|
||||
<ul>
|
||||
<li>The sequence identifier : <code>Id()</code></li>
|
||||
<li>THe sequence definition : <code>Definition()</code></li>
|
||||
</ul>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>sequence<span class="op">.</span>Id<span class="op">()</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="sidebar-item-container">
|
||||
<a href="./commands.html" class="sidebar-item-text sidebar-link">The *OBITools V4* commands</a>
|
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|
||||
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|
||||
<a href="./inupt.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">Specifying the data input to <em>OBITools</em> commands</span></a>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
|
||||
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|
||||
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|
||||
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|
||||
<div class="sidebar-item-container">
|
||||
<a href="./common_options.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></a>
|
||||
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|
||||
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|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./expressions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></a>
|
||||
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|
||||
</li>
|
||||
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|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_metabarcode_design.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">8</span> <span class="chapter-title">Metabarcode design and quality assessment</span></a>
|
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|
||||
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|
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|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_reformat.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span> <span class="chapter-title">File format conversions</span></a>
|
||||
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|
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|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></a>
|
||||
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|
||||
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|
||||
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|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_computation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span> <span class="chapter-title">Computations on sequences</span></a>
|
||||
</div>
|
||||
</li>
|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
|
||||
</div>
|
||||
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|
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<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./comm_utilities.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></a>
|
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||||
</ul>
|
||||
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<li class="sidebar-item sidebar-item-section">
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<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
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<a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">Appendices</a>
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<i class="bi bi-chevron-right ms-2"></i>
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<a href="./annexes.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">A</span> <span class="chapter-title">Annexes</span></a>
|
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|
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||||
<li class="sidebar-item">
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||||
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<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
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<!-- margin-sidebar -->
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<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
|
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<nav id="TOC" role="doc-toc" class="toc-active">
|
||||
<h2 id="toc-title">Table of contents</h2>
|
||||
|
||||
<ul>
|
||||
<li><a href="#biosequence" id="toc-biosequence" class="nav-link active" data-scroll-target="#biosequence">BioSequence</a>
|
||||
<ul class="collapse">
|
||||
<li><a href="#creating-new-instances" id="toc-creating-new-instances" class="nav-link" data-scroll-target="#creating-new-instances">Creating new instances</a></li>
|
||||
<li><a href="#end-of-life-of-a-biosequence-instance" id="toc-end-of-life-of-a-biosequence-instance" class="nav-link" data-scroll-target="#end-of-life-of-a-biosequence-instance">End of life of a <code>BioSequence</code> instance</a></li>
|
||||
<li><a href="#accessing-to-the-elements-of-a-sequence" id="toc-accessing-to-the-elements-of-a-sequence" class="nav-link" data-scroll-target="#accessing-to-the-elements-of-a-sequence">Accessing to the elements of a sequence</a></li>
|
||||
<li><a href="#the-annotations-of-a-sequence" id="toc-the-annotations-of-a-sequence" class="nav-link" data-scroll-target="#the-annotations-of-a-sequence">The annotations of a sequence</a></li>
|
||||
</ul></li>
|
||||
<li><a href="#the-sequence-iterator" id="toc-the-sequence-iterator" class="nav-link" data-scroll-target="#the-sequence-iterator">The sequence iterator</a>
|
||||
<ul class="collapse">
|
||||
<li><a href="#basic-usage-of-a-sequence-iterator" id="toc-basic-usage-of-a-sequence-iterator" class="nav-link" data-scroll-target="#basic-usage-of-a-sequence-iterator">Basic usage of a sequence iterator</a></li>
|
||||
<li><a href="#the-pipable-functions" id="toc-the-pipable-functions" class="nav-link" data-scroll-target="#the-pipable-functions">The <code>Pipable</code> functions</a></li>
|
||||
<li><a href="#the-teeable-functions" id="toc-the-teeable-functions" class="nav-link" data-scroll-target="#the-teeable-functions">The <code>Teeable</code> functions</a></li>
|
||||
</ul></li>
|
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</ul>
|
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<!-- main -->
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<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">The GO <em>OBITools</em> library</h1>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<div class="quarto-title-meta">
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<section id="biosequence" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="biosequence">BioSequence</h2>
|
||||
<p>The <code>BioSequence</code> class is used to represent biological sequences. It allows for storing : - the sequence itself as a <code>[]byte</code> - the sequencing quality score as a <code>[]byte</code> if needed - an identifier as a <code>string</code> - a definition as a <code>string</code> - a set of <em>(key, value)</em> pairs in a <code>map[sting]interface{}</code></p>
|
||||
<p>BioSequence is defined in the obiseq module and is included using the code</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<section id="creating-new-instances" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="creating-new-instances">Creating new instances</h3>
|
||||
<p>To create new instance, use</p>
|
||||
<ul>
|
||||
<li><code>MakeBioSequence(id string, sequence []byte, definition string) obiseq.BioSequence</code></li>
|
||||
<li><code>NewBioSequence(id string, sequence []byte, definition string) *obiseq.BioSequence</code></li>
|
||||
</ul>
|
||||
<p>Both create a <code>BioSequence</code> instance, but when the first one returns the instance, the second returns a pointer on the new instance. Two other functions <code>MakeEmptyBioSequence</code>, and <code>NewEmptyBioSequence</code> do the same job but provide an uninitialized objects.</p>
|
||||
<ul>
|
||||
<li><code>id</code> parameters corresponds to the unique identifier of the sequence. It mist be a string constituted of a single word (not containing any space).</li>
|
||||
<li><code>sequence</code> is the DNA sequence itself, provided as a <code>byte</code> array (<code>[]byte</code>).</li>
|
||||
<li><code>definition</code> is a <code>string</code>, potentially empty, but usualy containing a sentence explaining what is that sequence.</li>
|
||||
</ul>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewBiosequence<span class="op">(</span></span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"seq_GH0001"</span><span class="op">,</span></span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> bytes<span class="op">.</span>FromString<span class="op">(</span><span class="st">"ACGTGTCAGTCG"</span><span class="op">),</span></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"A short test sequence"</span><span class="op">,</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>When formated as fasta the parameters correspond to the following schema</p>
|
||||
<pre><code>>id definition containing potentially several words
|
||||
sequence</code></pre>
|
||||
</section>
|
||||
<section id="end-of-life-of-a-biosequence-instance" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="end-of-life-of-a-biosequence-instance">End of life of a <code>BioSequence</code> instance</h3>
|
||||
<p>When an instance of <code>BioSequence</code> is no longer in use, it is normally taken over by the GO garbage collector. If you know that an instance will never be used again, you can, if you wish, call the <code>Recycle</code> method on it to store the allocated memory elements in a <code>pool</code> to limit the allocation effort when many sequences are being handled. Once the recycle method has been called on an instance, you must ensure that no other method is called on it.</p>
|
||||
</section>
|
||||
<section id="accessing-to-the-elements-of-a-sequence" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="accessing-to-the-elements-of-a-sequence">Accessing to the elements of a sequence</h3>
|
||||
<p>The different elements of an <code>obiseq.BioSequence</code> must be accessed using a set of methods. For the three main elements provided during the creation of a new instance methodes are :</p>
|
||||
<ul>
|
||||
<li><code>Id() string</code></li>
|
||||
<li><code>Sequence() []byte</code></li>
|
||||
<li><code>Definition() string</code></li>
|
||||
</ul>
|
||||
<p>It exists pending method to change the value of these elements</p>
|
||||
<ul>
|
||||
<li><code>SetId(id string)</code></li>
|
||||
<li><code>SetSequence(sequence []byte)</code></li>
|
||||
<li><code>SetDefinition(definition string)</code></li>
|
||||
</ul>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||||
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||||
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewBiosequence<span class="op">(</span></span>
|
||||
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"seq_GH0001"</span><span class="op">,</span></span>
|
||||
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a> bytes<span class="op">.</span>FromString<span class="op">(</span><span class="st">"ACGTGTCAGTCG"</span><span class="op">),</span></span>
|
||||
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"A short test sequence"</span><span class="op">,</span></span>
|
||||
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a> <span class="op">)</span></span>
|
||||
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>Id<span class="op">())</span></span>
|
||||
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>SetId<span class="op">(</span><span class="st">"SPE01_0001"</span><span class="op">)</span></span>
|
||||
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>Id<span class="op">())</span></span>
|
||||
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<section id="different-ways-for-accessing-an-editing-the-sequence" class="level4">
|
||||
<h4 class="anchored" data-anchor-id="different-ways-for-accessing-an-editing-the-sequence">Different ways for accessing an editing the sequence</h4>
|
||||
<p>If <code>Sequence()</code>and <code>SetSequence(sequence []byte)</code> methods are the basic ones, several other methods exist.</p>
|
||||
<ul>
|
||||
<li><code>String() string</code> return the sequence directly converted to a <code>string</code> instance.</li>
|
||||
<li>The <code>Write</code> method family allows for extending an existing sequence following the buffer protocol.
|
||||
<ul>
|
||||
<li><code>Write(data []byte) (int, error)</code> allows for appending a byte array on 3’ end of the sequence.</li>
|
||||
<li><code>WriteString(data string) (int, error)</code> allows for appending a <code>string</code>.</li>
|
||||
<li><code>WriteByte(data byte) error</code> allows for appending a single <code>byte</code>.</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
<p>The <code>Clear</code> method empties the sequence buffer.</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"fmt"</span></span>
|
||||
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"</span></span>
|
||||
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> myseq <span class="op">:=</span> obiseq<span class="op">.</span>NewEmptyBiosequence<span class="op">()</span></span>
|
||||
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>WriteString<span class="op">(</span><span class="st">"accc"</span><span class="op">)</span></span>
|
||||
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> myseq<span class="op">.</span>WriteByte<span class="op">(</span><span class="dt">byte</span><span class="op">(</span><span class="ch">'c'</span><span class="op">))</span></span>
|
||||
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> fmt<span class="op">.</span>Println<span class="op">(</span>myseq<span class="op">.</span>String<span class="op">())</span></span>
|
||||
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
</section>
|
||||
<section id="sequence-quality-scores" class="level4">
|
||||
<h4 class="anchored" data-anchor-id="sequence-quality-scores">Sequence quality scores</h4>
|
||||
<p>Sequence quality scores cannot be initialized at the time of instance creation. You must use dedicated methods to add quality scores to a sequence.</p>
|
||||
<p>To be coherent the length of both the DNA sequence and que quality score sequence must be equal. But assessment of this constraint is realized. It is of the programmer responsability to check that invariant.</p>
|
||||
<p>While accessing to the quality scores relies on the method <code>Quality() []byte</code>, setting the quality need to call one of the following method. They run similarly to their sequence dedicated conterpart.</p>
|
||||
<ul>
|
||||
<li><code>SetQualities(qualities Quality)</code></li>
|
||||
<li><code>WriteQualities(data []byte) (int, error)</code></li>
|
||||
<li><code>WriteByteQualities(data byte) error</code></li>
|
||||
</ul>
|
||||
<p>In a way analogous to the <code>Clear</code> method, <code>ClearQualities()</code> empties the sequence of quality scores.</p>
|
||||
</section>
|
||||
</section>
|
||||
<section id="the-annotations-of-a-sequence" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="the-annotations-of-a-sequence">The annotations of a sequence</h3>
|
||||
<p>A sequence can be annotated with attributes. Each attribute is associated with a value. An attribute is identified by its name. The name of an attribute consists of a character string containing no spaces or blank characters. Values can be of several types.</p>
|
||||
<ul>
|
||||
<li>Scalar types:
|
||||
<ul>
|
||||
<li>integer</li>
|
||||
<li>numeric</li>
|
||||
<li>character</li>
|
||||
<li>boolean</li>
|
||||
</ul></li>
|
||||
<li>Container types:
|
||||
<ul>
|
||||
<li>vector</li>
|
||||
<li>map</li>
|
||||
</ul></li>
|
||||
</ul>
|
||||
<p>Vectors can contain any type of scalar. Maps are compulsorily indexed by strings and can contain any scalar type. It is not possible to have nested container type.</p>
|
||||
<p>Annotations are stored in an object of type <code>bioseq.Annotation</code> which is an alias of <code>map[string]interface{}</code>. This map can be retrieved using the <code>Annotations() Annotation</code> method. If no annotation has been defined for this sequence, the method returns an empty map. It is possible to test an instance of <code>BioSequence</code> using its <code>HasAnnotation() bool</code> method to see if it has any annotations associated with it.</p>
|
||||
<ul>
|
||||
<li>GetAttribute(key string) (interface{}, bool)</li>
|
||||
</ul>
|
||||
</section>
|
||||
</section>
|
||||
<section id="the-sequence-iterator" class="level2">
|
||||
<h2 class="anchored" data-anchor-id="the-sequence-iterator">The sequence iterator</h2>
|
||||
<p>The pakage <em>obiter</em> provides an iterator mecanism for manipulating sequences. The main class provided by this package is <code>obiiter.IBioSequence</code>. An <code>IBioSequence</code> iterator provides batch of sequences.</p>
|
||||
<section id="basic-usage-of-a-sequence-iterator" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="basic-usage-of-a-sequence-iterator">Basic usage of a sequence iterator</h3>
|
||||
<p>Many functions, among them functions reading sequences from a text file, return a <code>IBioSequence</code> iterator. The iterator class provides two main methods:</p>
|
||||
<ul>
|
||||
<li><code>Next() bool</code></li>
|
||||
<li><code>Get() obiiter.BioSequenceBatch</code></li>
|
||||
</ul>
|
||||
<p>The <code>Next</code> method moves the iterator to the next value, while the <code>Get</code> method returns the currently pointed value. Using them, it is possible to loop over the data as in the following code chunk.</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode go code-with-copy"><code class="sourceCode go"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="kw">import</span> <span class="op">(</span></span>
|
||||
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"</span></span>
|
||||
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="op">)</span></span>
|
||||
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="kw">func</span> main<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> mydata <span class="op">:=</span> obiformats<span class="op">.</span>ReadFastSeqFromFile<span class="op">(</span><span class="st">"myfile.fasta"</span><span class="op">)</span></span>
|
||||
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a> </span>
|
||||
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a> <span class="cf">for</span> mydata<span class="op">.</span>Next<span class="op">()</span> <span class="op">{</span></span>
|
||||
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> data <span class="op">:=</span> mydata<span class="op">.</span>Get<span class="op">()</span></span>
|
||||
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a> <span class="co">//</span></span>
|
||||
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a> <span class="co">// Whatever you want to do with the data chunk</span></span>
|
||||
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a> <span class="co">//</span></span>
|
||||
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a> <span class="op">}</span></span>
|
||||
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||||
<p>An <code>obiseq.BioSequenceBatch</code> instance is a set of sequences stored in an <code>obiseq.BioSequenceSlice</code> and a sequence number. The number of sequences in a batch is not defined. A batch can even contain zero sequences, if for example all sequences initially included in the batch have been filtered out at some stage of their processing.</p>
|
||||
</section>
|
||||
<section id="the-pipable-functions" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="the-pipable-functions">The <code>Pipable</code> functions</h3>
|
||||
<p>A function consuming a <code>obiiter.IBioSequence</code> and returning a <code>obiiter.IBioSequence</code> is of class <code>obiiter.Pipable</code>.</p>
|
||||
</section>
|
||||
<section id="the-teeable-functions" class="level3">
|
||||
<h3 class="anchored" data-anchor-id="the-teeable-functions">The <code>Teeable</code> functions</h3>
|
||||
<p>A function consuming a <code>obiiter.IBioSequence</code> and returning two <code>obiiter.IBioSequence</code> instance is of class <code>obiiter.Teeable</code>.</p>
|
||||
|
||||
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></span>
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<li><a href="#specifying-output-format" id="toc-specifying-output-format" class="nav-link active" data-scroll-target="#specifying-output-format"><span class="toc-section-number">5.1</span> Specifying output format</a></li>
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<h2 data-number="5.1" class="anchored" data-anchor-id="specifying-output-format"><span class="header-section-number">5.1</span> Specifying output format</h2>
|
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<p>Only two output sequence formats are supported by OBITools, Fasta and Fastq. Fastq is used when output sequences are associated with quality information. Otherwise, Fasta is the default format. However, it is possible to force the output format by using one of the following two options. Forcing the use of Fasta results in the loss of quality information. Conversely, when the Fastq format is forced with sequences that have no quality data, dummy qualities set to 40 for each nucleotide are added.</p>
|
||||
<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>
|
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|
||||
<li><code>--no-order</code> When several input files are provided, indicates that there is no order among them. (default: false). Using such option can increase a lot the processing of the data.</li>
|
||||
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|
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|
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<section id="the-fasta-and-fastq-annotations-format" class="level2" data-number="5.2">
|
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<h2 data-number="5.2" class="anchored" data-anchor-id="the-fasta-and-fastq-annotations-format"><span class="header-section-number">5.2</span> The Fasta and Fastq annotations format</h2>
|
||||
<p>OBITools extend the <a href="#the-fasta-sequence-format">Fasta</a> and <a href="#the-fastq-sequence-format">Fastq</a> formats by introducing a format for the title lines of these formats allowing to annotate every sequence. While the previous version of OBITools used an <em>ad-hoc</em> format for these annotation, this new version introduce the usage of the standard JSON format to store them.</p>
|
||||
<p>On input, OBITools automatically recognize the format of the annotations, but two options allows to force the parsing following one of them. You should normally not need to use these options.</p>
|
||||
<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>
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<a href="./index.html" class="sidebar-item-text sidebar-link">Preface</a>
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<a href="./installation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">Installation of the <em>OBITools</em></span></a>
|
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<a href="./formats.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">File formats usable with <em>OBITools</em></span></a>
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<a href="./tutorial.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">OBITools V4 Tutorial</span></a>
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<a href="./commands.html" class="sidebar-item-text sidebar-link">The *OBITools V4* commands</a>
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<a href="./inupt.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">Specifying the data input to <em>OBITools</em> commands</span></a>
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<a href="./output.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Controling OBITools outputs</span></a>
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<a href="./common_options.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span> <span class="chapter-title">Options common to most of the <em>OBITools</em> commands</span></a>
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<a href="./expressions.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span> <span class="chapter-title">OBITools expression language</span></a>
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<a href="./comm_annotation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span> <span class="chapter-title">Sequence annotations</span></a>
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|
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<a href="./comm_sampling.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span> <span class="chapter-title">Sequence sampling and filtering</span></a>
|
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<a href="./comm_utilities.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></a>
|
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|
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<span class="sidebar-item-text sidebar-link text-start">The GO *OBITools* library</span>
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<a href="./annexes.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">A</span> <span class="chapter-title">Annexes</span></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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||||
<div id="refs" class="references csl-bib-body hanging-indent" role="doc-bibliography">
|
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d1ab8a47978e8cbde063ec16bae609a9371d97ea
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Vendored
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"title": "1 Installation of the OBITools",
|
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"section": "1.2 Prerequisites",
|
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"text": "1.2 Prerequisites\nThe OBITools4 are developped using the GO programming language, we stick to the latest version of the language, today the \\(1.21.4\\). If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. Some parts of the soft are also written in C, therefore a recent C compiler is also requested, GCC on Linux or Windows, the Developer Tools on Mac.\nWhatever the installation you decide for, you will have to ensure that a C compiler is available on your system."
|
||||
"text": "1.2 Prerequisites\nThe OBITools4 are developped using the GO programming language, we stick to the latest version of the language, today the 1.21.41.21.4. If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. Some parts of the soft are also written in C, therefore a recent C compiler is also requested, GCC on Linux or Windows, the Developer Tools on Mac.\nWhatever the installation you decide for, you will have to ensure that a C compiler is available on your system."
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||||
"text": "3 The DNA sequence data\nSequences can be stored following various format. OBITools knows some of them. The central formats for sequence files manipulated by OBITools scripts are the FASTA 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 IUPAC code for encoding nucleotides.\nMoreover these two formats that can be used as input and output formats, OBITools4 can read the following format :"
|
||||
"section": "2.1 The DNA sequence data",
|
||||
"text": "2.1 The DNA sequence data\nSequences can be stored following various format. OBITools knows some of them. The central formats for sequence files manipulated by OBITools scripts are the FASTA 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 IUPAC code for encoding nucleotides.\nMoreover these two formats that can be used as input and output formats, OBITools4 can read the following format :\n\nEBML flat file format (use by ENA)\nGenbank flat file format\necoPCR output files\n\n\n2.1.1 The IUPAC Code\nThe International Union of Pure and Applied Chemistry (IUPAC) defined the standard code for representing protein or DNA sequences.\n\n\n\nCode\nNucleotide\n\n\n\n\nA\nAdenine\n\n\nC\nCytosine\n\n\nG\nGuanine\n\n\nT\nThymine\n\n\nU\nUracil\n\n\nR\nPurine (A or G)\n\n\nY\nPyrimidine (C, T, or U)\n\n\nM\nC or A\n\n\nK\nT, U, or G\n\n\nW\nT, U, or A\n\n\nS\nC or G\n\n\nB\nC, T, U, or G (not A)\n\n\nD\nA, T, U, or G (not C)\n\n\nH\nA, T, U, or C (not G)\n\n\nV\nA, C, or G (not T, not U)\n\n\nN\nAny base (A, C, G, T, or U)\n\n\n\n\n\n2.1.2 The FASTA sequence format\nThe FASTA format 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 FASTA program. OBITools use in more of the classical FASTA format an extended version of this format where structured data are included in the title line.\nIn FASTA format a sequence is represented by a title line beginning with a > character and the sequences by itself following the IUPAC code. The sequence is usually split other severals lines of the same length (expect for the last one)\n>my_sequence this is my pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\nThis is no special format for the title line excepting that this line should be unique. Usually the first word following the > 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\n>sequence_A this is my first pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n>sequence_B this is my second pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n>sequence_C this is my third pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n\n2.1.2.1 File extensions\nThere is no standard file extension for a FASTA file, but .fa and .fasta, are commonly used.\n\n\n\n2.1.3 The FASTQ sequence format1\nThe FASTQ format is a text file format for storing both biological sequences (only nucleic acid sequences) and the associated sequence quality scores. Every nucleotide of the sequence and its associated quality score are each encoded by a single ASCII character. This format was originally developed by the Wellcome Trust Sanger Institute to link a FASTA sequence file to the corresponding quality data, but is now became the de facto standard for storing results from high-throughput sequencers (Cock et al. 2010).\nOBITools considers that a FASTQ file uses four lines to encode a sequence record.\n\nLine 1 begins with a ‘@’ character and is followed by a sequence identifier and an optional description (like a FASTA title line).\nLine 2 is the sequence letters, in upper or lower case, but OBITools only write sequences as lower cases.\nLine 3 begins with a ‘+’ character and is optionally followed by the same sequence identifier (and any description) again.\nLine 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.\n\nA FASTQ file looks like this:\n@SEQ_ID\nGATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT\n+\n!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65\nThe character ‘!’ represents the lowest quality while ‘~’ is the highest. Here are the quality value characters in left-to-right increasing order of quality (ASCII):\n!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]\n^_`abcdefghijklmnopqrstuvwxyz{|}~\nIf the original Sanger FASTQ files also allowed the sequence and quality strings to be wrapped (split over multiple lines), it is not supported by OBITools as it make parsing complicated due to the unfortunate choice of “@” and “+” as markers (these characters can also occur in the quality string).\n\nSequence quality Line truncated
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|
||||
"text": "3.1 The IUPAC Code\nThe International Union of Pure and Applied Chemistry (IUPAC) defined the standard code for representing protein or DNA sequences.\n\n\n\nCode\nNucleotide\n\n\n\n\nA\nAdenine\n\n\nC\nCytosine\n\n\nG\nGuanine\n\n\nT\nThymine\n\n\nU\nUracil\n\n\nR\nPurine (A or G)\n\n\nY\nPyrimidine (C, T, or U)\n\n\nM\nC or A\n\n\nK\nT, U, or G\n\n\nW\nT, U, or A\n\n\nS\nC or G\n\n\nB\nC, T, U, or G (not A)\n\n\nD\nA, T, U, or G (not C)\n\n\nH\nA, T, U, or C (not G)\n\n\nV\nA, C, or G (not T, not U)\n\n\nN\nAny base (A, C, G, T, or U)"
|
||||
"section": "2.2 The taxonomy files",
|
||||
"text": "2.2 The taxonomy files\nMany OBITools are able to take into account taxonomic data. This is done by specifying a directory containing all :doc:NCBI taxonomy dump files <./taxdump>."
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"text": "3.2 The FASTA sequence format\nThe FASTA format 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 FASTA program. OBITools use in more of the classical FASTA format an extended version of this format where structured data are included in the title line.\nIn FASTA format a sequence is represented by a title line beginning with a > character and the sequences by itself following the IUPAC code. The sequence is usually split other severals lines of the same length (expect for the last one)\n>my_sequence this is my pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\nThis is no special format for the title line excepting that this line should be unique. Usually the first word following the > 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\n>sequence_A this is my first pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n>sequence_B this is my second pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n>sequence_C this is my third pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n\n3.2.1 File extensions\nThere is no standard file extension for a FASTA file, but .fa and .fasta, are commonly used."
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"section": "3.3 The FASTQ sequence format1",
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||||
"text": "3.3 The FASTQ sequence format1\nThe FASTQ format is a text file format for storing both biological sequences (only nucleic acid sequences) and the associated sequence quality scores. Every nucleotide of the sequence and its associated quality score are each encoded by a single ASCII character. This format was originally developed by the Wellcome Trust Sanger Institute to link a FASTA sequence file to the corresponding quality data, but is now became the de facto standard for storing results from high-throughput sequencers (Cock et al. 2010).\nOBITools considers that a FASTQ file uses four lines per sequence.\n\nLine 1 begins with a ‘@’ character and is followed by a sequence identifier and an optional description (like a FASTA title line).\nLine 2 is the sequence letters, in upper or lower case, but OBITools only write sequences as lower cases.\nLine 3 begins with a ‘+’ character and is optionally followed by the same sequence identifier (and any description) again.\nLine 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.\n\nA FASTQ file looks like this:\n@SEQ_ID\nGATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT\n+\n!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65\nThe character ‘!’ represents the lowest quality while ‘~’ is the highest. Here are the quality value characters in left-to-right increasing order of quality (ASCII):\n!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]\n^_`abcdefghijklmnopqrstuvwxyz{|}~\nIf the original Sanger FASTQ files also allowed the sequence and quality strings to be wrapped (split over multiple lines), it is not supported by OBITools as it make parsing complicated due to the unfortunate choice of “@” and “+” as markers (these characters can also occur in the quality string).\n\nSequence quality scores\nThe Phred quality value Q is an integer mapping of p (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:\n\\[\nQ_\\text{sanger} = -10 \\, \\log_{10} p\n\\]\nThe Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) earlier used a different mapping, encoding the odds \\(\\mathbf{p}/(1-\\mathbf{p})\\) instead of the probability \\(\\mathbf{p}\\):\n\\[\nQ_\\text{solexa-prior to v.1.3} = -10 \\; \\log_{10} \\frac{p}{1-p}\n\\]\nAlthough both mappings are asymptotically identical at higher quality values, they differ at lower quality levels (i.e., approximately \\(\\mathbf{p} > 0.05\\), or equivalently, \\(\\mathbf{Q} < 13\\)).\n\n\n\nFigure 3.1: Relationship between Q and p using the Sanger (red) and Solexa (black) equations (described above). The vertical dotted line indicates \\(\\mathbf{p}= 0.05\\), or equivalently, \\(Q = 13\\).\n\n\n\nEncoding\nThe FASTQ format had differente way of encoding the Phred quality score along the time. Here a breif history of these changes is presented. OBITools\n\nSanger 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).\nSolexa/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)\nStarting 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).\nStarting 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”.\n\n\nSequencing Control Software, Version 2.6, (Catalog # SY-960-2601, Part # 15009921 Rev. A, November 2009, page 30) states the following: 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. 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:\n\n@HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1\nTTAATTGGTAAATAAATCTCCTAATAGCTTAGATNTTACCTTNNNNNNNNNNTAGTTTCTTGAGA\nTTTGTTGGGGGAGACATTTTTGTGATTGCCTTGAT\n+HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1\nefcfffffcfeefffcffffffddf`feed]`]_Ba_^__[YBBBBBBBBBBRTT\\]][ dddd`\nddd^dddadd^BBBBBBBBBBBBBBBBBBBBBBBB\nAn alternative interpretation of this ASCII encoding has been proposed. ALine truncated
|
||||
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|
||||
"text": "2.3 The sample description file\nA key file for OBITools4 is the file describing all samples (PCR) analyzed in the processed sequencing library file. This file, often called the ngsfilter file, is a tab separated values (TSV) file. The format of this file is exactly identical to that used in OBITools2 and OBITools4.\n{tsv, .smaller} wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F\nAt least six columns must be present in every line of the file.\n\nThe first column contains the name of the experience:\nAn experiment name groups a set of sample together. Sequences belonging to the experiment are tagged with an attribute experiment containing the name of the experiment in their annotation.\nThe second column contains the sample identifier in the experiment\nThe sample identifier must be unique in the experiment. The obimultiplex and obitagpcr commands add to all the sequences bellonging to the same sample an attribute sample containing the sample identifier\nThe third column contains description of the tag used to identify sequences corresponding to this sample\nThe fourth column contains the forward primer sequence\nThe fifth column contains the reverse primer sequence\nThe sixth column must always contain the character F (full length)\n\n\n\n\n\nCock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and Peter M Rice. 2010. “The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa/Illumina FASTQ Variants.” Nucleic Acids Research 38 (6): 1767–71."
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"title": "3 OBITools V4 Tutorial",
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||||
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|
||||
"text": "3.2 Step by step analysis\n\n3.2.1 Recover full sequence reads from forward and reverse partial reads\nWhen 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.\nThe forward and reverse reads of the same fragment are at the same line position 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 obipairing utility that aligns the two reads and returns the reconstructed sequence.\nIn our case, the command is:\n\nobipairing --min-identity=0.8 \\\n --min-overlap=10 \\\n -F wolf_data/wolf_F.fastq \\\n -R wolf_data/wolf_R.fastq \\\n > results/wolf.fastq \n\nThe --min-identity and --min-overlap 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 mode attribute in the sequence header is set to joined instead of alignment.\n\n\n3.2.2 Remove unaligned sequence records\nUnaligned sequences (:pymode=joined) cannot be used. The following command allows removing them from the dataset:\n\nobigrep -p 'annotations.mode != \"join\"' \\\n results/wolf.fastq > results/wolf.ali.fastq\n\nThe -p requires a go like expression. annotations.mode != \"join\" means that if the value of the mode annotation of a sequence is different from join, the corresponding sequence record will be kept.\nThe first sequence record of wolf.ali.fastq can be obtained using the following command line:\n\nhead -n 4 results/wolf.ali.fastq\n\nThe folling piece of code appears on thew window of tour terminal.\n@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}\nccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg\n+\nCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\\RYU\\\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC\n\n\n3.2.3 Assign each sequence record to the corresponding sample/marker combination\nEach sequence record is assigned to its corresponding sample and marker using the data provided in a text file (here wolf_diet_ngsfilter.txt). 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: aattaac if the same tag has been used on each extremity of the PCR products, or aattaac:gaagtag if the tags were different), the sequence of the forward primer, the sequence of the reverse primer, the letter T or F for sample identification using the forward primer and tag only or using both primers and both tags, respectively (see obimultiplex for details).\n\nobimultiplex -t wolf_data/wolf_diet_ngsfilter.txt \\\n -u results/unidentified.fastq \\\n results/wolf.ali.fastq \\\n > results/wolf.ali.assigned.fastq\n\nThis command creates two files:\n\nunidentified.fastq containing all the sequence records that were not assigned to a sample/marker combination\nwolf.ali.assigned.fastq containing all the sequence records that were properly assigned to a sample/marker combination\n\nNote that each sequence record of the wolf.ali.assigned.fastq file contains only the barcode sequence as the sequences of primers and tags are removed by the obimultiplex program. Information concerning the experiment, sample, primers and tags is added as attributes in the sequence header.\nFor instance, the first sequence record of wolf.ali.assigned.fastq is:\n@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}\nttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n+\nCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\\RYU\\\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC\n\n\n3.2.4 Dereplicate reads into uniq sequences\nThe same DNA Line truncated
|
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"text": "3.2 Step by step analysis\n\n3.2.1 Recover full sequence reads from forward and reverse partial reads\nWhen 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.\nThe forward and reverse reads of the same fragment are at the same line position 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 obipairing utility that aligns the two reads and returns the reconstructed sequence.\nIn our case, the command is:\n\nobipairing --min-identity=0.8 \\\n --min-overlap=10 \\\n -F wolf_data/wolf_F.fastq \\\n -R wolf_data/wolf_R.fastq \\\n > results/wolf.fastq \n\nThe --min-identity and --min-overlap 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 mode attribute in the sequence header is set to joined instead of alignment.\n\n\n3.2.2 Remove unaligned sequence records\nUnaligned sequences (:pymode=joined) cannot be used. The following command allows removing them from the dataset:\n\nobigrep -p 'annotations.mode != \"join\"' \\\n results/wolf.fastq > results/wolf.ali.fastq\n\nThe -p requires a go like expression. annotations.mode != \"join\" means that if the value of the mode annotation of a sequence is different from join, the corresponding sequence record will be kept.\nThe first sequence record of wolf.ali.fastq can be obtained using the following command line:\n\nhead -n 4 results/wolf.ali.fastq\n\nThe folling piece of code appears on thew window of tour terminal.\n@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}\nccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg\n+\nCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\\RYU\\\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC\n\n\n3.2.3 Assign each sequence record to the corresponding sample/marker combination\nEach sequence record is assigned to its corresponding sample and marker using the data provided in a text file (here wolf_diet_ngsfilter.txt). 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: aattaac if the same tag has been used on each extremity of the PCR products, or aattaac:gaagtag if the tags were different), the sequence of the forward primer, the sequence of the reverse primer, the letter T or F for sample identification using the forward primer and tag only or using both primers and both tags, respectively (see obimultiplex for details).\n\nobimultiplex -t wolf_data/wolf_diet_ngsfilter.txt \\\n -u results/unidentified.fastq \\\n results/wolf.ali.fastq \\\n > results/wolf.ali.assigned.fastq\n\nThis command creates two files:\n\nunidentified.fastq containing all the sequence records that were not assigned to a sample/marker combination\nwolf.ali.assigned.fastq containing all the sequence records that were properly assigned to a sample/marker combination\n\nNote that each sequence record of the wolf.ali.assigned.fastq file contains only the barcode sequence as the sequences of primers and tags are removed by the obimultiplex program. Information concerning the experiment, sample, primers and tags is added as attributes in the sequence header.\nFor instance, the first sequence record of wolf.ali.assigned.fastq is:\n@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}\nttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n+\nCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\\RYU\\\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC\n\n\n3.2.4 Dereplicate reads into uniq sequences\nThe same DNA Line truncated
|
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},
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{
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"objectID": "inupt.html#specifying-input-format",
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"href": "inupt.html#specifying-input-format",
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"title": "4 Specifying the data input to OBITools commands",
|
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"section": "4.1 Specifying input format",
|
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"text": "4.1 Specifying input format\nFive sequence formats are accepted for input files. Fasta (Section 3.2) and Fastq (Section 3.3) 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 OBITools and allows to read ecoPCR outputs as sequence files.\n\n--ecopcr : Read data following the ecoPCR output format.\n--embl Read data following the EMBL flatfile format.\n--genbank Read data following the Genbank flatfile format.\n\nSeveral encoding schemes have been proposed for quality scores in Fastq format. Currently, OBITools considers Sanger encoding as the standard. For reasons of compatibility with older datasets produced with Solexa sequencers, it is possible, by using the following option, to force the use of the corresponding quality encoding scheme when reading these older files.\n\n--solexa Decodes quality string according to the Solexa specification. (default: false)"
|
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"text": "4.1 Specifying input format\nFive sequence formats are accepted for input files. Fasta (Section 2.1.2) and Fastq (Section 2.1.3) 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 OBITools and allows to read ecoPCR outputs as sequence files.\n\n--ecopcr : Read data following the ecoPCR output format.\n--embl Read data following the EMBL flatfile format.\n--genbank Read data following the Genbank flatfile format.\n\nSeveral encoding schemes have been proposed for quality scores in Fastq format. Currently, OBITools considers Sanger encoding as the standard. For reasons of compatibility with older datasets produced with Solexa sequencers, it is possible, by using the following option, to force the use of the corresponding quality encoding scheme when reading these older files.\n\n--solexa Decodes quality string according to the Solexa specification. (default: false)"
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},
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"objectID": "output.html#specifying-output-format",
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@@ -130,7 +123,7 @@
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"href": "expressions.html#function-defined-in-the-language",
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"title": "7 OBITools expression language",
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"section": "7.2 Function defined in the language",
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"text": "7.2 Function defined in the language\n\nInstrospection functions\n\nlen(x)\n\nIt is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like annotations, the number of elements in an array. The reurned value is an int.\n\ncontains(map,key)\n\nTests if the map contains a value assciated to key\n\n\n\n\nCast functions\n\nint(x)\n\nConverts if possible the x value to an integer value. The function returns an int.\n\nnumeric(x)\n\nConverts if possible the x value to a float value. The function returns a float.\n\nbool(x)\n\nConverts if possible the x value to a boolean value. The function returns a bool.\n\n\n\n\nString related functions\n\nprintf(format,...)\n\nAllows to combine several values to build a string. format follows the classical C printf syntax. The function returns a string.\n\nsubspc(x)\n\nsubstitutes every space in the x string by the underscore (_) character. The function returns a string.\n\n\n\n\nCondition function\n\nifelse(condition,val1,val2)\n\nThe condition value has to be a bool value. If it is true the function returns val1, otherwise, it is returning val2.\n\n\n\n\n7.2.1 Sequence analysis related function\n\ncomposition(sequence)\n\nThe nucleotide composition of the sequence is returned as as map indexed by a, c, g, or t and each value is the number of occurrences of that nucleotide. A fifth key others accounts for all others symboles.\n\ngcskew(sequence)\n\nComputes the excess of g compare to c of the sequence, known as the GC skew.\n\\[\nSkew_{GC}=\\frac{G-C}{G+C}\n\\]"
|
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"text": "7.2 Function defined in the language\n\nInstrospection functions\n\nlen(x)\n\nIt is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like annotations, the number of elements in an array. The reurned value is an int.\n\ncontains(map,key)\n\nTests if the map contains a value assciated to key\n\n\n\n\nCast functions\n\nint(x)\n\nConverts if possible the x value to an integer value. The function returns an int.\n\nnumeric(x)\n\nConverts if possible the x value to a float value. The function returns a float.\n\nbool(x)\n\nConverts if possible the x value to a boolean value. The function returns a bool.\n\n\n\n\nString related functions\n\nprintf(format,...)\n\nAllows to combine several values to build a string. format follows the classical C printf syntax. The function returns a string.\n\nsubspc(x)\n\nsubstitutes every space in the x string by the underscore (_) character. The function returns a string.\n\n\n\n\nCondition function\n\nifelse(condition,val1,val2)\n\nThe condition value has to be a bool value. If it is true the function returns val1, otherwise, it is returning val2.\n\n\n\n\n7.2.1 Sequence analysis related function\n\ncomposition(sequence)\n\nThe nucleotide composition of the sequence is returned as as map indexed by a, c, g, or t and each value is the number of occurrences of that nucleotide. A fifth key others accounts for all others symboles.\n\ngcskew(sequence)\n\nComputes the excess of g compare to c of the sequence, known as the GC skew.\nSkewGC=G−CG+C\nSkew_{GC}=\\frac{G-C}{G+C}"
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{
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"objectID": "expressions.html#accessing-to-the-sequence-annotations",
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@@ -179,7 +172,7 @@
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"href": "comm_computation.html#obipairing",
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"title": "11 Computations on sequences",
|
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"section": "11.1 obipairing",
|
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"text": "11.1 obipairing\n\nReplace the illuminapairedends original OBITools\n\n\nAlignment procedure\nobipairing is introducing a new alignment algorithm compared to the illuminapairedend command of the OBITools V2. Nethertheless this new algorithm has been design to produce the same results than the previous, except in very few cases.\nThe new algorithm is a two-step procedure. First, a FASTN-type algorithm (Lipman and Pearson 1985) identifies the best offset between the two matched readings. This identifies the region of overlap.\nIn the second step, the matching regions of the two reads are extracted along with a flanking sequence of \\(\\Delta\\) 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.\nUnless 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.\n\n\nThe scoring system\nIn 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.\nIf we consider a nucleotide read with a quality score \\(Q\\), the probability of misreading this base (\\(P_E\\)) is : \\[\nP_E = 10^{-\\frac{Q}{10}}\n\\]\nThus, when a given nucleotide \\(X\\) is observed with the quality score \\(Q\\). The probability that \\(X\\) is really an \\(X\\) is :\n\\[\nP(X=X) = 1 - P_E\n\\]\nOtherwise, \\(X\\) is actually one of the three other possible nucleotides (\\(X_{E1}\\), \\(X_{E2}\\) or \\(X_{E3}\\)). If we suppose that the three reading error have the same probability :\n\\[\nP(X=X_{E1}) = P(X=X_{E3}) = P(X=X_{E3}) = \\frac{P_E}{3}\n\\]\nAt each position in an alignment where the two nucleotides \\(X_1\\) and \\(X_2\\) face each other (not a gapped position), the probability of a true match varies depending on whether \\(X_1=X_2\\), an observed match, or \\(X_1 \\neq X_2\\), an observed mismatch.\nProbability of a true match when \\(X_1=X_2\\)\nThat probability can be divided in two parts. First \\(X_1\\) and \\(X_2\\) have been correctly read. The corresponding probability is :\n\\[\n\\begin{aligned}\nP_{TM} &= (1- PE_1)(1-PE_2)\\\\\n &=(1 - 10^{-\\frac{Q_1}{10} } )(1 - 10^{-\\frac{Q_2}{10}} )\n\\end{aligned}\n\\]\nSecondly, a match can occure if the true nucleotides read as \\(X_1\\) and \\(X_2\\) are not \\(X_1\\) and \\(X_2\\) but identical.\n\\[\n\\begin{aligned}\nP(X_1==X_{E1}) \\cap P(X_2==X_{E1}) &= \\frac{P_{E1} P_{E2}}{9} \\\\\nP(X_1==X_{Ex}) \\cap P(X_2==X_{Ex}) & = \\frac{P_{E1} P_{E2}}{3}\n\\end{aligned}\n\\]\nThe probability of a true match between \\(X_1\\) and \\(X_2\\) when \\(X_1 = X_2\\) an observed match :\n\\[\n\\begin{aligned}\nP(MATCH | X_1 = X_2) = (1- PE_1)(1-PE_2) + \\frac{P_{E1} P_{E2}}{3}\n\\end{aligned}\n\\]\nProbability of a true match when \\(X_1 \\neq X_2\\)\nThat probability can be divided in three parts.\n\n\\(X_1\\) has been correctly read and \\(X_2\\) is a sequencing error and is actually equal to \\(X_1\\). \\[\nP_a = (1-P_{E1})\\frac{P_{E2}}{3}\n\\]\n\\(X_2\\) has been correctly read and \\(X_1\\) is a sequencing error and is actually equal to \\(X_2\\). \\[\nP_b = (1-P_{E2})\\frac{P_{E1}}{3}\n\\]\n\\(X_1\\) and \\(X_2\\) corresponds to sequencing error but are actually the same base \\(X_{Ex}\\) \\[\nP_c = 2\\frac{P_{E1} P_{E2}}{9}\n\\]\n\nConsequently : \\[\n\\begin{aligned}\nP(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}\n\\end{aligned}\n\\]\nProbability of a match under the random model\nThe second considered model is a pure random model where every base is equiprobable, hence having a probability of occurrence of a nucleotide equals \\(0.25\\). Under that hypothesis\n\\[\nP(MATCH | \\text{Random model}) = 0.25\n\\]\nThe score is a log ration of likelyhood\nScore is define as the logarithm of the ratio between the likelyhood of the observations considering the sequencer error model over tha likelyhood u\n\n\n\n\n\nEvolution of the match and mismatch scores when the quality of base is 20 while the second range from 10 to 40."
|
||||
"text": "11.1 obipairing\n\nReplace the illuminapairedends original OBITools\n\n\nAlignment procedure\nobipairing is introducing a new alignment algorithm compared to the illuminapairedend command of the OBITools V2. Nethertheless this new algorithm has been design to produce the same results than the previous, except in very few cases.\nThe new algorithm is a two-step procedure. First, a FASTN-type algorithm (Lipman and Pearson 1985) identifies the best offset between the two matched readings. This identifies the region of overlap.\nIn the second step, the matching regions of the two reads are extracted along with a flanking sequence of Δ\\Delta 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.\nUnless 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.\n\n\nThe scoring system\nIn 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.\nIf we consider a nucleotide read with a quality score QQ, the probability of misreading this base (PEP_E) is : PE=10−Q10\nP_E = 10^{-\\frac{Q}{10}}\n\nThus, when a given nucleotide XX is observed with the quality score QQ. The probability that XX is really an XX is :\nP(X=X)=1−PE\nP(X=X) = 1 - P_E\n\nOtherwise, XX is actually one of the three other possible nucleotides (XE1X_{E1}, XE2X_{E2} or XE3X_{E3}). If we suppose that the three reading error have the same probability :\nP(X=XE1)=P(X=XE3)=P(X=XE3)=PE3\nP(X=X_{E1}) = P(X=X_{E3}) = P(X=X_{E3}) = \\frac{P_E}{3}\n\nAt each position in an alignment where the two nucleotides X1X_1 and X2X_2 face each other (not a gapped position), the probability of a true match varies depending on whether X1=X2X_1=X_2, an observed match, or X1≠X2X_1 \\neq X_2, an observed mismatch.\nProbability of a true match when X1=X2X_1=X_2\nThat probability can be divided in two parts. First X1X_1 and X2X_2 have been correctly read. The corresponding probability is :\nPTM=(1−PE1)(1−PE2)=(1−10−Q110)(1−10−Q210)\n\\begin{aligned}\nP_{TM} &= (1- PE_1)(1-PE_2)\\\\ \n &=(1 - 10^{-\\frac{Q_1}{10} } )(1 - 10^{-\\frac{Q_2}{10}} )\n\\end{aligned}\n\nSecondly, a match can occure if the true nucleotides read as X1X_1 and X2X_2 are not X1X_1 and X2X_2 but identical.\nP(X1==XE1)∩P(X2==XE1)=PE1PE29P(X1==XEx)∩P(X2==XEx)=PE1PE23\n\\begin{aligned}\nP(X_1==X_{E1}) \\cap P(X_2==X_{E1}) &= \\frac{P_{E1} P_{E2}}{9} \\\\\nP(X_1==X_{Ex}) \\cap P(X_2==X_{Ex}) & = \\frac{P_{E1} P_{E2}}{3}\n\\end{aligned}\n\nThe probability of a true match between X1X_1 and X2X_2 when X1=X2X_1 = X_2 an observed match :\nP(MATCH|X1=X2)=(1−PE1)(1−PE2)+PE1PE23\n\\begin{aligned}\nP(MATCH | X_1 = X_2) = (1- PE_1)(1-PE_2) + \\frac{P_{E1} P_{E2}}{3}\n\\end{aligned}\n\nProbability of a true match when X1≠X2X_1 \\neq X_2\nThat probability can be divided in three parts.\n\nX1X_1 has been correctly read and X2X_2 is a sequencing error and is actually equal to X1X_1. Pa=(1−PE1)PE23\nP_a = (1-P_{E1})\\frac{P_{E2}}{3}\n\nX2X_2 has been correctly read and X1X_1 is a sequencing error and is actually equal to X2X_2. Pb=(1−PE2)PE13\nP_b = (1-P_{E2})\\frac{P_{E1}}{3}\n\nX1X_1 and X2X_2 corresponds to sequencing error but are actually the same base XExX_{Ex} Pc=2PE1PE29\nP_c = 2\\frac{P_{E1} P_{E2}}{9}\n\n\nConsequently : P(MATCH|X1≠X2)=(1−PE1)PE23+(1−PE2)PE13+2PE1PE29\n\\begin{aligned}\nP(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}\n\\end{aligned}\n\nProbability of a match under the random model\nThe second considered model is a pure random model where every base is equiprobable, hence having a probability of occurrence of a nucleotide equals 0.250.25. Under that hypothesis\nP(MATCH|Random model)=0.25\nP(MATCH | \\text{Random model}) = 0.25\n\nThe score is a log ration of likelyhood\nScore is define as the logarithm of the ratio between the likelyhood of the observations considering the sequencer error model over tha likelyhood u\n\n\n\n\n\nEvolution of the match and mismatch scores when the quality of base is 20 while the second range from 10 to 40."
|
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"objectID": "comm_computation.html#obimultiplex",
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@@ -214,7 +207,7 @@
|
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"href": "comm_sampling.html#obigrep-filters-sequence-files-according-to-numerous-conditions",
|
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"title": "12 Sequence sampling and filtering",
|
||||
"section": "12.1 obigrep – filters sequence files according to numerous conditions",
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"text": "12.1 obigrep – filters sequence files according to numerous conditions\nThe obigrep command is somewhat analogous to the standard Unix grep command. It selects a subset of sequence records from a sequence file. A sequence record is a complex object consisting of an identifier, a set of attributes (a key, defined by its name, associated with a value), a definition, and the sequence itself. Instead of working text line by text line like the standard Unix tool, obigrep selection is done sequence record by sequence record. A large number of options allow you to refine the selection on any element of the sequence. obigrep allows you to specify multiple conditions simultaneously (which take on the value TRUE or FALSE) and only those sequence records which meet all conditions (all conditions are TRUE) are selected. obigrep is able to work on two paired read files. The selection criteria apply to one or the other of the readings in each pair depending on the mode chosen (--paired-mode option). In all cases the selection is applied in the same way to both files, thus maintaining their consistency.\n\n12.1.1 The options usable with obigrep\n\n12.1.1.1 Selecting sequences based on their caracteristics\nSequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.\nSelection based on the sequence\nSequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (e.g AACCTT). But the usage of regular patterns allows for looking for more complex pattern. As example, A[TG]C+G matches a A, followed by a T or a G, then one or several C and endly a G.\n\n--sequence|-s PATTERN\n\nRegular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available here.\n\nExamples:\n\nSelects only the sequence records that contain an EcoRI restriction site.\n\n\nobigrep -s 'GAATTC' seq1.fasta > seq2.fasta\n: Selects only the sequence records that contain a stretch of at least 10 A.\nobigrep -s 'A{10,}' seq1.fasta > seq2.fasta\n: Selects only the sequence records that do not contain ambiguous nucleotides.\nobigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta\n\n--min-count | -c COUNT\n\nonly sequences reprensenting at least COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to \\(1\\).\n\n--max-count | -C COUNT\n\nonly sequences reprensenting no more than COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to \\(1\\).\n\nExamples\n\nSelecting sequence records representing at least five reads in the dataset.\n\n\nobigrep -c 5 data_SPER01.fasta > data_norare_SPER01.fasta"
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"text": "12.1 obigrep – filters sequence files according to numerous conditions\nThe obigrep command is somewhat analogous to the standard Unix grep command. It selects a subset of sequence records from a sequence file. A sequence record is a complex object consisting of an identifier, a set of attributes (a key, defined by its name, associated with a value), a definition, and the sequence itself. Instead of working text line by text line like the standard Unix tool, obigrep selection is done sequence record by sequence record. A large number of options allow you to refine the selection on any element of the sequence. obigrep allows you to specify multiple conditions simultaneously (which take on the value TRUE or FALSE) and only those sequence records which meet all conditions (all conditions are TRUE) are selected. obigrep is able to work on two paired read files. The selection criteria apply to one or the other of the readings in each pair depending on the mode chosen (--paired-mode option). In all cases the selection is applied in the same way to both files, thus maintaining their consistency.\n\n12.1.1 The options usable with obigrep\n\n12.1.1.1 Selecting sequences based on their caracteristics\nSequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.\nSelection based on the sequence\nSequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (e.g AACCTT). But the usage of regular patterns allows for looking for more complex pattern. As example, A[TG]C+G matches a A, followed by a T or a G, then one or several C and endly a G.\n\n--sequence|-s PATTERN\n\nRegular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available here.\n\nExamples:\n\nSelects only the sequence records that contain an EcoRI restriction site.\n\n\nobigrep -s 'GAATTC' seq1.fasta > seq2.fasta\n: Selects only the sequence records that contain a stretch of at least 10 A.\nobigrep -s 'A{10,}' seq1.fasta > seq2.fasta\n: Selects only the sequence records that do not contain ambiguous nucleotides.\nobigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta\n\n--min-count | -c COUNT\n\nonly sequences reprensenting at least COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to 11.\n\n--max-count | -C COUNT\n\nonly sequences reprensenting no more than COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to 11.\n\nExamples\n\nSelecting sequence records representing at least five reads in the dataset.\n\n\nobigrep -c 5 data_SPER01.fasta > data_norare_SPER01.fasta"
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"objectID": "comm_utilities.html#obicount",
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