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<ul class="summary">
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<li class="chapter" data-level="1" data-path="the-obitools.html"><a href="the-obitools.html"><i class="fa fa-check"></i><b>1</b> The OBITools</a>
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<ul>
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<li class="chapter" data-level="1.1" data-path="the-obitools.html"><a href="the-obitools.html#aims-of-obitools"><i class="fa fa-check"></i><b>1.1</b> Aims of <em>OBITools</em></a></li>
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<li class="chapter" data-level="1.2" data-path="the-obitools.html"><a href="the-obitools.html#file-formats-usable-with-obitools"><i class="fa fa-check"></i><b>1.2</b> File formats usable with <em>OBITools</em></a>
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<ul>
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<li class="chapter" data-level="1.2.1" data-path="the-obitools.html"><a href="the-obitools.html#the-sequence-files"><i class="fa fa-check"></i><b>1.2.1</b> The sequence files</a></li>
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<li class="chapter" data-level="1.2.2" data-path="the-obitools.html"><a href="the-obitools.html#the-iupac-code"><i class="fa fa-check"></i><b>1.2.2</b> The IUPAC Code</a></li>
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<li class="chapter" data-level="1.2.3" data-path="the-obitools.html"><a href="the-obitools.html#classical-fasta"><i class="fa fa-check"></i><b>1.2.3</b> The <em>fasta</em> format</a></li>
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<li class="chapter" data-level="1.2.4" data-path="the-obitools.html"><a href="the-obitools.html#classical-fastq"><i class="fa fa-check"></i><b>1.2.4</b> The <em>fastq</em> sequence format</a></li>
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</ul></li>
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||||
<li class="chapter" data-level="1.3" data-path="the-obitools.html"><a href="the-obitools.html#file-extension"><i class="fa fa-check"></i><b>1.3</b> File extension</a></li>
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<li class="chapter" data-level="1.4" data-path="the-obitools.html"><a href="the-obitools.html#see-also"><i class="fa fa-check"></i><b>1.4</b> See also</a></li>
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<li class="chapter" data-level="1.5" data-path="the-obitools.html"><a href="the-obitools.html#references"><i class="fa fa-check"></i><b>1.5</b> References</a></li>
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</ul></li>
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<li class="chapter" data-level="2" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html"><i class="fa fa-check"></i><b>2</b> The <em>OBITools</em> commands</a>
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<ul>
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<li class="chapter" data-level="2.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#specifying-the-input-files-to-obitools-commands"><i class="fa fa-check"></i><b>2.1</b> Specifying the input files to <em>OBITools</em> commands</a></li>
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<li class="chapter" data-level="2.2" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#options-common-to-most-of-the-obitools-commands"><i class="fa fa-check"></i><b>2.2</b> Options common to most of the <em>OBITools</em> commands</a>
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<ul>
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<li class="chapter" data-level="2.2.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#specifying-input-format"><i class="fa fa-check"></i><b>2.2.1</b> Specifying input format</a></li>
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||||
<li class="chapter" data-level="2.2.2" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#specifying-output-format"><i class="fa fa-check"></i><b>2.2.2</b> Specifying output format</a></li>
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||||
<li class="chapter" data-level="2.2.3" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#format-of-the-annotations-in-fasta-and-fastq-files"><i class="fa fa-check"></i><b>2.2.3</b> Format of the annotations in Fasta and Fastq files</a></li>
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</ul></li>
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<li class="chapter" data-level="2.3" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#metabarcode-design-and-quality-assessment"><i class="fa fa-check"></i><b>2.3</b> Metabarcode design and quality assessment</a></li>
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||||
<li class="chapter" data-level="2.4" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#file-format-conversions"><i class="fa fa-check"></i><b>2.4</b> File format conversions</a></li>
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<li class="chapter" data-level="2.5" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#sequence-annotations"><i class="fa fa-check"></i><b>2.5</b> Sequence annotations</a></li>
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||||
<li class="chapter" data-level="2.6" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#computations-on-sequences"><i class="fa fa-check"></i><b>2.6</b> Computations on sequences</a>
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<ul>
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||||
<li class="chapter" data-level="2.6.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#obipairing"><i class="fa fa-check"></i><b>2.6.1</b> <code>obipairing</code></a></li>
|
||||
</ul></li>
|
||||
<li class="chapter" data-level="2.7" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#sequence-sampling-and-filtering"><i class="fa fa-check"></i><b>2.7</b> Sequence sampling and filtering</a>
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||||
<ul>
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||||
<li class="chapter" data-level="2.7.1" data-path="the-obitools-commands.html"><a href="the-obitools-commands.html#utilities"><i class="fa fa-check"></i><b>2.7.1</b> Utilities</a></li>
|
||||
</ul></li>
|
||||
</ul></li>
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||||
<li class="chapter" data-level="3" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html"><i class="fa fa-check"></i><b>3</b> Reference documentation for the GO <em>OBITools</em> library</a>
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||||
<ul>
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||||
<li class="chapter" data-level="3.1" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#biosequence"><i class="fa fa-check"></i><b>3.1</b> BioSequence</a>
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||||
<ul>
|
||||
<li class="chapter" data-level="3.1.1" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#creating-new-instances"><i class="fa fa-check"></i><b>3.1.1</b> Creating new instances</a></li>
|
||||
<li class="chapter" data-level="3.1.2" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#end-of-life-of-a-biosequence-instance"><i class="fa fa-check"></i><b>3.1.2</b> End of life of a <code>BioSequence</code> instance</a></li>
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||||
<li class="chapter" data-level="3.1.3" data-path="reference-documentation-for-the-go-obitools-library.html"><a href="reference-documentation-for-the-go-obitools-library.html#accessing-to-the-elements-of-a-sequence"><i class="fa fa-check"></i><b>3.1.3</b> Accessing to the elements of a sequence</a></li>
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||||
</ul></li>
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||||
</ul></li>
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||||
<li class="chapter" data-level="4" data-path="annexes.html"><a href="annexes.html"><i class="fa fa-check"></i><b>4</b> Annexes</a>
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<ul>
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||||
<li class="chapter" data-level="4.0.1" data-path="annexes.html"><a href="annexes.html#sequence-attributes"><i class="fa fa-check"></i><b>4.0.1</b> Sequence attributes</a></li>
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<h1>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">The GO <em>OBITools</em></a>
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<h1><span class="header-section-number">4</span> Annexes<a href="annexes.html#annexes" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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<div id="sequence-attributes" class="section level3 hasAnchor" number="4.0.1">
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<h3><span class="header-section-number">4.0.1</span> Sequence attributes<a href="annexes.html#sequence-attributes" class="anchor-section" aria-label="Anchor link to header"></a></h3>
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<div id="reserved-sequence-attributes" class="section level4 hasAnchor" number="4.0.1.1">
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<h4><span class="header-section-number">4.0.1.1</span> Reserved sequence attributes<a href="annexes.html#reserved-sequence-attributes" class="anchor-section" aria-label="Anchor link to header"></a></h4>
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||||
<div id="type-string" class="section level6 hasAnchor" number="4.0.1.1.1.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.1.1</span> Type : <code>string</code><a href="annexes.html#type-string" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<p>The attribute can contain 2 string values <code>"left"</code> or <code>"right".</code></p>
|
||||
</div>
|
||||
<div id="set-by-the-obipairing-tool" class="section level6 hasAnchor" number="4.0.1.1.1.2">
|
||||
<h6><span class="header-section-number">4.0.1.1.1.2</span> Set by the <em>obipairing</em> tool<a href="annexes.html#set-by-the-obipairing-tool" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<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>
|
||||
</div>
|
||||
</div>
|
||||
<div id="ali_length" class="section level5 hasAnchor" number="4.0.1.1.2">
|
||||
<h5><span class="header-section-number">4.0.1.1.2</span> <code>ali_length</code><a href="annexes.html#ali_length" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="set-by-the-obipairing-tool-1" class="section level6 hasAnchor" number="4.0.1.1.2.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.2.1</span> Set by the <em>obipairing</em> tool<a href="annexes.html#set-by-the-obipairing-tool-1" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<p>Length of the aligned parts when merging forward and reverse reads</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="count-the-number-of-sequence-occurrences" class="section level5 hasAnchor" number="4.0.1.1.3">
|
||||
<h5><span class="header-section-number">4.0.1.1.3</span> <code>count</code> : the number of sequence occurrences<a href="annexes.html#count-the-number-of-sequence-occurrences" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="set-by-the-obiuniq-tool" class="section level6 hasAnchor" number="4.0.1.1.3.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool<a href="annexes.html#set-by-the-obiuniq-tool" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<p>The <code>count</code> attribute indicates how-many strictly identical sequences
|
||||
have been merged in a single record. It contains an integer value. If it
|
||||
is absent this means that the sequence record represents a single
|
||||
occurrence of the sequence.</p>
|
||||
</div>
|
||||
<div id="getter-method-count" class="section level6 hasAnchor" number="4.0.1.1.3.2">
|
||||
<h6><span class="header-section-number">4.0.1.1.3.2</span> Getter : method <code>Count()</code><a href="annexes.html#getter-method-count" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<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>
|
||||
</div>
|
||||
</div>
|
||||
<div id="merged_" class="section level5 hasAnchor" number="4.0.1.1.4">
|
||||
<h5><span class="header-section-number">4.0.1.1.4</span> <code>merged_*</code><a href="annexes.html#merged_" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="type-mapstringint" class="section level6 hasAnchor" number="4.0.1.1.4.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.4.1</span> Type : <code>map[string]int</code><a href="annexes.html#type-mapstringint" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
</div>
|
||||
<div id="set-by-the-obiuniq-tool-1" class="section level6 hasAnchor" number="4.0.1.1.4.2">
|
||||
<h6><span class="header-section-number">4.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool<a href="annexes.html#set-by-the-obiuniq-tool-1" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<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>
|
||||
</div>
|
||||
</div>
|
||||
<div id="mode" class="section level5 hasAnchor" number="4.0.1.1.5">
|
||||
<h5><span class="header-section-number">4.0.1.1.5</span> <code>mode</code><a href="annexes.html#mode" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="set-by-the-obipairing-tool-2" class="section level6 hasAnchor" number="4.0.1.1.5.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.5.1</span> Set by the <em>obipairing</em> tool<a href="annexes.html#set-by-the-obipairing-tool-2" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<p><strong><code>obitag_ref_index</code></strong></p>
|
||||
</div>
|
||||
<div id="set-by-the-obirefidx-tool." class="section level6 hasAnchor" number="4.0.1.1.5.2">
|
||||
<h6><span class="header-section-number">4.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.<a href="annexes.html#set-by-the-obirefidx-tool." class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
<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>
|
||||
<div id="getter-method-count-1" class="section level6 hasAnchor" number="4.0.1.1.5.3">
|
||||
<h6><span class="header-section-number">4.0.1.1.5.3</span> Getter : method <code>Count()</code><a href="annexes.html#getter-method-count-1" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
</div>
|
||||
</div>
|
||||
<div id="pairing_mismatches" class="section level5 hasAnchor" number="4.0.1.1.6">
|
||||
<h5><span class="header-section-number">4.0.1.1.6</span> <code>pairing_mismatches</code><a href="annexes.html#pairing_mismatches" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="set-by-the-obipairing-tool-3" class="section level6 hasAnchor" number="4.0.1.1.6.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.6.1</span> Set by the <em>obipairing</em> tool<a href="annexes.html#set-by-the-obipairing-tool-3" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
</div>
|
||||
</div>
|
||||
<div id="score" class="section level5 hasAnchor" number="4.0.1.1.7">
|
||||
<h5><span class="header-section-number">4.0.1.1.7</span> <code>score</code><a href="annexes.html#score" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="set-by-the-obipairing-tool-4" class="section level6 hasAnchor" number="4.0.1.1.7.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.7.1</span> Set by the <em>obipairing</em> tool<a href="annexes.html#set-by-the-obipairing-tool-4" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
</div>
|
||||
</div>
|
||||
<div id="score_norm" class="section level5 hasAnchor" number="4.0.1.1.8">
|
||||
<h5><span class="header-section-number">4.0.1.1.8</span> <code>score_norm</code><a href="annexes.html#score_norm" class="anchor-section" aria-label="Anchor link to header"></a></h5>
|
||||
<div id="set-by-the-obipairing-tool-5" class="section level6 hasAnchor" number="4.0.1.1.8.1">
|
||||
<h6><span class="header-section-number">4.0.1.1.8.1</span> Set by the <em>obipairing</em> tool<a href="annexes.html#set-by-the-obipairing-tool-5" class="anchor-section" aria-label="Anchor link to header"></a></h6>
|
||||
|
||||
</div>
|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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<div class="sidebar-item-container">
|
||||
<a href="./intro.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">The OBITools</span></a>
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</div>
|
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</li>
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<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">The <em>OBITools</em> commands</span></a>
|
||||
</div>
|
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|
||||
<li class="sidebar-item">
|
||||
<div class="sidebar-item-container">
|
||||
<a href="./library.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
|
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|
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|
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<a href="./annexes.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">4</span> <span class="chapter-title">Annexes</span></a>
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<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
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<h2 id="toc-title">Table of contents</h2>
|
||||
|
||||
<ul>
|
||||
<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">4.0.1</span> Sequence attributes</a></li>
|
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|
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<h1 class="title d-none d-lg-block"><span class="chapter-number">4</span> <span class="chapter-title">Annexes</span></h1>
|
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</div>
|
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|
||||
|
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|
||||
<div class="quarto-title-meta">
|
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|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<section id="sequence-attributes" class="level3" data-number="4.0.1">
|
||||
<h3 data-number="4.0.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">4.0.1</span> Sequence attributes</h3>
|
||||
<section id="reserved-sequence-attributes" class="level4" data-number="4.0.1.1">
|
||||
<h4 data-number="4.0.1.1" class="anchored" data-anchor-id="reserved-sequence-attributes"><span class="header-section-number">4.0.1.1</span> Reserved sequence attributes</h4>
|
||||
<section id="ali_dir" class="level5" data-number="4.0.1.1.1">
|
||||
<h5 data-number="4.0.1.1.1" class="anchored" data-anchor-id="ali_dir"><span class="header-section-number">4.0.1.1.1</span> <code>ali_dir</code></h5>
|
||||
<section id="type-string" class="level6" data-number="4.0.1.1.1.1">
|
||||
<h6 data-number="4.0.1.1.1.1" class="anchored" data-anchor-id="type-string"><span class="header-section-number">4.0.1.1.1.1</span> Type : <code>string</code></h6>
|
||||
<p>The attribute can contain 2 string values <code>"left"</code> or <code>"right".</code></p>
|
||||
</section>
|
||||
<section id="set-by-the-obipairing-tool" class="level6" data-number="4.0.1.1.1.2">
|
||||
<h6 data-number="4.0.1.1.1.2" class="anchored" data-anchor-id="set-by-the-obipairing-tool"><span class="header-section-number">4.0.1.1.1.2</span> Set by the <em>obipairing</em> tool</h6>
|
||||
<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>
|
||||
</section>
|
||||
</section>
|
||||
<section id="ali_length" class="level5" data-number="4.0.1.1.2">
|
||||
<h5 data-number="4.0.1.1.2" class="anchored" data-anchor-id="ali_length"><span class="header-section-number">4.0.1.1.2</span> <code>ali_length</code></h5>
|
||||
<section id="set-by-the-obipairing-tool-1" class="level6" data-number="4.0.1.1.2.1">
|
||||
<h6 data-number="4.0.1.1.2.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-1"><span class="header-section-number">4.0.1.1.2.1</span> Set by the <em>obipairing</em> tool</h6>
|
||||
<p>Length of the aligned parts when merging forward and reverse reads</p>
|
||||
</section>
|
||||
</section>
|
||||
<section id="count-the-number-of-sequence-occurrences" class="level5" data-number="4.0.1.1.3">
|
||||
<h5 data-number="4.0.1.1.3" class="anchored" data-anchor-id="count-the-number-of-sequence-occurrences"><span class="header-section-number">4.0.1.1.3</span> <code>count</code> : the number of sequence occurrences</h5>
|
||||
<section id="set-by-the-obiuniq-tool" class="level6" data-number="4.0.1.1.3.1">
|
||||
<h6 data-number="4.0.1.1.3.1" class="anchored" data-anchor-id="set-by-the-obiuniq-tool"><span class="header-section-number">4.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool</h6>
|
||||
<p>The <code>count</code> attribute indicates how-many strictly identical sequences have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.</p>
|
||||
</section>
|
||||
<section id="getter-method-count" class="level6" data-number="4.0.1.1.3.2">
|
||||
<h6 data-number="4.0.1.1.3.2" class="anchored" data-anchor-id="getter-method-count"><span class="header-section-number">4.0.1.1.3.2</span> Getter : method <code>Count()</code></h6>
|
||||
<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>
|
||||
</section>
|
||||
</section>
|
||||
<section id="merged_" class="level5" data-number="4.0.1.1.4">
|
||||
<h5 data-number="4.0.1.1.4" class="anchored" data-anchor-id="merged_"><span class="header-section-number">4.0.1.1.4</span> <code>merged_*</code></h5>
|
||||
<section id="type-mapstringint" class="level6" data-number="4.0.1.1.4.1">
|
||||
<h6 data-number="4.0.1.1.4.1" class="anchored" data-anchor-id="type-mapstringint"><span class="header-section-number">4.0.1.1.4.1</span> Type : <code>map[string]int</code></h6>
|
||||
</section>
|
||||
<section id="set-by-the-obiuniq-tool-1" class="level6" data-number="4.0.1.1.4.2">
|
||||
<h6 data-number="4.0.1.1.4.2" class="anchored" data-anchor-id="set-by-the-obiuniq-tool-1"><span class="header-section-number">4.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool</h6>
|
||||
<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>
|
||||
</section>
|
||||
</section>
|
||||
<section id="mode" class="level5" data-number="4.0.1.1.5">
|
||||
<h5 data-number="4.0.1.1.5" class="anchored" data-anchor-id="mode"><span class="header-section-number">4.0.1.1.5</span> <code>mode</code></h5>
|
||||
<section id="set-by-the-obipairing-tool-2" class="level6" data-number="4.0.1.1.5.1">
|
||||
<h6 data-number="4.0.1.1.5.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-2"><span class="header-section-number">4.0.1.1.5.1</span> Set by the <em>obipairing</em> tool</h6>
|
||||
<p><strong><code>obitag_ref_index</code></strong></p>
|
||||
</section>
|
||||
<section id="set-by-the-obirefidx-tool." class="level6" data-number="4.0.1.1.5.2">
|
||||
<h6 data-number="4.0.1.1.5.2" class="anchored" data-anchor-id="set-by-the-obirefidx-tool."><span class="header-section-number">4.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.</h6>
|
||||
<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>
|
||||
</section>
|
||||
<section id="getter-method-count-1" class="level6" data-number="4.0.1.1.5.3">
|
||||
<h6 data-number="4.0.1.1.5.3" class="anchored" data-anchor-id="getter-method-count-1"><span class="header-section-number">4.0.1.1.5.3</span> Getter : method <code>Count()</code></h6>
|
||||
</section>
|
||||
</section>
|
||||
<section id="pairing_mismatches" class="level5" data-number="4.0.1.1.6">
|
||||
<h5 data-number="4.0.1.1.6" class="anchored" data-anchor-id="pairing_mismatches"><span class="header-section-number">4.0.1.1.6</span> <code>pairing_mismatches</code></h5>
|
||||
<section id="set-by-the-obipairing-tool-3" class="level6" data-number="4.0.1.1.6.1">
|
||||
<h6 data-number="4.0.1.1.6.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-3"><span class="header-section-number">4.0.1.1.6.1</span> Set by the <em>obipairing</em> tool</h6>
|
||||
</section>
|
||||
</section>
|
||||
<section id="score" class="level5" data-number="4.0.1.1.7">
|
||||
<h5 data-number="4.0.1.1.7" class="anchored" data-anchor-id="score"><span class="header-section-number">4.0.1.1.7</span> <code>score</code></h5>
|
||||
<section id="set-by-the-obipairing-tool-4" class="level6" data-number="4.0.1.1.7.1">
|
||||
<h6 data-number="4.0.1.1.7.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-4"><span class="header-section-number">4.0.1.1.7.1</span> Set by the <em>obipairing</em> tool</h6>
|
||||
</section>
|
||||
</section>
|
||||
<section id="score_norm" class="level5" data-number="4.0.1.1.8">
|
||||
<h5 data-number="4.0.1.1.8" class="anchored" data-anchor-id="score_norm"><span class="header-section-number">4.0.1.1.8</span> <code>score_norm</code></h5>
|
||||
<section id="set-by-the-obipairing-tool-5" class="level6" data-number="4.0.1.1.8.1">
|
||||
<h6 data-number="4.0.1.1.8.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-5"><span class="header-section-number">4.0.1.1.8.1</span> Set by the <em>obipairing</em> tool</h6>
|
||||
|
||||
|
||||
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|
||||
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<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span> <span class="chapter-title">The GO <em>OBITools</em> library</span></span>
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Reference in New Issue
Block a user