41 lines
18 KiB
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41 lines
18 KiB
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>OBITools4 Documentation on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/</link>
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<description>Recent content in OBITools4 Documentation on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<lastBuildDate>Fri, 04 Oct 2024 17:16:03 +0200</lastBuildDate>
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<atom:link href="http://metabar:8888/obidoc/index.xml" rel="self" type="application/rss+xml" />
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<item>
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<title>About</title>
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<link>http://metabar:8888/obidoc/docs/about/</link>
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<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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<guid>http://metabar:8888/obidoc/docs/about/</guid>
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<description><h2 id="what-are-obitools4">
 What are OBITools4?
 <a class="anchor" href="#what-are-obitools4">#</a>
</h2>
<p>The development of <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 began at 
 <a href="https://leca.osug.fr"><abbr title="LECA: Laboratoire d&#39;écologie Alpine - Laboratory for Alpine Ecology">LECA</abbr>
 
 </a> (
 <a href="https://www.univ-grenoble-alpes.fr/">University of Grenoble</a>) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as <code>grep</code>, <code>uniq</code> or <code>wc</code>, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.</p></description>
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</item>
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<item>
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<title>Regular Expressions</title>
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<link>http://metabar:8888/obidoc/docs/patterns/regular/</link>
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<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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<guid>http://metabar:8888/obidoc/docs/patterns/regular/</guid>
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<description><h1 id="regular-expressions">
 Regular Expressions
 <a class="anchor" href="#regular-expressions">#</a>
</h1>
<p>Regular expressions are a powerful tool for describing patterns in text. They are used in several <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 like <a href="http://metabar:8888/obidoc/obitools/obigrep/">
 <abbr title="obigrep: filter a sequence file"><code>obigrep</code></abbr>
 </a>, <a href="http://metabar:8888/obidoc/obitools/obiannotate/">
 <abbr title="obiannotate: edit sequence annotations"><code>obiannotate</code></abbr>
 </a> or <a href="http://metabar:8888/obidoc/obitools/obiscript/">
 <abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
 </a>.</p>
<h2 id="single-characters">
 Single characters
 <a class="anchor" href="#single-characters">#</a>
</h2>
<table>
 <thead>
 <tr>
 <th>Pattern</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>.</code></td>
 <td>any character, possibly including newline (flag s=true)</td>
 </tr>
 <tr>
 <td><code>[xyz]</code></td>
 <td>character class</td>
 </tr>
 <tr>
 <td><code>[^xyz]</code></td>
 <td>negated character class</td>
 </tr>
 <tr>
 <td><code>[[:alpha:]]</code></td>
 <td>ASCII character class</td>
 </tr>
 <tr>
 <td><code>[[:^alpha:]]</code></td>
 <td>negated ASCII character class</td>
 </tr>
 </tbody>
</table>
<h2 id="composites">
 Composites
 <a class="anchor" href="#composites">#</a>
</h2>
<table>
 <thead>
 <tr>
 <th>Pattern</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>xy</code></td>
 <td>x followed by y</td>
 </tr>
 <tr>
 <td><code>x|y</code></td>
 <td>x or y (prefer x)</td>
 </tr>
 </tbody>
</table>
<h2 id="repetitions">
 Repetitions
 <a class="anchor" href="#repetitions">#</a>
</h2>
<table>
 <thead>
 <tr>
 <th>Pattern</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>x*</code></td>
 <td>zero or more x, prefer more</td>
 </tr>
 <tr>
 <td><code>x+</code></td>
 <td>one or more x, prefer more</td>
 </tr>
 <tr>
 <td><code>x?</code></td>
 <td>zero or one x, prefer one</td>
 </tr>
 <tr>
 <td><code>x{n,m}</code></td>
 <
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</item>
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<item>
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<title>DNA Patterns</title>
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<link>http://metabar:8888/obidoc/docs/patterns/dnagrep/</link>
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<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
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<guid>http://metabar:8888/obidoc/docs/patterns/dnagrep/</guid>
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<description><h1 id="dna-patterns">
 DNA Patterns
 <a class="anchor" href="#dna-patterns">#</a>
</h1>
<p>DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 like <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
 <abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
 </a>, <a href="http://metabar:8888/obidoc/obitools/obipcr/">
 <abbr title="obipcr: the electronic PCR tool"><code>obipcr</code></abbr>
 </a> or <a href="http://metabar:8888/obidoc/obitools/obigrep/">
 <abbr title="obigrep: filter a sequence file"><code>obigrep</code></abbr>
 </a>. The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.</p></description>
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</item>
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<item>
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<title>Glossary of tags</title>
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<link>http://metabar:8888/obidoc/docs/commands/tags/</link>
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<pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
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<guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
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<description><h1 id="glossary-of-tags">
 Glossary of tags
 <a class="anchor" href="#glossary-of-tags">#</a>
</h1>
<h3 id="--d--">
 - D -
 <a class="anchor" href="#--d--">#</a>
</h3>
<ul>
<li>
<p><strong>definition</strong> :</p>
<blockquote>
<p>text information about the sequence present in the original sequence file.</p>
</blockquote>
</li>
<li>
<p><strong>direction</strong> :</p>
<blockquote>
<p>set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
</ul>
<h3 id="--f--">
 - F -
 <a class="anchor" href="#--f--">#</a>
</h3>
<ul>
<li>
<p><strong>forward_error</strong> :</p>
<blockquote>
<p>Number of mismatch between forward primer and priming site
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_match</strong> :</p>
<blockquote>
<p>Forward primer priming site sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_primer</strong> :</p>
<blockquote>
<p>Forward primer sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p></description>
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</item>
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</channel>
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</rss>
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