26 lines
14 KiB
XML
26 lines
14 KiB
XML
|
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||
|
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||
|
|
<channel>
|
||
|
|
<title>Patterns on OBITools4 documentation</title>
|
||
|
|
<link>http://metabar:8888/obidoc/docs/patterns/</link>
|
||
|
|
<description>Recent content in Patterns on OBITools4 documentation</description>
|
||
|
|
<generator>Hugo</generator>
|
||
|
|
<language>en-us</language>
|
||
|
|
<atom:link href="http://metabar:8888/obidoc/docs/patterns/index.xml" rel="self" type="application/rss+xml" />
|
||
|
|
<item>
|
||
|
|
<title>Regular Expressions</title>
|
||
|
|
<link>http://metabar:8888/obidoc/docs/patterns/regular/</link>
|
||
|
|
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
|
||
|
|
<guid>http://metabar:8888/obidoc/docs/patterns/regular/</guid>
|
||
|
|
<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>
 <
|
||
|
|
</item>
|
||
|
|
<item>
|
||
|
|
<title>DNA Patterns</title>
|
||
|
|
<link>http://metabar:8888/obidoc/docs/patterns/dnagrep/</link>
|
||
|
|
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
|
||
|
|
<guid>http://metabar:8888/obidoc/docs/patterns/dnagrep/</guid>
|
||
|
|
<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>
|
||
|
|
</item>
|
||
|
|
</channel>
|
||
|
|
</rss>
|