1836 lines
48 KiB
HTML
1836 lines
48 KiB
HTML
<!DOCTYPE html>
|
|
<html lang="en-us" dir="ltr">
|
|
<head>
|
|
<meta charset="UTF-8">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
<meta name="description" content="
|
|
Lua: the scripting language for OBITools
|
|
#
|
|
|
|
|
|
Lua is a scripting language. Its name means moon in Portuguese. Its purpose is to provide an interpreter that can be easily integrated into software to add scripting capabilities. OBITools provides the
|
|
obiscript
|
|
command for this purpose. The
|
|
obiscript
|
|
command allows a small script to be applied to each selected sequence in a sequence file. The Lua interpreter used by
|
|
obiscript
|
|
is
|
|
GopherLua Version 1.1.1 which implements Lua version 5.1.">
|
|
<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
|
|
<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
|
|
<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/docs/programming/lua/">
|
|
<meta property="og:site_name" content="OBITools4 documentation">
|
|
<meta property="og:title" content="Lua: for scripting OBITools">
|
|
<meta property="og:description" content="Lua: the scripting language for OBITools # Lua is a scripting language. Its name means moon in Portuguese. Its purpose is to provide an interpreter that can be easily integrated into software to add scripting capabilities. OBITools provides the obiscript command for this purpose. The obiscript command allows a small script to be applied to each selected sequence in a sequence file. The Lua interpreter used by obiscript is GopherLua Version 1.1.1 which implements Lua version 5.1.">
|
|
<meta property="og:locale" content="en_us">
|
|
<meta property="og:type" content="website">
|
|
<title>Lua: for scripting OBITools | OBITools4 documentation</title>
|
|
<link rel="icon" href="/obidoc/favicon.png" >
|
|
<link rel="manifest" href="/obidoc/manifest.json">
|
|
<link rel="canonical" href="http://metabar:8888/obidoc/docs/programming/lua/">
|
|
<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb+a3g=" crossorigin="anonymous">
|
|
<script defer src="/obidoc/fuse.min.js"></script>
|
|
<script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
|
|
|
|
<script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq+Or85BgKocXepm2Z+ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
|
|
<link rel="alternate" type="application/rss+xml" href="http://metabar:8888/obidoc/docs/programming/lua/index.xml" title="OBITools4 documentation" />
|
|
<!--
|
|
Made with Book Theme
|
|
https://github.com/alex-shpak/hugo-book
|
|
-->
|
|
<link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
|
|
</head>
|
|
<body dir="ltr">
|
|
<input type="checkbox" class="hidden toggle" id="menu-control" />
|
|
<input type="checkbox" class="hidden toggle" id="toc-control" />
|
|
<main class="container flex">
|
|
<aside class="book-menu">
|
|
<div class="book-menu-content">
|
|
|
|
<nav>
|
|
<h2 class="book-brand">
|
|
<a class="flex align-center" href="/obidoc/"><img src="/obidoc/obitools_logo.jpg" alt="Logo" class="book-icon" /><span>OBITools4 documentation</span>
|
|
</a>
|
|
</h2>
|
|
|
|
|
|
<div class="book-search hidden">
|
|
<input type="text" id="book-search-input" placeholder="Search" aria-label="Search" maxlength="64" data-hotkeys="s/" />
|
|
<div class="book-search-spinner hidden"></div>
|
|
<ul id="book-search-results"></ul>
|
|
</div>
|
|
<script>document.querySelector(".book-search").classList.remove("hidden")</script>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<span>Docs</span>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/about/" class="">About</a>
|
|
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/installation/" class="">Installation</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/principles/" class="">General operating principles</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-08756b4c1f14be6ee584ece005b9f621" class="toggle" />
|
|
<label for="section-08756b4c1f14be6ee584ece005b9f621" class="flex justify-between">
|
|
<a role="button" class="">File formats</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-933c2e64b905b84e22aa5273cea2d0bd" class="toggle" />
|
|
<label for="section-933c2e64b905b84e22aa5273cea2d0bd" class="flex justify-between">
|
|
<a role="button" class="">Sequence file formats</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/formats/fasta/" class="">FASTA file format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/formats/fastq/" class="">FASTQ file format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/formats/genbank/" class="">GenBank Flat File format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/formats/embl/" class="">EMBL Flat File format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/file_format/sequence_files/csv/" class="">CSV format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/formats/json/" class="">JSON format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/file_format/sequence_files/annotations/" class="">Annotation of sequences</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-0258ae1c222f9a38cc1b75254c93b0f4" class="toggle" />
|
|
<label for="section-0258ae1c222f9a38cc1b75254c93b0f4" class="flex justify-between">
|
|
<a role="button" class="">Taxonomy file formats</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/file_format/taxonomy_file/csv_taxdump/" class="">CSV formatted taxdump</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/" class="">NCBI taxdump</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/formats/csv/" class="">The CSV format</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-70b1e6e5ec7f3ccab643155fa50659b6" class="toggle" />
|
|
<label for="section-70b1e6e5ec7f3ccab643155fa50659b6" class="flex justify-between">
|
|
<a role="button" class="">Patterns</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/patterns/regular/" class="">Regular Expressions</a>
|
|
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/patterns/dnagrep/" class="">DNA Patterns</a>
|
|
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-8223f464911a1fe6c655972143684e93" class="toggle" />
|
|
<label for="section-8223f464911a1fe6c655972143684e93" class="flex justify-between">
|
|
<a role="button" class="">The OBITools4 commands</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/commands/options/" class="">Shared command options</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-8921ea65523c266b128dd4263232b0fc" class="toggle" />
|
|
<label for="section-8921ea65523c266b128dd4263232b0fc" class="flex justify-between">
|
|
<a role="button" class="">Basics</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obiannotate/" class="">obiannotate</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obicomplement/" class="">obicomplement</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obiconvert/" class="">obiconvert</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obicount/" class="">obicount</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obicsv/" class="">obicsv</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obidemerge/" class="">obidemerge</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obidistribute/" class="">obidistribute</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obigrep/" class="">obigrep</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obijoin/" class="">obijoin</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obisplit/" class="">obisplit</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obisummary/" class="">obisummary</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-dbdf1bb5377572439394e60e08c30f50" class="toggle" />
|
|
<label for="section-dbdf1bb5377572439394e60e08c30f50" class="flex justify-between">
|
|
<a role="button" class="">Demultiplexing samples</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obimultiplex/" class="">obimultiplex</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obitagpcr/" class="">obitagpcr</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-aa98fedd067b51150db59691a8ea8edd" class="toggle" />
|
|
<label for="section-aa98fedd067b51150db59691a8ea8edd" class="flex justify-between">
|
|
<a role="button" class="">Sequence alignments</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obiclean/" class="">obiclean</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-7433746525d8c2b29b033f765c869acd" class="toggle" />
|
|
<label for="section-7433746525d8c2b29b033f765c869acd" class="flex justify-between">
|
|
<a href="/obidoc/obitools/obipairing/" class="">obipairing</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/commands/alignments/obipairing/exact-alignment/" class="">Exact alignment</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obipcr/" class="">obipcr</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obirefidx/" class="">obirefidx</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obitag/" class="">obitag</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-5746f699d10490780dec8e30ab2dd3ce" class="toggle" />
|
|
<label for="section-5746f699d10490780dec8e30ab2dd3ce" class="flex justify-between">
|
|
<a role="button" class="">Taxonomy</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obitaxonomy/" class="">obitaxonomy</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-3f50c4fe7ab436a56ae92897d5444956" class="toggle" />
|
|
<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
|
|
<a role="button" class="">Advanced tools</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obiscript/" class="">obiscript</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-549be3934679fcb82a232f6bd5435563" class="toggle" />
|
|
<label for="section-549be3934679fcb82a232f6bd5435563" class="flex justify-between">
|
|
<a role="button" class="">Others</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obimicrosat/" class="">obimicrosat</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-ceca4455173761e30cbc0a6dc2327167" class="toggle" />
|
|
<label for="section-ceca4455173761e30cbc0a6dc2327167" class="flex justify-between">
|
|
<a role="button" class="">Experimentals</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obicleandb/" class="">obicleandb</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obiconsensus/" class="">obiconsensus</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/obitools/obilandmark/" class="">obilandmark</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/commands/tags/" class="">Glossary of tags</a>
|
|
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-9b1bcd52530c59dc4819b1f61c128f54" class="toggle" />
|
|
<label for="section-9b1bcd52530c59dc4819b1f61c128f54" class="flex justify-between">
|
|
<a role="button" class="">Cookbook</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<span>Programming OBITools</span>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/expression/" class="">Expression language</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-6d580829a667b5cca790b286d99a10fe" class="toggle" checked />
|
|
<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
|
|
<a href="/obidoc/docs/programming/lua/" class="active">Lua: for scripting OBITools</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<input type="checkbox" id="section-2fb081dac812d624eea5f4268fca9e26" class="toggle" />
|
|
<label for="section-2fb081dac812d624eea5f4268fca9e26" class="flex justify-between">
|
|
<a role="button" class="">Obitools Classes</a>
|
|
</label>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequence/" class="">BioSequence</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/taxon/" class="">Taxon</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
|
|
<li>
|
|
|
|
|
|
|
|
|
|
|
|
<a href="/obidoc/docs/programming/lua/obitools_classes/mutex/" class="">Mutex</a>
|
|
|
|
|
|
|
|
<ul>
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
</li>
|
|
|
|
|
|
</ul>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</nav>
|
|
|
|
|
|
|
|
|
|
<script>(function(){var e=document.querySelector("aside .book-menu-content");addEventListener("beforeunload",function(){localStorage.setItem("menu.scrollTop",e.scrollTop)}),e.scrollTop=localStorage.getItem("menu.scrollTop")})()</script>
|
|
|
|
|
|
|
|
</div>
|
|
</aside>
|
|
|
|
<div class="book-page">
|
|
<header class="book-header">
|
|
|
|
<div class="flex align-center justify-between">
|
|
<label for="menu-control">
|
|
<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
|
|
</label>
|
|
|
|
<h3>Lua: for scripting OBITools</h3>
|
|
|
|
<label for="toc-control">
|
|
|
|
<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
|
|
|
|
</label>
|
|
</div>
|
|
|
|
|
|
|
|
<aside class="hidden clearfix">
|
|
|
|
|
|
<nav id="TableOfContents">
|
|
<ul>
|
|
<li><a href="#lua-the-scripting-language-for-obitools">Lua: the scripting language for OBITools</a>
|
|
<ul>
|
|
<li><a href="#the-structure-of-a-lua-script-for-hahahugoshortcode68s4hbhb">The structure of a Lua script for HAHAHUGOSHORTCODE68s4HBHB</a>
|
|
<ul>
|
|
<li><a href="#the-begin-and-finish-function">The <code>begin</code> and finish function</a></li>
|
|
<li><a href="#the-worker-function">The <code>worker</code> function</a></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#the-obicontext-to-share-information">The <code>obicontext</code> to share information</a></li>
|
|
<li><a href="#the-obitools-classes">The OBITools classes</a>
|
|
<ul>
|
|
<li><a href="#the-biosequence-class">The <code>BioSequence</code> class</a></li>
|
|
<li><a href="#the-biosequenceslice-class">The <code>BioSequenceSlice</code> class</a></li>
|
|
<li><a href="#the-taxonomy-class">The <code>Taxonomy</code> class</a></li>
|
|
<li><a href="#the-taxon-class">The <code>Taxon</code> class</a></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#dealing-with-the-obitools4-multithreading">Dealing with the OBITools4 multithreading</a></li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</nav>
|
|
|
|
|
|
|
|
</aside>
|
|
|
|
|
|
</header>
|
|
|
|
|
|
|
|
<article class="markdown book-article"><h1 id="lua-the-scripting-language-for-obitools">
|
|
Lua: the scripting language for OBITools
|
|
<a class="anchor" href="#lua-the-scripting-language-for-obitools">#</a>
|
|
</h1>
|
|
<p>
|
|
<a href="https://www.lua.org/">Lua</a> is a scripting language. Its name means moon in Portuguese. Its purpose is to provide an interpreter that can be easily integrated into software to add scripting capabilities. OBITools provides the <a href="http://metabar:8888/obidoc/obitools/obiscript/">
|
|
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
|
|
</a> command for this purpose. The <a href="http://metabar:8888/obidoc/obitools/obiscript/">
|
|
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
|
|
</a> command allows a small script to be applied to each selected sequence in a sequence file. The Lua interpreter used by <a href="http://metabar:8888/obidoc/obitools/obiscript/">
|
|
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
|
|
</a> is
|
|
<a href="https://github.com/yuin/gopher-lua">GopherLua</a> Version 1.1.1 which implements Lua version 5.1.</p>
|
|
<p>The aim of this section is not to be a full introduction to
|
|
<a href="https://www.lua.org/">Lua</a>, but to show how to write a
|
|
<a href="https://www.lua.org/">Lua</a> script that can be used with <a href="http://metabar:8888/obidoc/obitools/obiscript/">
|
|
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
|
|
</a>. A full documentation of
|
|
<a href="https://www.lua.org/">Lua</a> is available on the official website of the language (
|
|
<a href="https://www.lua.org/manual/5.1">https://www.lua.org/manual/5.1</a>).</p>
|
|
<h2 id="the-structure-of-a-lua-script-for-hahahugoshortcode68s4hbhb">
|
|
The structure of a Lua script for <a href="http://metabar:8888/obidoc/obitools/obiscript/">
|
|
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
|
|
</a>
|
|
<a class="anchor" href="#the-structure-of-a-lua-script-for-hahahugoshortcode68s4hbhb">#</a>
|
|
</h2>
|
|
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="example.lua" download="example.lua">📄 example.lua</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<div class="highlight"><div style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;">
|
|
<table style="border-spacing:0;padding:0;margin:0;border:0;"><tr><td style="vertical-align:top;padding:0;margin:0;border:0;">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 1
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 2
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 3
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 4
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 5
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 6
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 7
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 8
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 9
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">10
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">11
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">12
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">13
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">14
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">15
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">16
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">17
|
|
</span></code></pre></td>
|
|
<td style="vertical-align:top;padding:0;margin:0;border:0;;width:100%">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-lua" data-lang="lua"><span style="display:flex;"><span><span style="color:#66d9ef">function</span> <span style="color:#a6e22e">begin</span>()
|
|
</span></span><span style="display:flex;"><span> obicontext.item(<span style="color:#e6db74">"compteur"</span>,<span style="color:#ae81ff">0</span>)
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">function</span> <span style="color:#a6e22e">worker</span>(sequence)
|
|
</span></span><span style="display:flex;"><span> samples <span style="color:#f92672">=</span> sequence:attribute(<span style="color:#e6db74">"merged_sample"</span>)
|
|
</span></span><span style="display:flex;"><span> samples[<span style="color:#e6db74">"tutu"</span>]<span style="color:#f92672">=</span><span style="color:#ae81ff">4</span>
|
|
</span></span><span style="display:flex;"><span> sequence:attribute(<span style="color:#e6db74">"merged_sample"</span>,samples)
|
|
</span></span><span style="display:flex;"><span> sequence:attribute(<span style="color:#e6db74">"toto"</span>,<span style="color:#ae81ff">44444</span>)
|
|
</span></span><span style="display:flex;"><span> nb <span style="color:#f92672">=</span> obicontext.inc(<span style="color:#e6db74">"compteur"</span>)
|
|
</span></span><span style="display:flex;"><span> sequence:id(<span style="color:#e6db74">"seq_"</span> <span style="color:#f92672">..</span> nb)
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">return</span> sequence
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">function</span> <span style="color:#a6e22e">finish</span>()
|
|
</span></span><span style="display:flex;"><span> print(<span style="color:#e6db74">"compteur = "</span> <span style="color:#f92672">..</span> obicontext.item(<span style="color:#e6db74">"compteur"</span>))
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">end</span></span></span></code></pre></td></tr></table>
|
|
</div>
|
|
</div></td>
|
|
|
|
</DIV>
|
|
|
|
<h3 id="the-begin-and-finish-function">
|
|
The <code>begin</code> and finish function
|
|
<a class="anchor" href="#the-begin-and-finish-function">#</a>
|
|
</h3>
|
|
<h3 id="the-worker-function">
|
|
The <code>worker</code> function
|
|
<a class="anchor" href="#the-worker-function">#</a>
|
|
</h3>
|
|
<h2 id="the-obicontext-to-share-information">
|
|
The <code>obicontext</code> to share information
|
|
<a class="anchor" href="#the-obicontext-to-share-information">#</a>
|
|
</h2>
|
|
<h2 id="the-obitools-classes">
|
|
The OBITools classes
|
|
<a class="anchor" href="#the-obitools-classes">#</a>
|
|
</h2>
|
|
<h3 id="the-biosequence-class">
|
|
The <code>BioSequence</code> class
|
|
<a class="anchor" href="#the-biosequence-class">#</a>
|
|
</h3>
|
|
<h3 id="the-biosequenceslice-class">
|
|
The <code>BioSequenceSlice</code> class
|
|
<a class="anchor" href="#the-biosequenceslice-class">#</a>
|
|
</h3>
|
|
<h3 id="the-taxonomy-class">
|
|
The <code>Taxonomy</code> class
|
|
<a class="anchor" href="#the-taxonomy-class">#</a>
|
|
</h3>
|
|
<h3 id="the-taxon-class">
|
|
The <code>Taxon</code> class
|
|
<a class="anchor" href="#the-taxon-class">#</a>
|
|
</h3>
|
|
<h2 id="dealing-with-the-obitools4-multithreading">
|
|
Dealing with the OBITools4 multithreading
|
|
<a class="anchor" href="#dealing-with-the-obitools4-multithreading">#</a>
|
|
</h2>
|
|
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="extrem_quality.lua" download="extrem_quality.lua">📄 extrem_quality.lua</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<div class="highlight"><div style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;">
|
|
<table style="border-spacing:0;padding:0;margin:0;border:0;"><tr><td style="vertical-align:top;padding:0;margin:0;border:0;">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 1
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 2
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 3
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 4
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 5
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 6
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 7
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 8
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f"> 9
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">10
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">11
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">12
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">13
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">14
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">15
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">16
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">17
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">18
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">19
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">20
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">21
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">22
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">23
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">24
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">25
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">26
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">27
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">28
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">29
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">30
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">31
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">32
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">33
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">34
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">35
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">36
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">37
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">38
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">39
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">40
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">41
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">42
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">43
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">44
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">45
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">46
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">47
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">48
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">49
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">50
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">51
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">52
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">53
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">54
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">55
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">56
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">57
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">58
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">59
|
|
</span></code></pre></td>
|
|
<td style="vertical-align:top;padding:0;margin:0;border:0;;width:100%">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-lua" data-lang="lua"><span style="display:flex;"><span><span style="color:#75715e">--</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- Script for obiscript extracting the qualities of</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- the first `size` and last `size` base pairs of </span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- all the reads longer than 2 x `size`</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">--</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- The result is a csv file on the stdout</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">--</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- obiscript -S ../qualities.lua FAZ61712_c61e82f1_69e58200_0_nolambda.fastq > xxxx</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- Import the io module</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">local</span> io <span style="color:#f92672">=</span> require(<span style="color:#e6db74">"io"</span>)
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#75715e">-- Set the output stream to the stdout of the Go program</span>
|
|
</span></span><span style="display:flex;"><span>io.output(io.stdout)
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span>size <span style="color:#f92672">=</span> <span style="color:#ae81ff">60</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">function</span> <span style="color:#a6e22e">begin</span>()
|
|
</span></span><span style="display:flex;"><span> obicontext.item(<span style="color:#e6db74">"locker"</span>, Mutex:new())
|
|
</span></span><span style="display:flex;"><span> header <span style="color:#f92672">=</span> <span style="color:#e6db74">"id"</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">for</span> i <span style="color:#f92672">=</span> <span style="color:#ae81ff">1</span>, size <span style="color:#66d9ef">do</span>
|
|
</span></span><span style="display:flex;"><span> header <span style="color:#f92672">=</span> header <span style="color:#f92672">..</span> <span style="color:#e6db74">", L"</span> <span style="color:#f92672">..</span> i
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">for</span> i <span style="color:#f92672">=</span> size, <span style="color:#ae81ff">1</span>, <span style="color:#f92672">-</span><span style="color:#ae81ff">1</span> <span style="color:#66d9ef">do</span>
|
|
</span></span><span style="display:flex;"><span> header <span style="color:#f92672">=</span> header <span style="color:#f92672">..</span> <span style="color:#e6db74">", R"</span> <span style="color:#f92672">..</span> i
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> obicontext.item(<span style="color:#e6db74">"locker"</span>):lock()
|
|
</span></span><span style="display:flex;"><span> print(header)
|
|
</span></span><span style="display:flex;"><span> obicontext.item(<span style="color:#e6db74">"locker"</span>):unlock()
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">function</span> <span style="color:#a6e22e">worker</span>(sequence)
|
|
</span></span><span style="display:flex;"><span> l <span style="color:#f92672">=</span> sequence:len()
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">if</span> l <span style="color:#f92672">></span> size <span style="color:#f92672">*</span> <span style="color:#ae81ff">2</span> <span style="color:#66d9ef">then</span>
|
|
</span></span><span style="display:flex;"><span> qualities <span style="color:#f92672">=</span> sequence:qualities()
|
|
</span></span><span style="display:flex;"><span> rep <span style="color:#f92672">=</span> sequence:id()
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">for</span> i <span style="color:#f92672">=</span> <span style="color:#ae81ff">1</span>, size <span style="color:#66d9ef">do</span>
|
|
</span></span><span style="display:flex;"><span> rep <span style="color:#f92672">=</span> rep <span style="color:#f92672">..</span> <span style="color:#e6db74">", "</span> <span style="color:#f92672">..</span> qualities[i]
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">for</span> i <span style="color:#f92672">=</span> size, <span style="color:#ae81ff">1</span>, <span style="color:#f92672">-</span><span style="color:#ae81ff">1</span> <span style="color:#66d9ef">do</span>
|
|
</span></span><span style="display:flex;"><span> rep <span style="color:#f92672">=</span> rep <span style="color:#f92672">..</span> <span style="color:#e6db74">", "</span> <span style="color:#f92672">..</span> qualities[l <span style="color:#f92672">-</span> i <span style="color:#f92672">+</span> <span style="color:#ae81ff">1</span>]
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> obicontext.item(<span style="color:#e6db74">"locker"</span>):lock()
|
|
</span></span><span style="display:flex;"><span> print(rep)
|
|
</span></span><span style="display:flex;"><span> obicontext.item(<span style="color:#e6db74">"locker"</span>):unlock()
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">end</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">return</span> BioSequenceSlice.new()
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">end</span></span></span></code></pre></td></tr></table>
|
|
</div>
|
|
</div></td>
|
|
|
|
</DIV>
|
|
|
|
</article>
|
|
|
|
|
|
|
|
<footer class="book-footer">
|
|
|
|
<div class="flex flex-wrap justify-between">
|
|
|
|
|
|
|
|
|
|
|
|
</div>
|
|
|
|
|
|
|
|
<script>(function(){function e(e){const t=window.getSelection(),n=document.createRange();n.selectNodeContents(e),t.removeAllRanges(),t.addRange(n)}document.querySelectorAll("pre code").forEach(t=>{t.addEventListener("click",function(){if(window.getSelection().toString())return;e(t.parentElement),navigator.clipboard&&navigator.clipboard.writeText(t.parentElement.textContent)})})})()</script>
|
|
|
|
|
|
|
|
|
|
</footer>
|
|
|
|
|
|
|
|
<div class="book-comments">
|
|
|
|
</div>
|
|
|
|
|
|
|
|
<label for="menu-control" class="hidden book-menu-overlay"></label>
|
|
</div>
|
|
|
|
|
|
<aside class="book-toc">
|
|
<div class="book-toc-content">
|
|
|
|
|
|
<nav id="TableOfContents">
|
|
<ul>
|
|
<li><a href="#lua-the-scripting-language-for-obitools">Lua: the scripting language for OBITools</a>
|
|
<ul>
|
|
<li><a href="#the-structure-of-a-lua-script-for-hahahugoshortcode68s4hbhb">The structure of a Lua script for HAHAHUGOSHORTCODE68s4HBHB</a>
|
|
<ul>
|
|
<li><a href="#the-begin-and-finish-function">The <code>begin</code> and finish function</a></li>
|
|
<li><a href="#the-worker-function">The <code>worker</code> function</a></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#the-obicontext-to-share-information">The <code>obicontext</code> to share information</a></li>
|
|
<li><a href="#the-obitools-classes">The OBITools classes</a>
|
|
<ul>
|
|
<li><a href="#the-biosequence-class">The <code>BioSequence</code> class</a></li>
|
|
<li><a href="#the-biosequenceslice-class">The <code>BioSequenceSlice</code> class</a></li>
|
|
<li><a href="#the-taxonomy-class">The <code>Taxonomy</code> class</a></li>
|
|
<li><a href="#the-taxon-class">The <code>Taxon</code> class</a></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#dealing-with-the-obitools4-multithreading">Dealing with the OBITools4 multithreading</a></li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</nav>
|
|
|
|
|
|
|
|
</div>
|
|
</aside>
|
|
|
|
</main>
|
|
|
|
|
|
</body>
|
|
</html>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|