MetabarcodingSchool/OBIJupyterHub
1
0
Fork 0
Code Issues Pull Requests 1 Actions Packages Projects Releases Wiki Activity
Files
30b7175702ea411825f8625838d1a7a63faf30fc
OBIJupyterHub/jupyterhub_volumes/web/obidoc/formats/json/index.html

1817 lines
51 KiB
HTML
Raw Normal View History

Make cleaning
2025-11-16 14:56:03 +01:00
<!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="
The JSON sequence file format
#
To facilitate the exchange of data between different systems, and to allow easy parsing of the data with all programming languages, OBITools offers to export sequence data in
JSON format. JSON output is requested by adding the --json-output option to the command line.
Converting FASTA to JSON format
#
Here it is an example of two sequences in
fasta
format:
📄 json_example.fasta
&gt;AB061527 {&#34;count&#34;:1,&#34;definition&#34;:&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;,&#34;family_name&#34;:&#34;Soricidae&#34;,&#34;family_taxid&#34;:9376,&#34;genus_name&#34;:&#34;Sorex&#34;,&#34;genus_taxid&#34;:9379,&#34;obicleandb_level&#34;:&#34;family&#34;,&#34;obicleandb_trusted&#34;:2.2137847111025621e-13,&#34;species_name&#34;:&#34;Sorex unguiculatus&#34;,&#34;species_taxid&#34;:62275,&#34;taxid&#34;:62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 {&#34;count&#34;:2,&#34;definition&#34;:&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;,&#34;family_name&#34;:&#34;Hominidae&#34;,&#34;family_taxid&#34;:9604,&#34;genus_name&#34;:&#34;Homo&#34;,&#34;genus_taxid&#34;:9605,&#34;obicleandb_level&#34;:&#34;genus&#34;,&#34;obicleandb_trusted&#34;:0,&#34;species_name&#34;:&#34;Homo sapiens&#34;,&#34;species_taxid&#34;:9606,&#34;taxid&#34;:9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
that you can convert in JSON with the
obiconvert
command:">
<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/formats/json/">
<meta property="og:site_name" content="OBITools4 documentation">
<meta property="og:title" content="JSON format">
<meta property="og:description" content="The JSON sequence file format # To facilitate the exchange of data between different systems, and to allow easy parsing of the data with all programming languages, OBITools offers to export sequence data in JSON format. JSON output is requested by adding the --json-output option to the command line.
Converting FASTA to JSON format # Here it is an example of two sequences in fasta format:
📄 json_example.fasta &gt;AB061527 {&#34;count&#34;:1,&#34;definition&#34;:&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;,&#34;family_name&#34;:&#34;Soricidae&#34;,&#34;family_taxid&#34;:9376,&#34;genus_name&#34;:&#34;Sorex&#34;,&#34;genus_taxid&#34;:9379,&#34;obicleandb_level&#34;:&#34;family&#34;,&#34;obicleandb_trusted&#34;:2.2137847111025621e-13,&#34;species_name&#34;:&#34;Sorex unguiculatus&#34;,&#34;species_taxid&#34;:62275,&#34;taxid&#34;:62275} ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat agcttaaaactcaaaggacttggcggtgctttatatccct &gt;AL355887 {&#34;count&#34;:2,&#34;definition&#34;:&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;,&#34;family_name&#34;:&#34;Hominidae&#34;,&#34;family_taxid&#34;:9604,&#34;genus_name&#34;:&#34;Homo&#34;,&#34;genus_taxid&#34;:9605,&#34;obicleandb_level&#34;:&#34;genus&#34;,&#34;obicleandb_trusted&#34;:0,&#34;species_name&#34;:&#34;Homo sapiens&#34;,&#34;species_taxid&#34;:9606,&#34;taxid&#34;:9606} ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac agcttaaaactcaaaggacctggcagttctttatatccct that you can convert in JSON with the obiconvert command:">
<meta property="og:locale" content="en_us">
<meta property="og:type" content="website">
<title>JSON format | 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/formats/json/">
<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb&#43;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&#43;Or85BgKocXepm2Z&#43;ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
<link rel="alternate" type="application/rss+xml" href="http://metabar:8888/obidoc/formats/json/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" checked />
<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" checked />
<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="active">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" />
<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
<a href="/obidoc/docs/programming/lua/" class="">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>JSON format</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="#the-json-sequence-file-format">The <em>JSON</em> sequence file format</a>
<ul>
<li><a href="#converting-fasta-to-json-format">Converting FASTA to JSON format</a></li>
<li><a href="#converting-fastq-to-json-format">Converting FASTQ to JSON format</a></li>
</ul>
</li>
</ul>
</nav>
</aside>
</header>
<article class="markdown book-article"><h1 id="the-json-sequence-file-format">
The <em>JSON</em> sequence file format
<a class="anchor" href="#the-json-sequence-file-format">#</a>
</h1>
<p>To facilitate the exchange of data between different systems, and to allow easy parsing of the data with all programming languages, <em>OBITools</em> offers to export sequence data in
<a href="https://en.wikipedia.org/wiki/JSON">JSON</a> format. JSON output is requested by adding the <code>--json-output</code> option to the command line.</p>
<h2 id="converting-fasta-to-json-format">
Converting FASTA to JSON format
<a class="anchor" href="#converting-fasta-to-json-format">#</a>
</h2>
<p>Here it is an example of two sequences in
<a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a>
format:</p>
<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="json_example.fasta" download="json_example.fasta">📄 json_example.fasta</a>
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
<pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;AB061527 {&#34;count&#34;:1,&#34;definition&#34;:&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;,&#34;family_name&#34;:&#34;Soricidae&#34;,&#34;family_taxid&#34;:9376,&#34;genus_name&#34;:&#34;Sorex&#34;,&#34;genus_taxid&#34;:9379,&#34;obicleandb_level&#34;:&#34;family&#34;,&#34;obicleandb_trusted&#34;:2.2137847111025621e-13,&#34;species_name&#34;:&#34;Sorex unguiculatus&#34;,&#34;species_taxid&#34;:62275,&#34;taxid&#34;:62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 {&#34;count&#34;:2,&#34;definition&#34;:&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;,&#34;family_name&#34;:&#34;Hominidae&#34;,&#34;family_taxid&#34;:9604,&#34;genus_name&#34;:&#34;Homo&#34;,&#34;genus_taxid&#34;:9605,&#34;obicleandb_level&#34;:&#34;genus&#34;,&#34;obicleandb_trusted&#34;:0,&#34;species_name&#34;:&#34;Homo sapiens&#34;,&#34;species_taxid&#34;:9606,&#34;taxid&#34;:9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
</code></pre></td>
</DIV>
<p>that you can convert in JSON with the <a href="http://metabar:8888/obidoc/obitools/obiconvert/">
<abbr title="obiconvert: convert format of a sequence file"><code>obiconvert</code></abbr>
</a> command:</p>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obiconvert --json-output json_example.fasta &gt; json_example.json
</span></span></code></pre></div><p>which produces the following JSON output:</p>
<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="json_example.json" download="json_example.json">📄 json_example.json</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></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-json" data-lang="json"><span style="display:flex;"><span>[
</span></span><span style="display:flex;"><span> {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;annotations&#34;</span>: {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;count&#34;</span>: <span style="color:#ae81ff">1</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;definition&#34;</span>: <span style="color:#e6db74">&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_name&#34;</span>: <span style="color:#e6db74">&#34;Soricidae&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_taxid&#34;</span>: <span style="color:#e6db74">&#34;9376&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_name&#34;</span>: <span style="color:#e6db74">&#34;Sorex&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_taxid&#34;</span>: <span style="color:#e6db74">&#34;9379&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;obicleandb_level&#34;</span>: <span style="color:#e6db74">&#34;family&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;obicleandb_trusted&#34;</span>: <span style="color:#ae81ff">2.2137847111025621e-13</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_name&#34;</span>: <span style="color:#e6db74">&#34;Sorex unguiculatus&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_taxid&#34;</span>: <span style="color:#e6db74">&#34;62275&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;taxid&#34;</span>: <span style="color:#e6db74">&#34;62275&#34;</span>
</span></span><span style="display:flex;"><span> },
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;id&#34;</span>: <span style="color:#e6db74">&#34;AB061527&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;sequence&#34;</span>: <span style="color:#e6db74">&#34;ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct&#34;</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:#f92672">&#34;annotations&#34;</span>: {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;count&#34;</span>: <span style="color:#ae81ff">2</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;definition&#34;</span>: <span style="color:#e6db74">&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_name&#34;</span>: <span style="color:#e6db74">&#34;Hominidae&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_taxid&#34;</span>: <span style="color:#e6db74">&#34;9604&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_name&#34;</span>: <span style="color:#e6db74">&#34;Homo&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_taxid&#34;</span>: <span style="color:#e6db74">&#34;9605&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;obicleandb_level&#34;</span>: <span style="color:#e6db74">&#34;genus&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;obicleandb_trusted&#34;</span>: <span style="color:#ae81ff">0</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_name&#34;</span>: <span style="color:#e6db74">&#34;Homo sapiens&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_taxid&#34;</span>: <span style="color:#e6db74">&#34;9606&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;taxid&#34;</span>: <span style="color:#e6db74">&#34;9606&#34;</span>
</span></span><span style="display:flex;"><span> },
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;id&#34;</span>: <span style="color:#e6db74">&#34;AL355887&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;sequence&#34;</span>: <span style="color:#e6db74">&#34;ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaacagcttaaaactcaaaggacctggcagttctttatatccct&#34;</span>
</span></span><span style="display:flex;"><span> }
</span></span><span style="display:flex;"><span>]
</span></span></code></pre></td></tr></table>
</div>
</div></td>
</DIV>
<h2 id="converting-fastq-to-json-format">
Converting FASTQ to JSON format
<a class="anchor" href="#converting-fastq-to-json-format">#</a>
</h2>
<p>To convert a
<a href="http://metabar:8888/obidoc/formats/fastq/">fastq</a>
file as the following example:</p>
<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="json_example.fasta" download="json_example.fasta">📄 json_example.fasta</a>
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
<pre tabindex="0"><code class="language-fastq" data-lang="fastq">&gt;AB061527 {&#34;count&#34;:1,&#34;definition&#34;:&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;,&#34;family_name&#34;:&#34;Soricidae&#34;,&#34;family_taxid&#34;:9376,&#34;genus_name&#34;:&#34;Sorex&#34;,&#34;genus_taxid&#34;:9379,&#34;obicleandb_level&#34;:&#34;family&#34;,&#34;obicleandb_trusted&#34;:2.2137847111025621e-13,&#34;species_name&#34;:&#34;Sorex unguiculatus&#34;,&#34;species_taxid&#34;:62275,&#34;taxid&#34;:62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 {&#34;count&#34;:2,&#34;definition&#34;:&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;,&#34;family_name&#34;:&#34;Hominidae&#34;,&#34;family_taxid&#34;:9604,&#34;genus_name&#34;:&#34;Homo&#34;,&#34;genus_taxid&#34;:9605,&#34;obicleandb_level&#34;:&#34;genus&#34;,&#34;obicleandb_trusted&#34;:0,&#34;species_name&#34;:&#34;Homo sapiens&#34;,&#34;species_taxid&#34;:9606,&#34;taxid&#34;:9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
</code></pre></td>
</DIV>
<p>use the equivalent command:</p>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obiconvert --json-output json_example.fastq &gt; json_example_qual.json
</span></span></code></pre></div><p>which produces the following JSON output:</p>
<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="json_example_qual.json" download="json_example_qual.json">📄 json_example_qual.json</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></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-json" data-lang="json"><span style="display:flex;"><span>[
</span></span><span style="display:flex;"><span> {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;annotations&#34;</span>: {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;count&#34;</span>: <span style="color:#ae81ff">1</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;definition&#34;</span>: <span style="color:#e6db74">&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_name&#34;</span>: <span style="color:#e6db74">&#34;Soricidae&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_taxid&#34;</span>: <span style="color:#e6db74">&#34;9376&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_name&#34;</span>: <span style="color:#e6db74">&#34;Sorex&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_taxid&#34;</span>: <span style="color:#e6db74">&#34;9379&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;obicleandb_level&#34;</span>: <span style="color:#e6db74">&#34;family&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_name&#34;</span>: <span style="color:#e6db74">&#34;Sorex unguiculatus&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_taxid&#34;</span>: <span style="color:#e6db74">&#34;62275&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;taxid&#34;</span>: <span style="color:#e6db74">&#34;62275&#34;</span>
</span></span><span style="display:flex;"><span> },
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;id&#34;</span>: <span style="color:#e6db74">&#34;AB061527&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;qualities&#34;</span>: <span style="color:#e6db74">&#34;BBFFBFFHHHHHFFFFFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;sequence&#34;</span>: <span style="color:#e6db74">&#34;ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat&#34;</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:#f92672">&#34;annotations&#34;</span>: {
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;count&#34;</span>: <span style="color:#ae81ff">2</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;definition&#34;</span>: <span style="color:#e6db74">&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_name&#34;</span>: <span style="color:#e6db74">&#34;Hominidae&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;family_taxid&#34;</span>: <span style="color:#e6db74">&#34;9604&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_name&#34;</span>: <span style="color:#e6db74">&#34;Homo&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;genus_taxid&#34;</span>: <span style="color:#e6db74">&#34;9605&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;obicleandb_level&#34;</span>: <span style="color:#e6db74">&#34;genus&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_name&#34;</span>: <span style="color:#e6db74">&#34;Homo sapiens&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;species_taxid&#34;</span>: <span style="color:#e6db74">&#34;9606&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;taxid&#34;</span>: <span style="color:#e6db74">&#34;9606&#34;</span>
</span></span><span style="display:flex;"><span> },
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;id&#34;</span>: <span style="color:#e6db74">&#34;AL355887&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;qualities&#34;</span>: <span style="color:#e6db74">&#34;@BBFFBFFHHHGGGFFFFFHHHJJJHHHHHHHHHJHHHHHHHHHHHHHHHHHHHHHHHHH&#34;</span>,
</span></span><span style="display:flex;"><span> <span style="color:#f92672">&#34;sequence&#34;</span>: <span style="color:#e6db74">&#34;ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac&#34;</span>
</span></span><span style="display:flex;"><span> }
</span></span><span style="display:flex;"><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="#the-json-sequence-file-format">The <em>JSON</em> sequence file format</a>
<ul>
<li><a href="#converting-fasta-to-json-format">Converting FASTA to JSON format</a></li>
<li><a href="#converting-fastq-to-json-format">Converting FASTQ to JSON format</a></li>
</ul>
</li>
</ul>
</nav>
</div>
</aside>
</main>
</body>
</html>
Reference in New Issue Copy Permalink