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The CSV (Coma-Separated Values) flat file format
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The
CSV format is a simple text format that is widely used for storing tabular data, such as spreadsheets, databases, and other data storage systems. It is a comma-separated values format, meaning that each value in a row is separated by a comma.
Each line of the file corresponds to a record that consists of the same number of fields. The first row of the file is a header row that contains the fields names. The field delimiter, the comma, can itself appear in a field using quotation marks around it, with &quot;.">
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<article class="markdown book-article"><h1 id="the-csv-coma-separated-values-flat-file-format">
The <em>CSV (Coma-Separated Values)</em> flat file format
<a class="anchor" href="#the-csv-coma-separated-values-flat-file-format">#</a>
</h1>
<p>The
<a href="https://en.wikipedia.org/wiki/Comma-separated_values">CSV</a> format is a simple text format that is widely used for storing tabular data, such as spreadsheets, databases, and other data storage systems. It is a comma-separated values format, meaning that each value in a row is separated by a comma.</p>
<p>Each line of the file corresponds to a record that consists of the same number of fields. The first row of the file is a header row that contains the fields names. The field delimiter, the comma, can itself appear in a field using quotation marks around it, with <code>&quot;</code>.</p>
<p>Here is an example with two sequences in a
<a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a>
file:</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="two_sequences.fasta" download="two_sequences.fasta">📄 two_sequences.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>The following command allows counting the number of records, and provides a CSV file:</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>obicount two_sequences.fasta
</span></span></code></pre></div><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-csv" data-lang="csv"><span style="display:flex;"><span><span style="color:#e6db74">entities</span>,<span style="color:#e6db74">n</span>
</span></span><span style="display:flex;"><span><span style="color:#e6db74">variants</span>,<span style="color:#e6db74">2</span>
</span></span><span style="display:flex;"><span><span style="color:#e6db74">reads</span>,<span style="color:#e6db74">3</span>
</span></span><span style="display:flex;"><span><span style="color:#e6db74">symbols</span>,<span style="color:#e6db74">200</span>
</span></span></code></pre></div><p>In a prettier presentation:</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>obicount two_sequences.fasta | csvlook
</span></span></code></pre></div><pre tabindex="0"><code>| entities | n |
| -------- | --- |
| variants | 2 |
| reads | 3 |
| symbols | 200 |
</code></pre><p>The CSV format of the result of <a href="http://metabar:8888/obidoc/obitools/obicount/">
<abbr title="obicount: counting sequence records"><code>obicount</code></abbr>
</a> is an easy way to make plots with <code>uplot</code>:</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>obicount two_sequences.fasta <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | uplot barplot -d, -H --xscale log10
</span></span></code></pre></div><pre tabindex="0"><code> n
┌ ┐
variants ┤■■■■ 2.0
reads ┤■■■■■■■ 3.0
symbols ┤■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 200.0
└ ┘
[log10]
</code></pre></article>
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