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obicount: counting sequence records
#
Description
#
Count the sequence records in a sequence file. It returns three pieces of information. The first is the number of sequence records. Each sequence record is associated with a count attribute (equal to 1 if absent), this number corresponds to the number of times that sequence has been observed in the non-dereplicated data set. In the following example, the first sequence record has no count attribute and therefore counts for 1, when the second sequence record has a count attribute equal to 2.">
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<meta property="og:description" content="obicount: counting sequence records # Description # Count the sequence records in a sequence file. It returns three pieces of information. The first is the number of sequence records. Each sequence record is associated with a count attribute (equal to 1 if absent), this number corresponds to the number of times that sequence has been observed in the non-dereplicated data set. In the following example, the first sequence record has no count attribute and therefore counts for 1, when the second sequence record has a count attribute equal to 2.">
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<h3>obicount</h3>
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<li><a href="#obicount-counting-sequence-records"><code>obicount</code>: counting sequence records</a>
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<li><a href="#description">Description</a></li>
<li><a href="#synopsis">Synopsis</a></li>
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<article class="markdown book-article"><h1 id="obicount-counting-sequence-records">
<code>obicount</code>: counting sequence records
<a class="anchor" href="#obicount-counting-sequence-records">#</a>
</h1>
<h2 id="description">
Description
<a class="anchor" href="#description">#</a>
</h2>
<p>Count the sequence records in a sequence file. It returns three pieces of information. The first is the number of sequence records. Each sequence record is associated with a <code>count</code> attribute (equal to 1 if absent), this number corresponds to the number of times that sequence has been observed in the non-dereplicated data set. In the following example, the first sequence record has no <code>count</code> attribute and therefore counts for 1, when the second sequence record has a <code>count</code> attribute equal to 2.</p>
<pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;AB061527 {&#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>
<p>Thus, the second value returned is the sum of the count values for all sequences, 3 for the presented example file. The last value is the number of nucleotides stored in the file, the sum of the sequence lengths, without accounting for the <code>count</code> tag.</p>
<script src="/obidoc/mermaid.min.js"></script>
<script>mermaid.initialize({
"flowchart": {
"useMaxWidth":true
},
"theme": "default"
}
)</script>
<pre class="mermaid workflow">
graph TD
A@{ shape: doc, label: "my_sequences.fastq" }
C[obicount]
D@{ shape: doc, label: "counts.csv" }
A --> C:::obitools
C --> D
classDef obitools fill:#99d57c
</pre>
<h2 id="synopsis">
Synopsis
<a class="anchor" href="#synopsis">#</a>
</h2>
<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 <span style="color:#f92672">[</span>--batch-size &lt;int&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--csv<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--debug<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--ecopcr<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--embl<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--fasta<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--fastq<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--force-one-cpu<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--genbank<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--help|-h|-?<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--input-OBI-header<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--input-json-header<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--max-cpu &lt;int&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--no-order<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof-goroutine &lt;int&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--pprof-mutex &lt;int&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--reads|-r<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--silent-warning<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--solexa<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--symbols|-s<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--u-to-t<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--variants|-v<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--version<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>&lt;args&gt;<span style="color:#f92672">]</span>
</span></span></code></pre></div><h2 id="options">
Options
<a class="anchor" href="#options">#</a>
</h2>
<h4 id="hahahugoshortcode20s2hbhb-specific-options">
<a href="http://metabar:8888/obidoc/obitools/obicount/">
<abbr title="obicount: counting sequence records"><code>obicount</code></abbr>
</a> specific options
<a class="anchor" href="#hahahugoshortcode20s2hbhb-specific-options">#</a>
</h4>
<ul>
<li>
<b><code class="language-bash">--variants</code></b>
| <b><code class="language-bash">-v</code></b>
: when present, output the only the number of sequence records in the file.
</li>
<li>
<b><code class="language-bash">--reads</code></b>
| <b><code class="language-bash">-r</code></b>
: when present, output only the sum of sequence counts in the file.
</li>
<li>
<b><code class="language-bash">--symbols</code></b>
| <b><code class="language-bash">-s</code></b>
: when present, output only the number of nucleotides in the file.
</li>
</ul>
<p>It is possible to combine two of the above options.</p>
<h4 id="controlling-the-input-data">
Controlling the input data
<a class="anchor" href="#controlling-the-input-data">#</a>
</h4>
<I>OBITools4</I> generally recognizes the input file format. It also recognizes
whether the input file is compressed using GZIP. But some rare files can be
misidentified, so the following options allow the user to force the format, thus
bypassing the format identification step.
<h5 id="the-file-format-options">
The file format options
<a class="anchor" href="#the-file-format-options">#</a>
</h5>
<ul>
<li>
<b><code class="language-bash">--fasta</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a> format.</li>
<li>
<b><code class="language-bash">--fastq</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/fastq/">fastq</a> format.</li>
<li>
<b><code class="language-bash">--embl</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/embl/">EMBL-ENA flatfile</a> format.</li>
<li>
<b><code class="language-bash">--csv</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/">CSV</a> format.</li>
<li>
<b><code class="language-bash">--genbank</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/genbank/">GenBank flatfile</a> format.</li>
<li><b><code class="language-bash">--ecopcr</code></b>: indicates that sequence data is in the old ecoPCR tabulated format.</li>
</ul>
<h5 id="controlling-the-way-obitools4-are-formatting-annotations">
Controlling the way <em>OBITools4</em> are formatting annotations
<a class="anchor" href="#controlling-the-way-obitools4-are-formatting-annotations">#</a>
</h5>
These options only apply to the <a href="http://metabar:8888/obidoc/formats/fasta/">FASTA</a> and <a href="http://metabar:8888/obidoc/formats/fastq/">FASTQ</a> formats
<ul>
<li><b><code class="language-bash">--input-OBI-header</code></b>: FASTA/FASTQ title line annotations follow the old OBI format.</li>
<li><b><code class="language-bash">--input-json-header</code></b>: FASTA/FASTQ title line annotations follow the JSON format.</li>
</ul>
<h5 id="controlling-quality-score-decoding">
Controlling quality score decoding
<a class="anchor" href="#controlling-quality-score-decoding">#</a>
</h5>
This option only applies to the <a href="http://metabar:8888/obidoc/formats/fastq/">FASTQ</a> formats
<ul>
<li><b><code class="language-bash">--solexa</code></b>: decodes quality string according to the old Solexa specification. (default: the standard Sanger encoding is used, env: <strong>OBISSOLEXA</strong>)</li>
</ul>
<h4 id="general-options">
General options
<a class="anchor" href="#general-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--help</code></b>
| <b><code class="language-bash">-h|-?</code></b>
: shows this help.</li>
<li><b><code class="language-bash">--version</code></b>: prints the version and exits.</li>
<li><b><code class="language-bash">--silent-warning</code></b>: This option tells obitools to stop displaying warnings.
This behaviour can be controlled by setting the <strong>OBIWARNINGS</strong> environment variable.</li>
</ul>
<h4 id="computation-related-options">
Computation related options
<a class="anchor" href="#computation-related-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--max-cpu</code></b> &lt;INTEGER>: <em>OBITools</em> can take advantage of your computer&rsquo;s multi-core
architecture by parallelizing the computation across all available CPUs.
Computing on more CPUs usually requires more memory to perform the
computation. Reducing the number of CPUs used to perform a calculation
is also a way to indirectly control the amount of memory used by the
process. The number of CPUs used by <em>OBITools</em> can also be controlled
by setting the <strong>OBIMAXCPU</strong> environment variable.</li>
<li><b><code class="language-bash">--force-one-cpu</code></b>: forces the use of a single CPU core for parallel processing (default: false).</li>
<li><b><code class="language-bash">--batch-size</code></b> &lt;INTEGER>: number of sequence per batch for parallel processing (default: 1000, env: <strong>OBIBATCHSIZE</strong>)</li>
</ul>
<h4 id="debug-related-options">
Debug related options
<a class="anchor" href="#debug-related-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--debug</code></b>: enables debug mode, by setting log level to debug (default: false, env: <strong>OBIDEBUG</strong>)</li>
<li><b><code class="language-bash">--pprof</code></b>: enables pprof server. Look at the log for details. (default: false).</li>
<li><b><code class="language-bash">--pprof-mutex</code></b> &lt;INTEGER>: enables profiling of mutex lock. (default: 10, env: <strong>OBIPPROFMUTEX</strong>)</li>
<li><b><code class="language-bash">--pprof-goroutine</code></b> &lt;INTEGER>: enables profiling of goroutine blocking profile. (default: 6060, env: <strong>OBIPPROFGOROUTINE</strong>)</li>
</ul>
<h2 id="examples">
Examples
<a class="anchor" href="#examples">#</a>
</h2>
<p>By default, the <a href="http://metabar:8888/obidoc/obitools/obicount/">
<abbr title="obicount: counting sequence records"><code>obicount</code></abbr>
</a> command will output the number of sequence records (variants), sum of counts (reads), and number of nucleotides (symbols) in the sequence 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 my_sequence_file.fasta
</span></span></code></pre></div><pre tabindex="0"><code>INFO[0000] Number of workers set 16
INFO[0000] Found 1 files to process
INFO[0000] xxx.fastq.gz mime type: text/fastq
entities,n
variants,43221
reads,43221
symbols,4391530
</code></pre><p>The output is in CSV format and can be transformed into Markdown for a prettier output using the
<a href="https://github.com/brentp/csvtomd"><code>csvtomd</code></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>obicount my_sequence_file.fasta | csvtomd
</span></span></code></pre></div><pre tabindex="0"><code>entities | n
----------|---------
variants | 43221
reads | 43221
symbols | 4391530
</code></pre><p>The conversion can also be done with the <code>csvlook</code> command from the
<a href="https://csvkit.readthedocs.io/">csvkit</a> package.</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 my_sequence_file.fasta | csvlook
</span></span></code></pre></div><pre tabindex="0"><code>| entities | n |
| -------- | --------- |
| variants | 43 221 |
| reads | 43 221 |
| symbols | 4 391 530 |
</code></pre><p>When using the <code>--variants</code>, <code>--reads</code> or <code>--symbols</code> option, the output only contains the number(s) corresponding to the specified option(s).</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 -v --reads my_sequence_file.fasta | csvlook
</span></span></code></pre></div><pre tabindex="0"><code>| entities | n |
| -------- | ------ |
| variants | 43 221 |
| reads | 43 221 |
</code></pre><p>As for all the OBITools commands, a GZIP compressed input file can be used.</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 my_sequence_file.fasta.gz | csvlook
</span></span></code></pre></div><pre tabindex="0"><code>| entities | n |
| -------- | --------- |
| variants | 43 221 |
| reads | 43 221 |
| symbols | 4 391 530 |
</code></pre></article>
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<li><a href="#obicount-counting-sequence-records"><code>obicount</code>: counting sequence records</a>
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<li><a href="#description">Description</a></li>
<li><a href="#synopsis">Synopsis</a></li>
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