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Customising the execution of OBITools
#
OBITools are a set of UNIX commands that can be used from a UNIX shell. They can be used interactively from a terminal, or as part of a shell script to automate a data analysis pipeline. Each OBITools command implements an algorithm to process the data. For example, the
obicount
command implements an algorithm to count the number of sequences in a sequence file.">
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<h3>Shared command options</h3>
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<li><a href="#customising-the-execution-of-obitools">Customising the execution of <em>OBITools</em></a>
<ul>
<li><a href="#multiple-ways-to-specify-the-same-option">Multiple ways to specify the same option</a></li>
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<article class="markdown book-article"><h1 id="customising-the-execution-of-obitools">
Customising the execution of <em>OBITools</em>
<a class="anchor" href="#customising-the-execution-of-obitools">#</a>
</h1>
<p><em>OBITools</em> are a set of UNIX commands that can be used from a UNIX shell. They can be used interactively from a terminal, or as part of a shell script to automate a data analysis pipeline. Each <em>OBITools</em> command implements an algorithm to process the data. For example, the <a href="http://metabar:8888/obidoc/obitools/obicount/">
<abbr title="obicount: counting sequence records"><code>obicount</code></abbr>
</a> command implements an algorithm to count the number of sequences in a sequence 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>
<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><pre tabindex="0"><code>entities,n
variants,2
reads,3
symbols,200
</code></pre><p>In addition to its name, an <em>OBITools</em> command has a number of options that allow you to customise its behaviour. For example, the <a href="http://metabar:8888/obidoc/obitools/obicount/">
<abbr title="obicount: counting sequence records"><code>obicount</code></abbr>
</a> command has the <code>--symbols</code> option, which tells it to count only the total number of nucleotides 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 --symbols two_sequences.fasta
</span></span></code></pre></div><pre tabindex="0"><code>entities,n
symbols,200
</code></pre><p>If you compare the two outputs, you will notice that the first version of the <a href="http://metabar:8888/obidoc/obitools/obicount/">
<abbr title="obicount: counting sequence records"><code>obicount</code></abbr>
</a> command without the <code>--symbols</code> option counts the total number of nucleotides, but also the number of sequence variants and the number of reads, while the second version with the <code>--symbols</code> option counts only the total number of nucleotides.</p>
<h2 id="multiple-ways-to-specify-the-same-option">
Multiple ways to specify the same option
<a class="anchor" href="#multiple-ways-to-specify-the-same-option">#</a>
</h2>
<p>Unix options are specified on the command line by adding then after the command name. They can take two forms:</p>
<ul>
<li>The long option name, which is the name of the option preceded by two hyphens, for example <code>--help</code>.</li>
<li>For some options, such as the <code>help</code> option, there is also a short version of the option. This consists of a single character preceded by a single hyphen, for example <code>-h</code>.</li>
</ul>
<p>If multiple forms of the same option exist, they are separated in the documentation by a vertical bar <code>|</code>, <em>e.g.</em> the option <code>help</code> exists in its long form <code>--help</code> and in one of its short forms <code>-h</code> or <code>-?</code>. These different forms are represented as follows <code>--help|-h|-?</code>.</p>
<h2 id="specifying-an-option-through-environment-variables">
Specifying an option through environment variables
<a class="anchor" href="#specifying-an-option-through-environment-variables">#</a>
</h2>
<p>Options such as <code>--max-cpu</code>, which specifies the maximum number of CPU cores used by <em>OBITools</em>, can be specified when running the 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 --max-cpu<span style="color:#f92672">=</span><span style="color:#ae81ff">4</span> my_sequence.fasta
</span></span></code></pre></div><p>or by declaring an environment variable. For this example, the environment variable corresponding to the <code>--max-cpu</code> option is <code>OBIMAXCPU</code>. When using
<a href="https://en.wikipedia.org/wiki/Bash_%28Unix_shell%29">bash</a> or
<a href="https://en.wikipedia.org/wiki/Z_shell">zsh</a> shells, the environment variable can be set using the <code>export</code> 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>export OBIMAXCPU<span style="color:#f92672">=</span><span style="color:#ae81ff">4</span>
</span></span></code></pre></div><p>Once the environment variable is set, any <em>OBITools</em> command run in the same shell session will use the value of four CPU cores, in this case without the need to specify the <code>--max-cpu</code> option.</p>
<p>Some <em>OBITools</em> options are shared by most of the commands. These options are listed in the following table.</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="controlling-the-output-data">
Controlling the output data
<a class="anchor" href="#controlling-the-output-data">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--compress</code></b>
| <b><code class="language-bash">-Z</code></b>
: output is compressed using gzip. (default: false)</li>
<li><b><code class="language-bash">--no-order</code></b>: the <em>OBITools</em> ensure that the order between the input file and
the output file does not change. When multiple files are processed,
they are processed one at a time.
If the <strong>&ndash;no-order</strong> option is added to a command, multiple input
files can be opened at the same time and their contents processed
in parallel. This usually increases processing speed, but does not
guarantee the order of the sequences in the output file.
Also, processing multiple files in parallel may require more memory
to perform the computation.</li>
<li>
<b><code class="language-bash">--fasta-output</code></b>: writes sequence data in <a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a> format (default if quality data is not available).</li>
<li>
<b><code class="language-bash">--fastq-output</code></b>: writes sequence data in <a href="http://metabar:8888/obidoc/formats/fastq/">fastq</a> format (default if quality data is available).</li>
<li><b><code class="language-bash">--json-output</code></b>: writes sequence data in JSON format.</li>
<li><b><code class="language-bash">--out</code></b>
| <b><code class="language-bash">-o</code></b>
&lt;FILENAME>: filename used for saving the output (default: &ldquo;-&rdquo;, the standard output)</li>
<li><b><code class="language-bash">--output-OBI-header</code></b>
| <b><code class="language-bash">-O</code></b>
: writes output FASTA/FASTQ title line annotations in OBI format (default: JSON).</li>
<li><b><code class="language-bash">--output-json-header</code></b>: writew output FASTA/FASTQ title line annotations in JSON format (the default format).</li>
<li><b><code class="language-bash">--skip-empty</code></b>: sequences of length equal to zero are removed from the output (default: false).</li>
<li><b><code class="language-bash">--no-progressbar</code></b>: deactivates progress bar display (default: false).</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>
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