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obisummary: generate summary statistics
#
Description
#
Generate summary statistics describing the sequence content of a sequence file.
Synopsis
#
obisummary [--batch-size &lt;int&gt;] [--csv] [--debug] [--ecopcr] [--embl]
[--fasta] [--fastq] [--force-one-cpu] [--genbank] [--help|-h|-?]
[--input-OBI-header] [--input-json-header] [--json-output]
[--map &lt;string&gt;]... [--max-cpu &lt;int&gt;] [--no-order] [--pprof]
[--pprof-goroutine &lt;int&gt;] [--pprof-mutex &lt;int&gt;] [--silent-warning]
[--solexa] [--u-to-t] [--version] [--yaml-output] [&lt;args&gt;]
Options
#
obisummary
specific options
#
--map &lt;string&gt;: Name of a map attribute.
--yaml-output &lt;string&gt;: Print results as YAML record. (default: false)
Controlling the input data
#
OBITools4 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.
The file format options
#
--fasta: indicates that sequence data is in fasta format.
--fastq: indicates that sequence data is in fastq format.
--embl: indicates that sequence data is in EMBL-ENA flatfile format.
--csv: indicates that sequence data is in CSV format.
--genbank: indicates that sequence data is in GenBank flatfile format.
--ecopcr: indicates that sequence data is in the old ecoPCR tabulated format.
Controlling the way OBITools4 are formatting annotations
#
These options only apply to the FASTA and FASTQ formats
--input-OBI-header: FASTA/FASTQ title line annotations follow the old OBI format.
--input-json-header: FASTA/FASTQ title line annotations follow the JSON format.
Controlling quality score decoding
#
This option only applies to the FASTQ formats
--solexa: decodes quality string according to the old Solexa specification. (default: the standard Sanger encoding is used, env: OBISSOLEXA)
Controlling the output data
#
--compress
| -Z
: output is compressed using gzip. (default: false)
--no-order: the OBITools 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 &ndash;no-order 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.
--fasta-output: writes sequence data in fasta format (default if quality data is not available).
--fastq-output: writes sequence data in fastq format (default if quality data is available).
--json-output: writes sequence data in JSON format.
--out
| -o
&lt;FILENAME&gt;: filename used for saving the output (default: &ldquo;-&rdquo;, the standard output)
--output-OBI-header
| -O
: writes output FASTA/FASTQ title line annotations in OBI format (default: JSON).
--output-json-header: writew output FASTA/FASTQ title line annotations in JSON format (the default format).
--skip-empty: sequences of length equal to zero are removed from the output (default: false).
--no-progressbar: deactivates progress bar display (default: false).
General options
#
--help
| -h|-?
: shows this help.
--version: prints the version and exits.
--silent-warning: This option tells obitools to stop displaying warnings.
This behaviour can be controlled by setting the OBIWARNINGS environment variable.
Computation related options
#
--max-cpu &lt;INTEGER&gt;: OBITools 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 OBITools can also be controlled
by setting the OBIMAXCPU environment variable.
--force-one-cpu: forces the use of a single CPU core for parallel processing (default: false).
--batch-size &lt;INTEGER&gt;: number of sequence per batch for parallel processing (default: 1000, env: OBIBATCHSIZE)
Debug related options
#
--debug: enables debug mode, by setting log level to debug (default: false, env: OBIDEBUG)
--pprof: enables pprof server. Look at the log for details. (default: false).
--pprof-mutex &lt;INTEGER&gt;: enables profiling of mutex lock. (default: 10, env: OBIPPROFMUTEX)
--pprof-goroutine &lt;INTEGER&gt;: enables profiling of goroutine blocking profile. (default: 6060, env: OBIPPROFGOROUTINE)
Examples
#
obisummary --help
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<meta property="og:description" content="obisummary: generate summary statistics # Description # Generate summary statistics describing the sequence content of a sequence file.
Synopsis # obisummary [--batch-size &lt;int&gt;] [--csv] [--debug] [--ecopcr] [--embl] [--fasta] [--fastq] [--force-one-cpu] [--genbank] [--help|-h|-?] [--input-OBI-header] [--input-json-header] [--json-output] [--map &lt;string&gt;]... [--max-cpu &lt;int&gt;] [--no-order] [--pprof] [--pprof-goroutine &lt;int&gt;] [--pprof-mutex &lt;int&gt;] [--silent-warning] [--solexa] [--u-to-t] [--version] [--yaml-output] [&lt;args&gt;] Options # obisummary specific options # --map &lt;string&gt;: Name of a map attribute. --yaml-output &lt;string&gt;: Print results as YAML record. (default: false) Controlling the input data # OBITools4 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. The file format options # --fasta: indicates that sequence data is in fasta format. --fastq: indicates that sequence data is in fastq format. --embl: indicates that sequence data is in EMBL-ENA flatfile format. --csv: indicates that sequence data is in CSV format. --genbank: indicates that sequence data is in GenBank flatfile format. --ecopcr: indicates that sequence data is in the old ecoPCR tabulated format. Controlling the way OBITools4 are formatting annotations # These options only apply to the FASTA and FASTQ formats --input-OBI-header: FASTA/FASTQ title line annotations follow the old OBI format. --input-json-header: FASTA/FASTQ title line annotations follow the JSON format. Controlling quality score decoding # This option only applies to the FASTQ formats --solexa: decodes quality string according to the old Solexa specification. (default: the standard Sanger encoding is used, env: OBISSOLEXA) Controlling the output data # --compress | -Z : output is compressed using gzip. (default: false) --no-order: the OBITools 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 –no-order 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. --fasta-output: writes sequence data in fasta format (default if quality data is not available). --fastq-output: writes sequence data in fastq format (default if quality data is available). --json-output: writes sequence data in JSON format. --out | -o &lt;FILENAME&gt;: filename used for saving the output (default: “-”, the standard output) --output-OBI-header | -O : writes output FASTA/FASTQ title line annotations in OBI format (default: JSON). --output-json-header: writew output FASTA/FASTQ title line annotations in JSON format (the default format). --skip-empty: sequences of length equal to zero are removed from the output (default: false). --no-progressbar: deactivates progress bar display (default: false). General options # --help | -h|-? : shows this help. --version: prints the version and exits. --silent-warning: This option tells obitools to stop displaying warnings. This behaviour can be controlled by setting the OBIWARNINGS environment variable. Computation related options # --max-cpu &lt;INTEGER&gt;: OBITools can take advantage of your computer’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 OBITools can also be controlled by setting the OBIMAXCPU environment variable. --force-one-cpu: forces the use of a single CPU core for parallel processing (default: false). --batch-size &lt;INTEGER&gt;: number of sequence per batch for parallel processing (default: 1000, env: OBIBATCHSIZE) Debug related options # --debug: enables debug mode, by setting log level to debug (default: false, env: OBIDEBUG) --pprof: enables pprof server. Look at the log for details. (default: false). --pprof-mutex &lt;INTEGER&gt;: enables profiling of mutex lock. (default: 10, env: OBIPPROFMUTEX) --pprof-goroutine &lt;INTEGER&gt;: enables profiling of goroutine blocking profile. (default: 6060, env: OBIPPROFGOROUTINE) Examples # obisummary --help">
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<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
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<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
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<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
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<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
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<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
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<span>Programming OBITools</span>
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<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
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<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>
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<li><a href="#obisummary-generate-summary-statistics"><code>obisummary</code>: generate summary statistics</a>
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<li><a href="#description">Description</a></li>
<li><a href="#synopsis">Synopsis</a></li>
<li><a href="#options">Options</a>
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<article class="markdown book-article"><h1 id="obisummary-generate-summary-statistics">
<code>obisummary</code>: generate summary statistics
<a class="anchor" href="#obisummary-generate-summary-statistics">#</a>
</h1>
<h2 id="description">
Description
<a class="anchor" href="#description">#</a>
</h2>
<p>Generate summary statistics describing the sequence content of a sequence file.</p>
<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>obisummary <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></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--fasta<span style="color:#f92672">]</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>--json-output<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--map &lt;string&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--max-cpu &lt;int&gt;<span style="color:#f92672">]</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></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--pprof-goroutine &lt;int&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof-mutex &lt;int&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--silent-warning<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--solexa<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--u-to-t<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--version<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--yaml-output<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="hahahugoshortcode28s0hbhb-specific-options">
<a href="http://metabar:8888/obidoc/obitools/obisummary/">
<abbr title="obisummary: generate summary statistics"><code>obisummary</code></abbr>
</a> specific options
<a class="anchor" href="#hahahugoshortcode28s0hbhb-specific-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--map</code></b> &lt;string>: Name of a map attribute.</li>
<li><b><code class="language-bash">--yaml-output</code></b> &lt;string>: Print results as YAML record. (default: false)</li>
</ul>
<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>
<h2 id="examples">
Examples
<a class="anchor" href="#examples">#</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>obisummary --help
</span></span></code></pre></div></article>
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