MetabarcodingSchool/OBIJupyterHub
1
0
Fork 0
Code Issues Pull Requests 1 Actions Packages Projects Releases Wiki Activity
Files
30b7175702ea411825f8625838d1a7a63faf30fc
OBIJupyterHub/jupyterhub_volumes/web/obidoc/obitools/obiscript/index.html
Eric Coissac 30b7175702 Make cleaning
2025-11-17 14:18:13 +01:00

2157 lines
56 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters
This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.
<!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="
obiscript: apply a LUA script on sequences
#
Description
#
Apply a LUA script to each sequence in a sequence file.
Synopsis
#
obiscript [--allows-indels] [--approx-pattern &lt;PATTERN&gt;]...
[--attribute|-a &lt;KEY=VALUE&gt;]... [--batch-size &lt;int&gt;]
[--compressed|-Z] [--csv] [--debug] [--definition|-D &lt;PATTERN&gt;]...
[--ecopcr] [--embl] [--fail-on-taxonomy] [--fasta] [--fasta-output]
[--fastq] [--fastq-output] [--force-one-cpu] [--genbank]
[--has-attribute|-A &lt;KEY&gt;]... [--help|-h|-?] [--id-list &lt;FILENAME&gt;]
[--identifier|-I &lt;PATTERN&gt;]... [--ignore-taxon|-i &lt;TAXID&gt;]...
[--input-OBI-header] [--input-json-header] [--inverse-match|-v]
[--json-output] [--max-count|-C &lt;COUNT&gt;] [--max-cpu &lt;int&gt;]
[--max-length|-L &lt;LENGTH&gt;] [--min-count|-c &lt;COUNT&gt;]
[--min-length|-l &lt;LENGTH&gt;] [--no-order] [--no-progressbar]
[--only-forward] [--out|-o &lt;FILENAME&gt;] [--output-OBI-header|-O]
[--output-json-header]
[--paired-mode &lt;forward|reverse|and|or|andnot|xor&gt;]
[--paired-with &lt;FILENAME&gt;] [--pattern-error &lt;int&gt;] [--pprof]
[--pprof-goroutine &lt;int&gt;] [--pprof-mutex &lt;int&gt;]
[--predicate|-p &lt;EXPRESSION&gt;]... [--raw-taxid]
[--require-rank &lt;RANK_NAME&gt;]... [--restrict-to-taxon|-r &lt;TAXID&gt;]...
[--script|-S &lt;string&gt;] [--sequence|-s &lt;PATTERN&gt;]... [--skip-empty]
[--solexa] [--taxonomy|-t &lt;string&gt;] [--template] [--update-taxid]
[--valid-taxid] [--version] [&lt;args&gt;]
Options
#
obiscript
mandatory option
#
--script
| -S
&lt;STRING&gt;: The script to execute.
Other
obiscript
specific option
#
--template: Print on the standard output a script template.
Selecting sequence records
#
Selection based on the sequence
#
Strict matching
#
--sequence
| -s
&lt;PATTERN&gt;: A Regular expression pattern used to match the sequence.
Only the entries whose sequence matches the pattern are kept.
Regular expression patterns are case-insensitive.
Approximate matching
#
--approx-pattern &lt;PATTERN&gt;: A DNA pattern used to match the sequence.
Only the entries whose sequence matches the pattern are kept.
DNA patterns are case-insensitive. They can be matched allowing
for errors: mismatches or insertions or deletions.
--allows-indels: allows for indels during pattern DNA pattern matching (see --approx-pattern option).
--pattern-error &lt;INTEGER&gt;: maximum number of errors allowed when searching for patterns in DNA (default 0, see --approx-pattern option).
Selection based on the sequence identifier
#
--identifier
| -I
&lt;REGEX&gt;: Regular expression pattern to be
tested against the sequence identifier.
The pattern is case-insensitive.
--id-list &lt;FILENAME&gt;: points to a text file containing the list of sequence record identifiers to be selected.
The file format consists in a single identifier per line.
Selection based on the sequence definition
#
--definition
| -D
&lt;REGEX&gt;: Regular expression pattern to be tested against the sequence definition.
The pattern is case-insensitive.
Selection based on the sequence properties
#
--min-count
| -c
&lt;COUNT&gt;: selects the sequence records for which the number of occurrences (i.e the count attribute) is equal to or greater than the defined minimum count.
--max-count
| -C
&lt;COUNT&gt;: Select the sequence records for which the occurrence count (i.e the count attribute) is equal to or smaller than the defined maximum count.
--min-length
| -l
&lt;LENGTH&gt;: selects the sequence records for which the sequence length is equal to or
greater than the defined minimum sequence length.
--max-length
| -L
&lt;LENGTH&gt;: selects sequence records for which the sequence length is equal to or less than the defined maximum sequence length.
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
#
obiscript --help
">
<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/obitools/obiscript/">
<meta property="og:site_name" content="OBITools4 documentation">
<meta property="og:title" content="obiscript">
<meta property="og:description" content="obiscript: apply a LUA script on sequences # Description # Apply a LUA script to each sequence in a sequence file.
Synopsis # obiscript [--allows-indels] [--approx-pattern &lt;PATTERN&gt;]... [--attribute|-a &lt;KEY=VALUE&gt;]... [--batch-size &lt;int&gt;] [--compressed|-Z] [--csv] [--debug] [--definition|-D &lt;PATTERN&gt;]... [--ecopcr] [--embl] [--fail-on-taxonomy] [--fasta] [--fasta-output] [--fastq] [--fastq-output] [--force-one-cpu] [--genbank] [--has-attribute|-A &lt;KEY&gt;]... [--help|-h|-?] [--id-list &lt;FILENAME&gt;] [--identifier|-I &lt;PATTERN&gt;]... [--ignore-taxon|-i &lt;TAXID&gt;]... [--input-OBI-header] [--input-json-header] [--inverse-match|-v] [--json-output] [--max-count|-C &lt;COUNT&gt;] [--max-cpu &lt;int&gt;] [--max-length|-L &lt;LENGTH&gt;] [--min-count|-c &lt;COUNT&gt;] [--min-length|-l &lt;LENGTH&gt;] [--no-order] [--no-progressbar] [--only-forward] [--out|-o &lt;FILENAME&gt;] [--output-OBI-header|-O] [--output-json-header] [--paired-mode &lt;forward|reverse|and|or|andnot|xor&gt;] [--paired-with &lt;FILENAME&gt;] [--pattern-error &lt;int&gt;] [--pprof] [--pprof-goroutine &lt;int&gt;] [--pprof-mutex &lt;int&gt;] [--predicate|-p &lt;EXPRESSION&gt;]... [--raw-taxid] [--require-rank &lt;RANK_NAME&gt;]... [--restrict-to-taxon|-r &lt;TAXID&gt;]... [--script|-S &lt;string&gt;] [--sequence|-s &lt;PATTERN&gt;]... [--skip-empty] [--solexa] [--taxonomy|-t &lt;string&gt;] [--template] [--update-taxid] [--valid-taxid] [--version] [&lt;args&gt;] Options # obiscript mandatory option # --script | -S &lt;STRING&gt;: The script to execute. Other obiscript specific option # --template: Print on the standard output a script template. Selecting sequence records # Selection based on the sequence # Strict matching # --sequence | -s &lt;PATTERN&gt;: A Regular expression pattern used to match the sequence. Only the entries whose sequence matches the pattern are kept. Regular expression patterns are case-insensitive. Approximate matching # --approx-pattern &lt;PATTERN&gt;: A DNA pattern used to match the sequence. Only the entries whose sequence matches the pattern are kept. DNA patterns are case-insensitive. They can be matched allowing for errors: mismatches or insertions or deletions. --allows-indels: allows for indels during pattern DNA pattern matching (see --approx-pattern option). --pattern-error &lt;INTEGER&gt;: maximum number of errors allowed when searching for patterns in DNA (default 0, see --approx-pattern option). Selection based on the sequence identifier # --identifier | -I &lt;REGEX&gt;: Regular expression pattern to be tested against the sequence identifier. The pattern is case-insensitive. --id-list &lt;FILENAME&gt;: points to a text file containing the list of sequence record identifiers to be selected. The file format consists in a single identifier per line. Selection based on the sequence definition # --definition | -D &lt;REGEX&gt;: Regular expression pattern to be tested against the sequence definition. The pattern is case-insensitive. Selection based on the sequence properties # --min-count | -c &lt;COUNT&gt;: selects the sequence records for which the number of occurrences (i.e the count attribute) is equal to or greater than the defined minimum count. --max-count | -C &lt;COUNT&gt;: Select the sequence records for which the occurrence count (i.e the count attribute) is equal to or smaller than the defined maximum count. --min-length | -l &lt;LENGTH&gt;: selects the sequence records for which the sequence length is equal to or greater than the defined minimum sequence length. --max-length | -L &lt;LENGTH&gt;: selects sequence records for which the sequence length is equal to or less than the defined maximum sequence length. 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 # obiscript --help">
<meta property="og:locale" content="en_us">
<meta property="og:type" content="website">
<title>obiscript | 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/obitools/obiscript/">
<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/obitools/obiscript/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" />
<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" />
<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="">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" checked />
<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" checked />
<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
<a role="button" class="">Advanced tools</a>
</label>
<ul>
<li>
<a href="/obidoc/obitools/obiscript/" class="active">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>obiscript</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="#obiscript-apply-a-lua-script-on-sequences"><code>obiscript</code>: apply a LUA script on sequences</a>
<ul>
<li><a href="#description">Description</a></li>
<li><a href="#synopsis">Synopsis</a></li>
<li><a href="#options">Options</a>
<ul>
<li></li>
</ul>
</li>
<li><a href="#examples">Examples</a></li>
</ul>
</li>
</ul>
</nav>
</aside>
</header>
<article class="markdown book-article"><h1 id="obiscript-apply-a-lua-script-on-sequences">
<code>obiscript</code>: apply a LUA script on sequences
<a class="anchor" href="#obiscript-apply-a-lua-script-on-sequences">#</a>
</h1>
<h2 id="description">
Description
<a class="anchor" href="#description">#</a>
</h2>
<p>Apply a LUA script to each sequence in 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>obiscript <span style="color:#f92672">[</span>--allows-indels<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--approx-pattern &lt;PATTERN&gt;<span style="color:#f92672">]</span>...
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--attribute|-a &lt;KEY<span style="color:#f92672">=</span>VALUE&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--batch-size &lt;int&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--compressed|-Z<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>--definition|-D &lt;PATTERN&gt;<span style="color:#f92672">]</span>...
</span></span><span style="display:flex;"><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>--fail-on-taxonomy<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--fasta<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--fasta-output<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>--fastq-output<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></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--has-attribute|-A &lt;KEY&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--help|-h|-?<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--id-list &lt;FILENAME&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--identifier|-I &lt;PATTERN&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--ignore-taxon|-i &lt;TAXID&gt;<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>--inverse-match|-v<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--json-output<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--max-count|-C &lt;COUNT&gt;<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>--max-length|-L &lt;LENGTH&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--min-count|-c &lt;COUNT&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--min-length|-l &lt;LENGTH&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--no-order<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--no-progressbar<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--only-forward<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--out|-o &lt;FILENAME&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--output-OBI-header|-O<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--output-json-header<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--paired-mode &lt;forward|reverse|and|or|andnot|xor&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--paired-with &lt;FILENAME&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pattern-error &lt;int&gt;<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></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--predicate|-p &lt;EXPRESSION&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--raw-taxid<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--require-rank &lt;RANK_NAME&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--restrict-to-taxon|-r &lt;TAXID&gt;<span style="color:#f92672">]</span>...
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--script|-S &lt;string&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--sequence|-s &lt;PATTERN&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--skip-empty<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>--taxonomy|-t &lt;string&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--template<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--update-taxid<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--valid-taxid<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="hahahugoshortcode7s0hbhb-mandatory-option">
<a href="http://metabar:8888/obidoc/obitools/obiscript/">
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
</a> mandatory option
<a class="anchor" href="#hahahugoshortcode7s0hbhb-mandatory-option">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--script</code></b>
| <b><code class="language-bash">-S</code></b>
&lt;STRING>: The script to execute.
</li>
</ul>
<h4 id="other-hahahugoshortcode7s2hbhb-specific-option">
Other <a href="http://metabar:8888/obidoc/obitools/obiscript/">
<abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
</a> specific option
<a class="anchor" href="#other-hahahugoshortcode7s2hbhb-specific-option">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--template</code></b>: Print on the standard output a script template.
</li>
</ul>
<h4 id="selecting-sequence-records">
Selecting sequence records
<a class="anchor" href="#selecting-sequence-records">#</a>
</h4>
<h5 id="selection-based-on-the-sequence">
Selection based on the sequence
<a class="anchor" href="#selection-based-on-the-sequence">#</a>
</h5>
<h6 id="strict-matching">
Strict matching
<a class="anchor" href="#strict-matching">#</a>
</h6>
<ul>
<li><b><code class="language-bash">--sequence</code></b>
| <b><code class="language-bash">-s</code></b>
&lt;PATTERN>: A <a href="/obidoc/docs/patterns/regular">Regular expression pattern</a> used to match the sequence.
Only the entries whose sequence matches the pattern are kept.
Regular expression patterns are case-insensitive.</li>
</ul>
<h6 id="approximate-matching">
Approximate matching
<a class="anchor" href="#approximate-matching">#</a>
</h6>
<ul>
<li><b><code class="language-bash">--approx-pattern</code></b> &lt;PATTERN>: A <a href="/obidoc/docs/patterns/dnagrep">DNA pattern</a> used to match the sequence.
Only the entries whose sequence matches the pattern are kept.
DNA patterns are case-insensitive. They can be matched allowing
for errors: mismatches or insertions or deletions.</li>
<li><b><code class="language-bash">--allows-indels</code></b>: allows for indels during pattern DNA pattern matching (see <code>--approx-pattern</code> option).
</li>
<li><b><code class="language-bash">--pattern-error</code></b> &lt;INTEGER>: maximum number of errors allowed when searching for patterns in DNA (default 0, see <code>--approx-pattern</code> option).
</ul>
<h5 id="selection-based-on-the-sequence-identifier">
Selection based on the sequence identifier
<a class="anchor" href="#selection-based-on-the-sequence-identifier">#</a>
</h5>
<ul>
<li><b><code class="language-bash">--identifier</code></b>
| <b><code class="language-bash">-I</code></b>
&lt;REGEX>: <a href="/obidoc/docs/patterns/regular">Regular expression pattern</a> to be
tested against the sequence identifier.
The pattern is case-insensitive.</li>
<li><b><code class="language-bash">--id-list</code></b> &lt;FILENAME>: <FILENAME> points to a text file containing the list of sequence record identifiers to be selected.
The file format consists in a single identifier per line.</li>
</ul>
<h5 id="selection-based-on-the-sequence-definition">
Selection based on the sequence definition
<a class="anchor" href="#selection-based-on-the-sequence-definition">#</a>
</h5>
<ul>
<li><b><code class="language-bash">--definition</code></b>
| <b><code class="language-bash">-D</code></b>
&lt;REGEX>: <a href="/obidoc/docs/patterns/regular">Regular expression pattern</a> to be tested against the sequence definition.
The pattern is case-insensitive.</li>
</ul>
<h5 id="selection-based-on-the-sequence-properties">
Selection based on the sequence properties
<a class="anchor" href="#selection-based-on-the-sequence-properties">#</a>
</h5>
<ul>
<li><b><code class="language-bash">--min-count</code></b>
| <b><code class="language-bash">-c</code></b>
&lt;COUNT>: selects the sequence records for which the number of occurrences (<em>i.e</em> the <em>count</em> attribute) is equal to or greater than the defined minimum count.</li>
<li><b><code class="language-bash">--max-count</code></b>
| <b><code class="language-bash">-C</code></b>
&lt;COUNT>: Select the sequence records for which the occurrence count (<em>i.e</em> the <em>count</em> attribute) is equal to or smaller than the defined maximum count.</li>
<li><b><code class="language-bash">--min-length</code></b>
| <b><code class="language-bash">-l</code></b>
&lt;LENGTH>: selects the sequence records for which the sequence length is equal to or
greater than the defined minimum sequence length.</li>
<li><b><code class="language-bash">--max-length</code></b>
| <b><code class="language-bash">-L</code></b>
&lt;LENGTH>: selects sequence records for which the sequence length is equal to or less than the defined maximum sequence length.</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>obiscript --help
</span></span></code></pre></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="#obiscript-apply-a-lua-script-on-sequences"><code>obiscript</code>: apply a LUA script on sequences</a>
<ul>
<li><a href="#description">Description</a></li>
<li><a href="#synopsis">Synopsis</a></li>
<li><a href="#options">Options</a>
<ul>
<li></li>
</ul>
</li>
<li><a href="#examples">Examples</a></li>
</ul>
</li>
</ul>
</nav>
</div>
</aside>
</main>
</body>
</html>
Reference in New Issue View Git Blame Copy Permalink