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psm-convert.html
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<!DOCTYPE html>
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<title>psm-convert</title>
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<div id="content" class="autogenerated">
<!-- START CONTENT -->
<h1>psm-convert</h1>
<h2>Usage:</h2>
<p><code>crux psm-convert [options] <input PSM file> <output format></code></p>
<h2>Description:</h2>
Reads in a file containing peptide-spectrum matches (PSMs) in one of the variety of supported formats and outputs the same PSMs in a different format
<h2>Input:</h2>
<ul>
<li><code>input PSM file</code> – The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format</li>
<li><code>output format</code> – The desired format of the output file. Legal values are tsv, html, sqt, pin, pepxml, mzidentml.</li>
</ul>
<h2>Output:</h2>
<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
<ul>
<li><code>psm-convert.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
<li><code>psm-convert.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
</ul>
<h2>Options:</h2>
<ul style="list-style-type: none;">
<li class="nobullet">
<h3>psm-convert options</h3>
<ul>
<li class="nobullet"><code>--input-format auto|tsv|sqt|pepxml|mzidentml</code> – Legal values are auto, tsv, sqt, pepxml or mzidentml format. Default = <code>auto</code>.</li>
<li class="nobullet"><code>--distinct-matches T|F</code> – Whether matches/ion are distinct (as opposed to total). Default = <code>true</code>.</li>
<li class="nobullet"><code>--protein-database <string></code> – The name of the file in FASTA format. Default = <code><empty></code>.</li>
</ul>
</li>
<li class="nobullet">
<h3>Input and output</h3>
<ul>
<li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
<li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
<li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
<li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
</ul>
</li>
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<p>
The original version of Crux was written by Chris Park and Aaron Klammer
under the supervision
of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
MacCoss</a>
and <a href="http://noble.gs.washington.edu/~noble">Prof. William
Stafford Noble</a> in the Department of Genome Sciences at the
University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>
<br />The complete list of contributors
can be found <a href="../contributors.html">here</a>.
<br />
<br />
Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> awards R01 GM096306 and P41 GM103533.
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