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<div class="title">Digestor </div> </div>
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<div class="textblock"><p>Digests a protein database in-silico. </p>
<center></center><center><table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> Digestor <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
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<td valign="middle" align="center" rowspan="1">none (FASTA input) </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDFilter.html">IDFilter</a> (peptide blacklist) </td></tr>
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</center><p>This application is used to digest a protein database to get all peptides given a cleavage enzyme. At the moment only trypsin is supported.</p>
<p>The output can be used as a blacklist filter input to <a class="el" href="TOPP_IDFilter.html">IDFilter</a>, to remove certain peptides.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
Digestor -- Digests a protein database in-silico.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
Digestor <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'fasta')
-out <file>* Output file (peptides) (valid formats: 'idXML', 'fasta')
-out_type <type> Set this if you cannot control the filename of 'out', e.g., in TOPPAS. (valid:
'idXML', 'fasta')
-missed_cleavages <number> The number of allowed missed cleavages (default: '1' min: '0')
-min_length <number> Minimum length of peptide (default: '6')
-max_length <number> Maximum length of peptide (default: '40')
-enzyme <string> The type of digestion enzyme (default: 'Trypsin' valid: 'Trypsin', 'none')
Common UTIL options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+Digestor</span><span class="node_description">Digests a protein database in-silico.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'Digestor'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file</span><span class="item_tags">input file</span><span class="item_restrictions">*.fasta</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output file (peptides)</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML,*.fasta</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_type</span><span class="item_value"></span>
<span class="item_description">Set this if you cannot control the filename of 'out', e.g., in TOPPAS.</span><span class="item_tags"></span><span class="item_restrictions">idXML,fasta</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">missed_cleavages</span><span class="item_value">1</span>
<span class="item_description">The number of allowed missed cleavages</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">min_length</span><span class="item_value">6</span>
<span class="item_description">Minimum length of peptide</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_length</span><span class="item_value">40</span>
<span class="item_description">Maximum length of peptide</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">enzyme</span><span class="item_value">Trypsin</span>
<span class="item_description">The type of digestion enzyme</span><span class="item_tags"></span><span class="item_restrictions">Trypsin,none</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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