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<TITLE>Conversion between OpenMS XML formats and text formats</TITLE>
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<div class="title">Conversion between <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> XML formats and text formats </div> </div>
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<div class="textblock"><h1><a class="anchor" id="TOPP_example_convert_export"></a>
Export of OpenMS XML formats</h1>
<p>As TOPP offers no functionality for statistical analysis, this step is normally done using external statistics packages. <br/>
In order to export the OpenMS XML formats into an appropriate format for these packages the TOPP <b>TextExporter</b> can be used.</p>
<p>It converts the the following OpenMS XML formats to text files:</p>
<ul>
<li>featureXML</li>
<li>idXML</li>
<li>consensusXML</li>
</ul>
<p>The use of the <b>TextExporter</b> is very simple: </p>
<div class="fragment"><div class="line">TextExporter -in <a class="code" href="namespaceOpenMS_1_1Internal_1_1ClassTest.html#a835c194d7465ac0e608fc154c9e9ef80">infile</a>.idXML -out outfile.txt</div>
</div><!-- fragment --><h1><a class="anchor" id="TOPP_example_convert_import_feature"></a>
Import of feature data to OpenMS</h1>
<p>OpenMS offers a lot of visualization and analysis functionality for feature data. <br/>
Feature data in text format, e.g. from other analysis tools, can be imported using the <b>TextImporter</b>. The default mode accepts comma separated values containing the following columns: RT, m/z, intensity. Additionally meta data columns may follow. If meta data is used, meta data column names have to be specified in a header line. Without headers: </p>
<pre class="fragment">1201 503.123 1435000
1201 1006.246 1235200</pre><p> Or with headers: </p>
<pre class="fragment">RT m/z Int isHeavy myMeta
1201 503.123 1435000 true 2
1201 1006.246 1235200 maybe 1</pre><p>Example invocation: </p>
<div class="fragment"><div class="line">TextImporter -in <a class="code" href="namespaceOpenMS_1_1Internal_1_1ClassTest.html#a835c194d7465ac0e608fc154c9e9ef80">infile</a>.txt -out outfile.featureXML</div>
</div><!-- fragment --><p>The tool also supports data from msInspect,SpecArray and Kroenik(Hardkloer sibling), just specify the -mode option accordingly.</p>
<h1><a class="anchor" id="TOPP_example_convert_import_id"></a>
Import of protein/peptide identification data to OpenMS</h1>
<p>Peptide/protein identification data from several identification engines can be converted to idXML format using the <b>IDFileConverter</b> tool.</p>
<p>It can currently read the following formats:</p>
<ul>
<li>Sequest output folder</li>
<li>pepXML file</li>
<li>idXML file</li>
</ul>
<p>It can currently write the folling formats:</p>
<ul>
<li>pepXML</li>
<li>idXML</li>
</ul>
<p>This example shows how to convert pepXML to idXML: </p>
<div class="fragment"><div class="line">IDFileConverter -in <a class="code" href="namespaceOpenMS_1_1Internal_1_1ClassTest.html#a835c194d7465ac0e608fc154c9e9ef80">infile</a>.pepXML -out outfile.idXML</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 11:19:25 using doxygen 1.8.5</font></TD>
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