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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVReader.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
using namespace OpenMS;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_ConvertTraMLToTSV ConvertTraMLToTSV
@brief Converts TraML files to OpenSWATH transition TSV files
The OpenSWATH transition TSV files will have the following headers, all fields are separated by tabs:
<ul>
<li> PrecursorMz (float) </li>
<li> ProductMz (float) </li>
<li> Tr_calibrated (float) </li>
<li> transition_name (free text, needs to be unique for each transition [in this file]) </li>
<li> Collision Energy (float) </li>
<li> LibraryIntensity (float) </li>
<li> transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) </li>
<li> decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) </li>
<li> PeptideSequence (free text, sequence only (no modifications) ) </li>
<li> ProteinName (free text) </li>
<li> Annotation (free text, e.g. y7) </li>
<li> FullUniModPeptideName (free text, should contain modifications*) </li>
<li> PrecursorCharge (integer, contains the charge of the precursor) </li>
<li> GroupLabel (free text, e.g. heavy or light) </li>
<li> UniprotID (free text) </li>
<li> FragmentType (free text, contains the type of the fragment, e.g. "b" or "y") </li>
<li> FragmentCharge (integer, contains the fragment charge) </li>
<li> FragmentSeriesNumber (integer, e.g. for y7 use "7" here) </li>
</ul>
* modifications are returned in UniMod annotation.
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPConvertTraMLToTSV : public TOPPBase
{
public:
TOPPConvertTraMLToTSV() :
TOPPBase("ConvertTraMLToTSV", "Converts a TraML file to an OpenSWATH transition TSV file")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Input TraML file");
setValidFormats_("in", StringList::create("TraML"));
registerOutputFile_("out", "<file>", "", "Output OpenSWATH transition TSV file");
setValidFormats_("out", StringList::create("csv"));
}
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in");
String out = getStringOption_("out");
const char * tr_file = out.c_str();
TraMLFile traml;
TargetedExperiment targeted_exp;
std::cout << "Reading " << in << std::endl;
traml.load(in, targeted_exp);
TransitionTSVReader tsv_reader = TransitionTSVReader();
tsv_reader.setLogType(log_type_);
tsv_reader.convertTargetedExperimentToTSV(tr_file, targeted_exp);
std::cout << "Writing " << out << std::endl;
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPConvertTraMLToTSV tool;
return tool.main(argc, argv);
}
/// @endcond
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