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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/APPLICATIONS/TOPPBase.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
using namespace OpenMS;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_MRMMapper MRMMapper
@brief MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
<CENTER>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> potential predecessor tools </td>
<td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ MRMMapper \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> potential successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_FileFilter </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> @ref TOPP_OpenSwathAnalyzer </td>
</tr>
</table>
</CENTER>
This tool reads an mzML containing chromatograms (presumably measured on an
SRM instrument) and a TraML file that contains the data that was used to
generate the instrument method to measure said data. It then maps the
transitions in the TraML file to the chromatograms found in the mzML file
and stores the mapping by replacing the "id" paramter in the mzML with the
"id" of the transition in the TraML file. It removes chromatograms for
which it cannot find a mapping and throws an error if more than one
transitions maps to a chromatogram.
In strict mode (default) it also throws an error it not all chromatograms
could be found in the TraML file.
The thus mapped file can then be used in a downstream analysis.
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_MRMMapper.cli
<B>The algorithm parameters for the Analyzer filter are:</B>
@htmlinclude TOPP_MRMMapper.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPMRMMapper
: public TOPPBase
{
public:
TOPPMRMMapper() :
TOPPBase("MRMMapper", "MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)", true)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "Input file containing chromatograms (converted mzXML file)");
setValidFormats_("in", StringList::create("mzML"));
registerInputFile_("tr", "<file>", "", "transition file");
setValidFormats_("tr", StringList::create("TraML"));
registerOutputFile_("out", "<file>", "", "Output file containing mapped chromatograms");
setValidFormats_("out", StringList::create("mzML"));
registerDoubleOption_("precursor_tolerance", "<double>", 0.1, "Precursor tolerance when mapping (in Th)", false);
registerDoubleOption_("product_tolerance", "<double>", 0.1, "Product tolerance when mapping (in Th)", false);
registerFlag_("no-strict", "run in non-strict mode and allow some chromatograms to not be mapped.");
}
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in");
String tr_file = getStringOption_("tr");
String out = getStringOption_("out");
DoubleReal map_precursor_tol_ = getDoubleOption_("precursor_tolerance");
DoubleReal map_product_tol_ = getDoubleOption_("product_tolerance");
bool nostrict = getFlag_("no-strict");
OpenMS::TargetedExperiment targeted_exp;
OpenMS::MSExperiment<ChromatogramPeak> chromatogram_map;
OpenMS::MSExperiment<ChromatogramPeak> output;
TraMLFile().load(tr_file, targeted_exp);
MzMLFile().load(in, chromatogram_map);
// copy all meta data from old chromatogram
output = chromatogram_map;
output.clear(false);
std::vector<MSChromatogram<ChromatogramPeak> > empty_chromats;
output.setChromatograms(empty_chromats);
int notmapped = 0;
for (Size i = 0; i < chromatogram_map.getChromatograms().size(); i++)
{
// try to find the best matching transition for this chromatogram
bool mapped_already = false;
MSChromatogram<ChromatogramPeak> chromatogram = chromatogram_map.getChromatograms()[i];
for (Size j = 0; j < targeted_exp.getTransitions().size(); j++)
{
if (fabs(chromatogram.getPrecursor().getMZ() - targeted_exp.getTransitions()[j].getPrecursorMZ()) < map_precursor_tol_ &&
fabs(chromatogram.getProduct().getMZ() - targeted_exp.getTransitions()[j].getProductMZ()) < map_product_tol_)
{
// std::cout << "Mapping chromatogram " << i << " to transition " << j << " (" << targeted_exp.getTransitions()[j].getNativeID() << ")"
// " with precursor mz " << chromatogram.getPrecursor().getMZ() << " / " << targeted_exp.getTransitions()[j].getPrecursorMZ() <<
// " and product mz " << chromatogram.getProduct().getMZ() << " / " << targeted_exp.getTransitions()[j].getProductMZ() << std::endl;
// ensure: map every chromatogram to only one transition
if (mapped_already)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Already mapped chromatogram " + String(i) + \
" with " + String(chromatogram.getPrecursor().getMZ()) + \
" -> " + String(chromatogram.getProduct().getMZ()) + \
"! Maybe try to decrease your mapping tolerance.");
}
mapped_already = true;
// Create precursor and set the peptide sequence
Precursor precursor = chromatogram.getPrecursor();
String pepref = targeted_exp.getTransitions()[j].getPeptideRef();
for (Size pep_idx = 0; pep_idx < targeted_exp.getPeptides().size(); pep_idx++)
{
const OpenMS::TargetedExperiment::Peptide * pep = &targeted_exp.getPeptides()[pep_idx];
if (pep->id == pepref)
{
precursor.setMetaValue("peptide_sequence", pep->sequence);
break;
}
}
// add precursor to spectrum
chromatogram.setPrecursor(precursor);
// Set the id of the chromatogram, using the id of the transition (this gives directly the mapping of the two)
chromatogram.setNativeID(targeted_exp.getTransitions()[j].getNativeID());
}
}
// ensure: map every chromatogram to at least one transition
if (!mapped_already)
{
std::cerr << "Did not find a mapping for chromatogram " + String(i) + " with " + String(chromatogram.getPrecursor().getMZ()) + \
" -> " + String(chromatogram.getProduct().getMZ()) + "! Maybe try to increase your mapping tolerance." << std::endl;
notmapped++;
if (!nostrict)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Did not find a mapping for chromatogram " + String(i) + "! Maybe try to increase your mapping tolerance.");
}
}
else
{
output.addChromatogram(chromatogram);
}
}
if (notmapped > 0)
{
std::cerr << "Could not find mapping for " << notmapped << " chromatogram(s) " << std::endl;
}
// add all data processing information to all the chromatograms
DataProcessing dp;
dp = getProcessingInfo_(DataProcessing::FORMAT_CONVERSION);
std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = output.getChromatograms();
for (Size i=0; i<chromatograms.size(); ++i)
{
chromatograms[i].getDataProcessing().push_back(dp);
}
output.setChromatograms(chromatograms);
MzMLFile().store(out, output);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPMRMMapper tool;
return tool.main(argc, argv);
}
/// @endcond
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