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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: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/DTAFile.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_DTAExtractor DTAExtractor
@brief Extracts scans of an mzML file to several files in DTA format.
<center>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. predecessor tools </td>
<td VALIGN="middle" ROWSPAN=2> \f$ \longrightarrow \f$ DTAExtractor \f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> pot. successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> any signal-/preprocessing tool </td>
<td VALIGN="middle" ALIGN = "center" ROWSPAN=1> - </td>
</tr>
</table>
</center>
The retention time, the m/z ratio (for MS level > 1) and the file extension are appended to the output file name.
You can limit the exported spectra by m/z range, retention time range or MS level.
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_DTAExtractor.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_DTAExtractor.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPDTAExtractor :
public TOPPBase
{
public:
TOPPDTAExtractor() :
TOPPBase("DTAExtractor", "Extracts spectra of an MS run file to several files in DTA format.")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "input file ");
setValidFormats_("in", StringList::create("mzML"));
registerStringOption_("out", "<file>", "", "base name of DTA output files (RT, m/z and extension are appended)");
registerStringOption_("mz", "[min]:[max]", ":", "m/z range of precursor peaks to extract.\n"
"This option is ignored for MS level 1", false);
registerStringOption_("rt", "[min]:[max]", ":", "retention time range of spectra to extract", false);
registerStringOption_("level", "i[,j]...", "1,2,3", "MS levels to extract", false);
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
//ranges
String mz, rt, tmp;
double mz_l, mz_u, rt_l, rt_u;
vector<UInt> levels;
//initialize ranges
mz_l = rt_l = -1 * numeric_limits<double>::max();
mz_u = rt_u = numeric_limits<double>::max();
rt = getStringOption_("rt");
mz = getStringOption_("mz");
String level = getStringOption_("level");
//convert bounds to numbers
try
{
//rt
parseRange_(rt, rt_l, rt_u);
writeDebug_("rt lower/upper bound: " + String(rt_l) + " / " + String(rt_u), 1);
//mz
parseRange_(mz, mz_l, mz_u);
writeDebug_("mz lower/upper bound: " + String(mz_l) + " / " + String(mz_u), 1);
//levels
tmp = level;
if (level.has(',')) //several levels given
{
vector<String> tmp2;
level.split(',', tmp2);
for (vector<String>::iterator it = tmp2.begin(); it != tmp2.end(); ++it)
{
levels.push_back(it->toInt());
}
}
else //one level given
{
levels.push_back(level.toInt());
}
String tmp3("MS levels: ");
tmp3 = tmp3 + *(levels.begin());
for (vector<UInt>::iterator it = ++levels.begin(); it != levels.end(); ++it)
{
tmp3 = tmp3 + ", " + *it;
}
writeDebug_(tmp3, 1);
}
catch (Exception::ConversionError & /*e*/)
{
writeLog_(String("Invalid boundary '") + tmp + "' given. Aborting!");
printUsage_();
return ILLEGAL_PARAMETERS;
}
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MSExperiment<Peak1D> exp;
MzMLFile f;
f.setLogType(log_type_);
f.getOptions().setRTRange(DRange<1>(rt_l, rt_u));
f.load(in, exp);
DTAFile dta;
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
for (MSExperiment<Peak1D>::iterator it = exp.begin(); it != exp.end(); ++it)
{
//check for MS-level
bool in_level_range = false;
for (vector<UInt>::iterator it2 = levels.begin(); it2 != levels.end(); ++it2)
{
if (it->getMSLevel() == *it2)
{
in_level_range = true;
}
}
if (!in_level_range) continue;
//store spectra
if (it->getMSLevel() > 1)
{
double mz_value = 0.0;
if (!it->getPrecursors().empty()) mz_value = it->getPrecursors()[0].getMZ();
if (mz_value < mz_l || mz_value > mz_u)
{
continue;
}
dta.store(out + "_RT" + String(it->getRT()) + "_MZ" + String(mz_value) + ".dta", *it);
}
else
{
dta.store(out + "_RT" + String(it->getRT()) + ".dta", *it);
}
}
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPDTAExtractor tool;
return tool.main(argc, argv);
}
/// @endcond
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