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// File: test_timsxicextractor.cpp
// Created by: Olivier Langella
// Created on: 3/2/2021
//
/*******************************************************************************
* Copyright (c) 2021 Olivier Langella
*<olivier.langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
// Run using this command line:
// tests/catch2-only-tests "Creating mass spectrum via TIMS XIC extraction from
// timsdata" -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/benchmark/catch_benchmark.hpp>
#include <QDebug>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/msrun/private/timsmsrunreader.h>
#include <pappsomspp/core/msrun/private/timsmsrunreaderms2.h>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/processing/filters/filtersuitestring.h>
#include <pappsomspp/core/xicextractor/msrunxicextractorfactory.h>
#include <pappsomspp/core/processing/uimonitor/uimonitortext.h>
#include <pappsomspp/core/vendors/tims/timsddaprecursors.h>
#include "tests/tests-config.h"
#include "../common.h"
#include <time.h>
using namespace pappso;
TEST_CASE("Creating mass spectrum via TIMS XIC extraction from timsdata",
"[massSpecTimsXicExtractor]")
{
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
#if USE_PAPPSO_TREE == 1
QString file_path_name;
// file_path_name =
//"/home/rusconi/devel/dataForMzml/bruker/20210126_HeLa.d/"
//"1-26-2021_1_QC_HeLa10ng_826.d/analysis.tdf";
file_path_name =
"/gorgone/pappso/jouy/raw/2021_Tims_TOF/20211124_HeLa/"
"11-25-2021_1_HeLa200ng_2321.d/analysis.tdf";
// file_path_name =
//"/home/rusconi/devel/dataForMzml/bruker/2021_Tims_TOF/20211124_HeLa/"
//"11-25-2021_1_HeLa200ng_2321.d/analysis.tdf";
qDebug() << "The file to use as a test base is: " << file_path_name;
// When not in debug mode.
std::cout << __FILE__ << ":" << __LINE__
<< " The file to use as a test base is: "
<< file_path_name.toStdString() << std::endl;
pappso::MsFileAccessor accessor(file_path_name, "a1");
qDebug() << "Setting the preferred file reader type to tims2.";
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
pappso::MsRunReaderSPtr p_msreader =
accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
REQUIRE(p_msreader != nullptr);
REQUIRE(accessor.getFileReaderType() == Enums::FileReaderType::tims_ms2);
pappso::TimsMsRunReaderMs2 *tims_reader =
dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_msreader.get());
REQUIRE(tims_reader != nullptr);
pappso::TimsDataSp tims_data = tims_reader->getTimsDataSPtr();
// std::vector<std::size_t> precursor_list = {132929};
std::vector<std::size_t> precursor_list = {31693};
// Now craft the mz list. We have an acquisition m/z range from 100 to 1700.
std::vector<pappso_double> mz_list;
// Seed the lower m/z value of the m/z range and push it back to the mz_list.
double mz = 100;
mz_list.push_back(mz);
// We'll need a precision.
PrecisionPtr precision_p = PrecisionFactory::getPpmInstance(30);
// Compute the last mz value accounting for the delta (we do not want to
// over-trip the 1700 hard limit.
double last_mz = 1700;
last_mz -= 2 * precision_p->delta(last_mz);
while(mz < last_mz)
{
mz += 2 * precision_p->delta(mz);
mz_list.push_back(mz);
}
qDebug() << "The mz_list now has " << mz_list.size() << " m/z values.";
std::cout << "The mz_list now has " << mz_list.size() << " m/z values.";
std::vector<pappso::XicCoordSPtr> xic_list;
std::vector<pappso::XicCoordSPtr> xic_coord_list;
clock_t start = clock();
for(auto precursor_id : precursor_list)
{
XicCoordSPtr xic_coord_tims_struct_sp =
tims_data.get()
->getTimsDdaPrecursorsPtr()
->getXicCoordTimsFromPrecursorId(precursor_id,
PrecisionFactory::getPpmInstance(30))
.initializeAndClone();
xic_list.push_back(xic_coord_tims_struct_sp);
}
for(pappso::pappso_double mz : mz_list)
{
pappso::XicCoordSPtr new_xic_coord =
xic_list[0].get()->initializeAndClone();
new_xic_coord.get()->mzRange =
pappso::MzRange(mz, PrecisionFactory::getPpmInstance(30.0));
xic_coord_list.push_back(new_xic_coord);
}
MsRunXicExtractorInterfaceSp xic_extractor =
MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(
p_msreader);
xic_extractor.get()->setXicExtractMethod(Enums::XicExtractMethod::sum);
QTextStream outputStream(stdout, QIODevice::WriteOnly);
UiMonitorText monitor(outputStream);
INFO("monitor.setStatus");
monitor.setStatus("Now starting the actual XIC extraction");
INFO("extractXicCoordSPtrList start");
// DO THE EXTRACTION!!
xic_extractor.get()->extractXicCoordSPtrList(monitor, xic_coord_list);
INFO("extractXicCoordSPtrList stop");
qInfo() << QString("Time taken: %1\n")
.arg((double)(clock() - start) / CLOCKS_PER_SEC);
// At this point we have tens of thousands of XICs performed each time over
// the whole set of frames of the acquisition.
// A XIC is a total ion current chromatogram for a given m/z value over the
// whole rt range. The XIC is a Trace, with x:rt y:int. And there is such a
// Trace for each m/z value in the mz_list above.
// If we want a full mass spectral integration over the whole acquisiion, all
// we need to do is iterate in the xic_coord_list, get the m/z value for each
// item in this list and sum all the y values of the XIC Trace.
Trace full_mass_spectrum_trace;
for(auto xic_coord : xic_coord_list)
{
double mz = xic_coord->mzRange.getMz();
double sum_y = xic_coord.get()->xicSptr.get()->sumY();
full_mass_spectrum_trace.push_back(DataPoint(mz, sum_y));
}
std::cout << "The full mass spectrum for the acquisition:\n"
<< full_mass_spectrum_trace.toString().toStdString();
#elif USE_PAPPSO_TREE == 1
std::cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl;
#endif
}
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