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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/>.
*
******************************************************************************/
// make test ARGS="-V -I 1,1"
// ./tests/catch2-only-tests [TimsXicExtractor] -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/timsmsrunreaderms2.h>
#include <pappsomspp/core/msrun/private/timsmsrunreader.h>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/processing/filters/filtersuitestring.h>
#include <pappsomspp/core/xicextractor/msrunxicextractorfactory.h>
#include <pappsomspp/core/processing/uimonitor/uimonitortextpercent.h>
#include <pappsomspp/core/vendors/tims/timsddaprecursors.h>
#include "tests/tests-config.h"
#include "../common.h"
#include <time.h>
using namespace pappso;
TEST_CASE("Extracting XIC from timsdata", "[TimsXicExtractor]")
{
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
#if USEPAPPSOTREE == 1
QString file_path_name;
/*
file_path_name =
"/gorgone/pappso/fichiers_fabricants/Bruker/tims_doc/tdf-sdk/"
"example_data/"
"200ngHeLaPASEF_2min_compressed.d/analysis.tdf";
*/
// 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 =
"/backup2/"
"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();
pappso::MsFileAccessor accessor(file_path_name, "a1");
accessor.setPreferredFileReaderType(Enums::MsDataFormat::brukerTims,
Enums::FileReaderType::tims_ms2);
WARN("get reader");
pappso::MsRunReaderSPtr p_msreader =
accessor.msRunReaderSPtr(accessor.getMsRunIds().front());
WARN("get reader OK");
REQUIRE(p_msreader != nullptr);
REQUIRE(accessor.getFileReaderType() == Enums::FileReaderType::tims_ms2);
pappso::TimsMsRunReaderMs2 *tims2_reader =
dynamic_cast<pappso::TimsMsRunReaderMs2 *>(p_msreader.get());
REQUIRE(tims2_reader != nullptr);
pappso::TimsDataSp tims_data = tims2_reader->getTimsDataSPtr();
std::vector<std::size_t> precursor_list = {2159};
std::vector<pappso_double> mz_list = {
466.738, 467.239, 420, 421, 422, 423, 424, 425, 426};
std::vector<pappso::XicCoordSPtr> xic_list;
std::vector<pappso::XicCoordSPtr> xic_struct_list;
clock_t start = clock();
for(auto precursor_id : precursor_list)
{
xic_list.push_back(
tims_data.get()
->getTimsDdaPrecursorsPtr()
->getXicCoordTimsFromPrecursorId(
precursor_id, PrecisionFactory::getPpmInstance(30.0))
.initializeAndClone());
}
for(pappso::pappso_double mz : mz_list)
{
pappso::XicCoordSPtr new_xic_struct =
xic_list[0].get()->initializeAndClone();
new_xic_struct.get()->mzRange =
pappso::MzRange(mz, PrecisionFactory::getPpmInstance(30.0));
xic_struct_list.push_back(new_xic_struct);
}
WARN("buildMsRunXicExtractorSp");
MsRunXicExtractorInterfaceSp xic_extractor =
MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(
p_msreader);
WARN("buildMsRunXicExtractorSp OK");
xic_extractor.get()->setXicExtractMethod(Enums::XicExtractMethod::sum);
QTextStream outputStream(stdout, QIODevice::WriteOnly);
UiMonitorTextPercent monitor(outputStream);
WARN("monitor.setStatus");
monitor.setStatus("Actually starting the XIC extraction.");
WARN("extractXicCoordSPtrList start");
xic_extractor.get()->extractXicCoordSPtrListParallelized(monitor,
xic_struct_list);
WARN("extractXicCoordSPtrList stop");
qInfo() << QString("Time taken: %1\n")
.arg((double)(clock() - start) / CLOCKS_PER_SEC);
for(auto &&xic_struct : xic_struct_list)
{
REQUIRE(xic_struct.get() != nullptr);
QFile fileods(QString("%1/tims_xic_%2.ods")
.arg(CMAKE_BINARY_DIR)
.arg(xic_struct.get()->mzRange.getMz()));
OdsDocWriter writer(&fileods);
writer.writeLine();
writer.writeCell("rtTarget");
writer.writeCell(xic_struct.get()->rtTarget);
writer.writeLine();
XicOdsWriter xic_writer(writer);
xic_writer.write(*xic_struct.get()->xicSptr.get());
writer.close();
fileods.close();
}
#elif USEPAPPSOTREE == 1
std::cout << std::endl << "..:: NO test TIMS TDF parsing ::.." << std::endl;
#endif
}
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