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/*******************************************************************************
* Copyright (c) 2024 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/>.
*
******************************************************************************/
// ./tests/proteincode/catch2-only-proteincode [specglob] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <QString>
#include <pappsomspp/core/massspectrum/massspectrum.h>
#include <pappsomspp/core/processing/filters/filterresample.h>
#include <pappsomspp/core/processing/filters/filterpass.h>
#include <pappsomspp/core/processing/specglob/spectralalignment.h>
#include <pappsomspp/core/processing/filters/filterchargedeconvolution.h>
#include <pappsomspp/core/utils.h>
#include "proteincode_lib.h"
#include "../common.h"
#include "tests/tests-config.h"
TEST_CASE("trim peptide on localized protein region.", "[specglob]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION(
"..:: scan_15780 spectrum easy met on fasta file AIADGSIIDIIR "
"::..",
"[specglob]")
{
pappso::PeptideSp sampler(std::make_shared<pappso::Peptide>("AIADGSIIDIIR"));
pappso::specglob::PeptideSpectraCsp peptide_spectra =
std::make_shared<pappso::specglob::PeptideSpectrum>(sampler);
pappso::QualifiedMassSpectrum spectrum_simple = readQualifiedMassSpectrumMgf(
QString(CMAKE_SOURCE_DIR)
.append("/tests/data/scans/20120906_balliau_extract_1_A01_urnb-1_15780.mgf"));
PrecisionPtr precision_ptr = pappso::PrecisionFactory::getDaltonInstance(0.02);
pappso::FilterChargeDeconvolution(precision_ptr)
.filter(*(spectrum_simple.getMassSpectrumSPtr().get()));
pappso::FilterResampleKeepGreater(150).filter(*(spectrum_simple.getMassSpectrumSPtr().get()));
pappso::FilterGreatestY(120).filter(*(spectrum_simple.getMassSpectrumSPtr().get()));
pappso::specglob::ExperimentalSpectrumCsp experimental_spectrum =
std::make_shared<pappso::specglob::ExperimentalSpectrum>(spectrum_simple, precision_ptr);
pappso::specglob::SpectralAlignment spectral_alignment(pappso::specglob::ScoreValues(),
precision_ptr);
spectral_alignment.align(peptide_spectra, experimental_spectrum);
REQUIRE(spectral_alignment.getMaxScore() == 24);
// INFOS:
// ;AIADGSSAMLLDLLR++++-289,11;7;11;[A][I][A][D][G][S][S][A][M][-289,11]LLDLLR_[-0,00];[A]IADGSSAM[-289,11]LLDLLR;1;0,00;27;0.3224648627994288
REQUIRE(spectral_alignment.backTrack().toStdString() ==
"[A][I]ADGSIID[I][I][R]_[-0.00452147]");
pappso::specglob::PeptideModel peptide_model = spectral_alignment.buildPeptideModel();
REQUIRE(peptide_model.toProForma().toStdString() ==
"[-0.0045]?AIADGSIIDIIR");
peptide_model.eliminateComplementaryDelta(precision_ptr);
REQUIRE(peptide_model.toProForma().toStdString() == "[-0.0045]?AIADGSIIDIIR");
peptide_model.matchExperimentalPeaks(precision_ptr);
REQUIRE(peptide_model.getCountSharedPeaks() == 11);
}
SECTION(
"..:: scan_3302 spectrum easy met on fasta file GKQQVM[MOD:00719]VGYSDSGK "
"::..",
"[specglob]")
{
pappso::PeptideSp sampler(std::make_shared<pappso::Peptide>("GKQQVMVGYSDSGK"));
pappso::specglob::PeptideSpectraCsp peptide_spectra =
std::make_shared<pappso::specglob::PeptideSpectrum>(sampler);
pappso::QualifiedMassSpectrum spectrum_simple = readQualifiedMassSpectrumMgf(
QString(CMAKE_SOURCE_DIR)
.append("/tests/data/scans/"
"20120906_balliau_extract_1_A08_teal-2_scan_3302.mgf"));
pappso::FilterGreatestY(80).filter(*(spectrum_simple.getMassSpectrumSPtr().get()));
PrecisionPtr precision_ptr = pappso::PrecisionFactory::getDaltonInstance(0.02);
pappso::specglob::ExperimentalSpectrumCsp experimental_spectrum =
std::make_shared<pappso::specglob::ExperimentalSpectrum>(spectrum_simple, precision_ptr);
pappso::specglob::SpectralAlignment spectral_alignment(pappso::specglob::ScoreValues(),
precision_ptr);
spectral_alignment.align(peptide_spectra, experimental_spectrum);
// INFOS:
// ;AIADGSSAMLLDLLR++++-289,11;7;11;[A][I][A][D][G][S][S][A][M][-289,11]LLDLLR_[-0,00];[A]IADGSSAM[-289,11]LLDLLR;1;0,00;27;0.3224648627994288
REQUIRE(spectral_alignment.backTrack().toStdString() ==
"[128.095]G[K][-128.095]QQV[M][15.9994]VGYSDSGK_[-0.0038543]");
REQUIRE(spectral_alignment.getMaxScore() == 52);
pappso::specglob::PeptideModel peptide_model = spectral_alignment.buildPeptideModel();
REQUIRE(peptide_model.toProForma().toStdString() ==
"[-0.0039]?G[+128.0946]K[-128.0953]QQVM[+15.9994]VGYSDSGK");
peptide_model.eliminateComplementaryDelta(precision_ptr);
REQUIRE(peptide_model.toProForma().toStdString() == "[-0.0045]?GKQQVM[+15.9994]VGYSDSGK");
peptide_model.matchExperimentalPeaks(precision_ptr);
REQUIRE(peptide_model.getCountSharedPeaks() == 14);
writeSpectralAlignmentMatrix("alignment_matrix_3302_good_seq.ods", spectral_alignment);
}
SECTION(
"..:: trim peptide GKQQVM[MOD:00719]VGYSDSGK "
"::..",
"[specglob]")
{
pappso::QualifiedMassSpectrum spectrum_simple = readQualifiedMassSpectrumMgf(
QString(CMAKE_SOURCE_DIR)
.append("/tests/data/scans/"
"20120906_balliau_extract_1_A08_teal-2_scan_3302.mgf"));
pappso::FilterGreatestY(80).filter(*(spectrum_simple.getMassSpectrumSPtr().get()));
PrecisionPtr precision_ptr = pappso::PrecisionFactory::getDaltonInstance(0.02);
pappso::specglob::ExperimentalSpectrumCsp experimental_spectrum =
std::make_shared<pappso::specglob::ExperimentalSpectrum>(spectrum_simple, precision_ptr);
pappso::specglob::SpectralAlignment spectral_alignment(pappso::specglob::ScoreValues(),
precision_ptr);
pappso::PeptideSp sampler(
std::make_shared<pappso::Peptide>("FSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEM"));
pappso::specglob::PeptideSpectraCsp peptide_spectra =
std::make_shared<pappso::specglob::PeptideSpectrum>(sampler);
spectral_alignment.align(peptide_spectra, experimental_spectrum);
REQUIRE(spectral_alignment.getMaxScore() == 0);
// INFOS:
// ;AIADGSSAMLLDLLR++++-289,11;7;11;[A][I][A][D][G][S][S][A][M][-289,11]LLDLLR_[-0,00];[A]IADGSSAM[-289,11]LLDLLR;1;0,00;27;0.3224648627994288
// REQUIRE(spectral_alignment.backTrack().toStdString() ==
// "[128.095]G[K][-128.095]QQV[M][15.9994]VGYSDSGK_[-0.0038543]");
REQUIRE_THROWS_AS(spectral_alignment.buildPeptideModel(), pappso::PappsoException);
// REQUIRE(peptide_model.toProForma().toStdString() ==
// "G[+128.0946]K[-128.0953]QQVM[+15.9994]VGYSDSGK");
writeSpectralAlignmentMatrix("alignment_matrix_3302.ods", spectral_alignment);
spectral_alignment.align(peptide_spectra, experimental_spectrum);
REQUIRE(spectral_alignment.getMaxScore() == 0);
pappso::specglob::PeptideModel peptide_model = spectral_alignment.rtrim(precision_ptr);
REQUIRE(spectral_alignment.getMaxScore() == 59);
REQUIRE(spectral_alignment.backTrack().toStdString() ==
"KG[K][-128.095]QQV[M][15.9994]VGYSDSGK_[-0.0041749]");
// GKQQVM[MOD:00719]VGYSDSGK
REQUIRE(peptide_model.toProForma().toStdString() == "[-0.0045]?GKQQVM[+15.9994]VGYSDSGK");
peptide_model.matchExperimentalPeaks(precision_ptr);
peptide_model.removeBracketsForAlignedAA();
REQUIRE(peptide_model.toProForma().toStdString() == "[-0.0045]?GKQQVM[+15.9994]VGYSDSGK");
peptide_model.matchExperimentalPeaks(precision_ptr);
REQUIRE(peptide_model.getCountSharedPeaks() == 14);
REQUIRE(peptide_model.getMass() ==
Catch::Approx(experimental_spectrum.get()->getPrecursorMass()).margin(0.01));
pappso::Aa metox(Enums::AminoAcidChar::methionine);
metox.addAaModification(pappso::AaModification::getInstance("MOD:00719"));
peptide_model.checkForAaModification(metox, precision_ptr);
REQUIRE(peptide_model.toProForma().toStdString() == "GKQQVM[MOD:00719]VGYSDSGK");
REQUIRE(peptide_model.getMass() ==
Catch::Approx(experimental_spectrum.get()->getPrecursorMass()).margin(0.01));
}
}
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