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//
// File: test_c13n15.cpp
// Created by: Olivier Langella
// Created on: 12/7/2023
//
/*******************************************************************************
* Copyright (c) 2023 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/catch2-only-benchmarks [proteincode] -s --benchmark-samples 5
#define CATCH_CONFIG_ENABLE_BENCHMARKING
#include <catch2/catch_test_macros.hpp>
#include <catch2/benchmark/catch_benchmark.hpp>
#include <QDebug>
#include <pappsomspp/core/exception/exceptionnotfound.h>
#include <pappsomspp/core/exception/exceptionoutofrange.h>
#include <pappsomspp/core/protein/protein.h>
#include <pappsomspp/core/protein/proteinintegercode.h>
#include <pappsomspp/core/massspectrum/qualifiedmassspectrum.h>
#include <pappsomspp/core/processing/filters/filterresample.h>
#include <pappsomspp/core/processing/filters/filterpass.h>
#include <pappsomspp/core/processing/filters/filterchargedeconvolution.h>
#include <pappsomspp/core/processing/filters/filterpeakdelta.h>
#include <pappsomspp/core/amino_acid/aastringcodemassmatching.h>
#include <pappsomspp/core/fasta/fastareader.h>
#include "../common.h"
#include "tests/tests-config.h"
#include "../proteincode/proteincode_lib.h"
TEST_CASE("proteincode test suite.", "[proteincode]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: scan spectrum on fasta file ::..", "[proteincodes]")
{
std::cout << std::endl
<< "..:: Test Fasta big file indexer ::.." << std::endl;
QFile file2(QString(CMAKE_SOURCE_DIR)
.append("/tests/data/fasta/Genome_Z_mays_5a.small.fasta"));
FastaProteinArrayHandler protein_handler;
pappso::FastaReader reader(protein_handler);
reader.parse(file2);
// compute spectrum code :
pappso::MassSpectrum spectrum = readMgf(
QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
pappso::FilterResampleKeepGreater(160).filter(spectrum);
pappso::FilterChargeDeconvolution(
pappso::PrecisionFactory::getDaltonInstance(0.02))
.filter(spectrum);
//.applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100);
pappso::FilterGreatestY(100).filter(spectrum);
pappso::FilterPeakDelta filter_peak_delta;
filter_peak_delta.filter(spectrum);
pappso::FilterGreatestY(200).filter(spectrum);
std::vector<double> mass_list = spectrum.xValues();
// ok spectrum code
pappso::AaCode aa_code;
aa_code.addAaModification('C',
pappso::AaModification::getInstance("MOD:00397"));
pappso::AaStringCodec aa_codec(aa_code);
pappso::ProteinSp max_protein;
double max_score = 0;
//
pappso::AaStringCodeMassMatching aaMatching(
aa_code, 7, pappso::PrecisionFactory::getDaltonInstance(0.01));
std::vector<uint32_t> code_list_from_spectrum =
aaMatching.getAaCodeFromMassList(mass_list);
std::vector<pappso::ProteinIntegerCode> arr_codedProtein;
REQUIRE(protein_handler.getProteinArray().size() == 3041);
BENCHMARK("fasta protein coder")
{
/* mode debug 2325604b33c648c7621fc637f4838e0654a9a2b3
* --benchmark-samples 5
* fasta protein coder 5 1 14.6394 s
2.92579 s 2.89503 s 2.97303 s
44.3713 ms 17.6264 ms 63.129 ms
*/
for(auto &protein : protein_handler.getProteinArray())
{
pappso::ProteinSp protein_sp = protein.makeProteinSp();
qDebug() << protein_sp.get()->getAccession();
// pappso::ProteinIntegerCode protein_code(protein_sp, aa_codec, 5);
arr_codedProtein.push_back({protein_sp, aa_codec, 5});
}
};
// std::vector<uint32_t> code_list = code_list_from_spectrum;
std::sort(code_list_from_spectrum.begin(), code_list_from_spectrum.end());
code_list_from_spectrum.erase(std::unique(code_list_from_spectrum.begin(),
code_list_from_spectrum.end()),
code_list_from_spectrum.end());
BENCHMARK("protein convolution")
{
for(auto &protein_code : arr_codedProtein)
{
/* mode debug cd443161fbbb3cd2f15c7f92cb94b6cef9cb0c0f
* --benchmark-samples 5
* protein convolution 5 1 1.28755 m
15.9592 s 15.6614 s 16.2533 s
356.477 ms 196.799 ms 477.38 ms
*/
auto vec_score = protein_code.convolution(code_list_from_spectrum);
double score = *std::max(vec_score.begin(), vec_score.end());
if(score > max_score)
{
max_score = score;
max_protein = protein_code.getProteinSp();
}
}
};
REQUIRE(max_protein.get()->getAccession().toStdString() ==
"GRMZM2G151344_P01"); //GRMZM2G083841_P01
}
}
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