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//
// File: test_aa.cpp
// Created by: Olivier Langella
// Created on: 7/3/2015
//
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.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/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
// make test ARGS="-V -I 1,1"
// ./tests/catch2-only-tests [Aa] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
#include <QDebug>
#include <QString>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/amino_acid/aa.h>
#include <iostream>
#include <pappsomspp/core/obo/obopsimod.h>
#include <pappsomspp/core/obo/filterobopsimodtermlabel.h>
#include <pappsomspp/core/obo/filterobopsimodsink.h>
#include <pappsomspp/core/obo/filterobopsimodtermdiffmono.h>
#include <pappsomspp/core/exception/exceptionnotfound.h>
#include <pappsomspp/core/exception/exceptionoutofrange.h>
#include <pappsomspp/core/obo/filterobopsimodmap.h>
#include <pappsomspp/core/obo/obounimod.h>
#include <pappsomspp/core/obo/obopsimod.h>
#include <pappsomspp/core/exception/exceptionnotpossible.h>
using namespace pappso;
using namespace std;
TEST_CASE("Amino Acid test suite.", "[Aa]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: test Formula ::..", "[Aa]")
{
pappso::FilterOboPsiModMap obo_unimod_map;
pappso::OboUnimod unimod_parser(obo_unimod_map);
pappso::FilterOboPsiModMap obo_psimod_map;
pappso::OboPsiMod psimod_parser(obo_psimod_map);
pappso::OboPsiModTerm pterm = obo_psimod_map.getOboPsiModTermWithAccession("MOD:00394");
pappso::ChemicalFormula formula;
formula.setOboPsiModTerm(pterm);
REQUIRE(formula.getMass() == Catch::Approx(42.010564684));
pterm = obo_psimod_map.getOboPsiModTermWithAccession("MOD:00022");
REQUIRE(pterm.getAccession() == "MOD:00022");
formula.setOboPsiModTerm(pterm);
REQUIRE(pterm.m_formula.toStdString() == "C 5 H 9 N 1 O 1 S 1");
REQUIRE(formula.getMass() == Catch::Approx(131.0404850886));
REQUIRE(formula.getMass() == Catch::Approx(pterm.m_massMono));
pappso::AaModificationP mod = AaModification::getInstanceInsertionAccessionByAaLetter('M');
REQUIRE(mod->getMass() == Catch::Approx(131.0404850886));
pterm = obo_psimod_map.getOboPsiModTermWithAccession("MOD:00582");
formula.setOboPsiModTerm(pterm);
REQUIRE(pterm.m_diffFormula.toStdString() == "(12)C -6 (13)C 6 (14)N -2 (15)N 2");
REQUIRE(formula.getMass() == Catch::Approx(8.0141988136));
// UNIMOD:259 == MOD:00582
pterm = obo_unimod_map.getOboPsiModTermWithAccession("UNIMOD:259");
REQUIRE(pterm.isUnimod());
formula.setOboPsiModTerm(pterm);
REQUIRE(pterm.m_diffFormula.toStdString() == "C(-6) 13C(6) N(-2) 15N(2)");
REQUIRE(formula.getMass() == Catch::Approx(8.0141988136));
// UNIMOD:21
pterm = obo_unimod_map.getOboPsiModTermWithAccession("UNIMOD:21");
REQUIRE(pterm.isUnimod());
formula.setOboPsiModTerm(pterm);
REQUIRE(pterm.m_diffFormula.toStdString() == "H O(3) P");
REQUIRE(formula.getMass() == Catch::Approx(79.9663308889));
pterm = obo_unimod_map.getOboPsiModTermWithName("Acetyl");
REQUIRE(pterm.isUnimod());
formula.setOboPsiModTerm(pterm);
REQUIRE(pterm.m_diffFormula.toStdString() == "H(2) C(2) O");
REQUIRE(formula.getMass() == Catch::Approx(42.010564684));
pappso::AaModificationP modp = AaModification::getInstance("Acetyl");
REQUIRE(modp->getAccession().toStdString() == "UNIMOD:1");
modp = AaModification::getInstance("Phospho");
REQUIRE(modp->getAccession().toStdString() == "UNIMOD:21");
REQUIRE(formula.getMass() == Catch::Approx(pterm.m_diffMono));
// iTRAQ4plex
pterm = obo_unimod_map.getOboPsiModTermWithName("iTRAQ4plex");
REQUIRE(pterm.isUnimod());
formula.setOboPsiModTerm(pterm);
REQUIRE(pterm.m_diffFormula.toStdString() == "H(12) C(4) 13C(3) N 15N O");
REQUIRE(formula.getMass() == Catch::Approx(144.1020624229));
REQUIRE(formula.getMass() == Catch::Approx(pterm.m_diffMono));
}
SECTION("..:: test PSI-MOD removal ::..", "[Aa]")
{
//%S << std::endl << "..:: AA init ::.." << std::endl;
// OboPsiMod test;
Aa leucine('L');
REQUIRE(leucine.getMass() == Catch::Approx(113.084063979));
leucine.addAaModification(AaModification::getInstanceRemovalAccessionByAaLetter('L'));
REQUIRE(leucine.getMass() == Catch::Approx(0.0));
leucine.addAaModification(AaModification::getInstanceInsertionAccessionByAaLetter('M'));
REQUIRE(leucine.getMass() == Catch::Approx(131.0404850886));
REQUIRE(leucine.toProForma().toStdString() == "L[MOD:00022][MOD:01641]");
REQUIRE(leucine.getTotalModificationMass() == Catch::Approx(17.9564211096));
leucine.removeAllButInternalModification();
REQUIRE(leucine.toProForma().toStdString() == "L");
}
SECTION("..:: AA init ::..", "[Aa]")
{
//%S << std::endl << "..:: AA init ::.." << std::endl;
// OboPsiMod test;
Aa leucine('L');
MzRange mz_range(leucine.getMass(), PrecisionFactory::getPpmInstance(1));
std::cout << "leucine: " << QString::number(leucine.getMass(), 'g', 10).toStdString()
<< std::endl;
std::cout << "leucine number of N15 : " << leucine.getNumberOfIsotope(Enums::Isotope::N15)
<< std::endl;
std::cout << mz_range.toString().toStdString() << std::endl;
/*
if(!mz_range.contains(pappso_double(131.094635) - MASSH2O))
{
std::cerr << QString::number(leucine.getMass(), 'g', 10).toStdString()
<< " != 131.094635 - H2O";
return 1;
}
*/
REQUIRE(mz_range.contains(pappso_double(131.094635) - MASSH2O));
Aa alanine('A');
/*
if(!MzRange(alanine.getMass(), PrecisionFactory::getPpmInstance(1))
.contains(pappso_double(89.047676 - MASSH2O)))
{
std::cerr << QString::number(alanine.getMass(), 'g', 10).toStdString()
<< " != " << (89.047676 - MASSH2O);
return 1;
}
*/
REQUIRE(MzRange(alanine.getMass(), PrecisionFactory::getPpmInstance(1))
.contains(pappso_double(89.047676 - MASSH2O)));
alanine.addAaModification(AaModification::getInstanceCustomizedMod(18.022316354654));
// SUCCESS
// qDebug() << alanine.getModificationList();
alanine.addAaModification(AaModification::getInstance("MOD:00397"));
// alanine.addAaModification(AaModification::getInstance("fdgMOD:00397"));
FilterOboPsiModSink term_list;
FilterOboPsiModTermLabel filter_label(term_list, QString("Carba*"));
OboPsiMod psimod(filter_label);
std::cout << "term_list.size= " << term_list.size() << std::endl;
REQUIRE(term_list.size() == 12);
MzRange range(pappso_double(57.02), PrecisionFactory::getDaltonInstance(pappso_double(0.02)));
std::cout << range.getMz() << std::endl;
std::cout << "choses "
<< MzRange(pappso_double(57.02),
PrecisionFactory::getDaltonInstance(pappso_double(0.02)))
.toString()
.toStdString()
<< std::endl;
FilterOboPsiModSink term_listb;
FilterOboPsiModTermDiffMono filter_labelb(
term_listb,
MzRange(pappso_double(57.02), PrecisionFactory::getDaltonInstance(pappso_double(0.02))));
OboPsiMod psimodb(filter_labelb);
for(auto term : term_listb.getOboPsiModTermList())
{
//%S << term._accession.toStdString() << " " << mz(term._diff_mono)
// << std::endl;
}
std::cout << "term_listb.size= " << term_listb.size() << std::endl;
REQUIRE(term_listb.size() == 8);
Aa alaninebis('A');
REQUIRE(alaninebis.getNumberOfAtom(Enums::AtomIsotopeSurvey::C) == 3);
REQUIRE(alaninebis.getNumberOfAtom(Enums::AtomIsotopeSurvey::H) == 5);
// xref: DiffFormula: "C 2 H 3 N 1 O 1"
alaninebis.addAaModification(AaModification::getInstance("MOD:00397"));
REQUIRE(alaninebis.getNumberOfAtom(Enums::AtomIsotopeSurvey::C) == 5);
REQUIRE(alaninebis.getNumberOfAtom(Enums::AtomIsotopeSurvey::H) == 8);
REQUIRE(alaninebis.toAbsoluteString().toStdString() == "A(MOD:00397)");
alaninebis.addAaModification(AaModification::getInstanceCustomizedMod(18.022316354654));
// SUCCESS
REQUIRE_FALSE(alanine < alaninebis);
REQUIRE_FALSE(alaninebis < alanine);
REQUIRE(alanine == alaninebis);
Aa alanineter('A');
qDebug() << "TEST";
alanineter.addAaModification(AaModification::getInstance("MOD:00397"));
REQUIRE_FALSE(alanine == alanineter);
REQUIRE_FALSE(alanine < alanineter);
}
SECTION("..:: Test Modifications ::..")
{
AaModificationP mod = AaModification::getInstance("MOD:00397");
std::cout << " MOD:00397 mass=" << QString::number(mod->getMass(), 'g', 15).toStdString()
<< std::endl;
// 57.021464
// MOD:00429
mod = AaModification::getInstance("MOD:00429");
std::cout << " MOD:00429 mass=" << QString::number(mod->getMass(), 'g', 15).toStdString()
<< std::endl;
// 28.0313
// MOD:00382
mod = AaModification::getInstance("MOD:00382");
std::cout << " MOD:00382 mass=" << QString::number(mod->getMass(), 'g', 15).toStdString()
<< std::endl;
//-20.026215
REQUIRE(mod->getMass() == Catch::Approx(-20.026215));
// MOD:00234
mod = AaModification::getInstance("MOD:00234");
std::cout << " MOD:00234 mass=" << QString::number(mod->getMass(), 'g', 15).toStdString()
<< std::endl;
// 305.068156
// MOD:00838
mod = AaModification::getInstance("MOD:00838");
std::cout << " MOD:00838 mass=" << QString::number(mod->getMass(), 'g', 15).toStdString()
<< std::endl;
for(auto amino_acid : pappso::Aa::getAminoAcidCharList())
{
pappso::Aa aa_enumi(amino_acid);
std::cout << " " << (char)amino_acid << " "
<< QString::number(aa_enumi.getMass(), 'g', 15).toStdString() << std::endl;
}
/*
* A 71.037113785565
5: R 156.101111025652
5: C 103.009184785565
5: D 115.026943024685
5: E 129.042593089167
5: F 147.068413914529
5: G 57.021463721083
5: H 137.058911859647
5: I 113.084063979011
5: K 128.094963016052
5: L 113.084063979011
5: M 131.040484914529
5: N 114.042927442166
5: P 97.052763850047
5: Q 128.058577506648
5: R 156.101111025652
5: S 87.032028405125
5: T 101.047678469607
5: V 99.068413914529
5: W 186.07931295157
5: Y 163.063328534089
5: U 168.964198469607
5: O 255.158291550141
*/
REQUIRE(pappso::Aa('A').getMass() == Catch::Approx(71.0371137856));
REQUIRE(pappso::Aa('R').getMass() == Catch::Approx(156.101111025652));
REQUIRE(pappso::Aa('C').getMass() == Catch::Approx(103.0091849597));
REQUIRE(pappso::Aa('D').getMass() == Catch::Approx(115.026943024685));
// AaModification::getInstance("MOD:00397_wrong");
REQUIRE_THROWS_AS(AaModification::getInstance("MOD:00397_wrong"), pappso::ExceptionNotFound);
}
/*
return 0;
*/
}
|
