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|
// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Fabian Kriegel, Frederic Lehnert $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
#include <OpenMS/SIMULATION/DigestSimulation.h>
///////////////////////////
#include <OpenMS/SIMULATION/LABELING/SILACLabeler.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
void createTestFeatureMapSimVector_(FeatureMapSimVector& feature_maps, bool add3rd)
{
feature_maps.clear();
FeatureMapSim fm1,fm2,fm3;
ProteinHit prothit1,prothit2,prothit3,prothit4,prothit5,prothit6,prothit7,prothit8,prothit9,prothit10, prothit11, prothit12;
// create first map
prothit1.setSequence("AAAAAAAKAAAAA"); // 2 Fragmente AAAAAAAK und AAAAA und kommt in allen Channels vor
prothit1.setMetaValue("description", "test sequence 1");
prothit1.setAccession("ACC1");
prothit1.setMetaValue("intensity", 200.0);
prothit2.setSequence("CNARCNCNCN"); // 2 Fragmente CNAR und CNCNCN und kommt in allen Channels vor
prothit2.setMetaValue("description", "test sequence 2");
prothit2.setAccession("ACC2");
prothit2.setMetaValue("intensity", 80.0);
prothit3.setSequence("CNHAADDAAAAA"); // ungelabelt, einzelnes Fragment
prothit3.setMetaValue("description", "test sequence 3");
prothit3.setAccession("ACC3");
prothit3.setMetaValue("intensity", 100.0);
prothit12.setSequence("VNAAAAAARVNCNCNAAAA"); // Ergebniss: CNAAAAAAR(Label Medium_R) , CNCNCNAAAA (einmal kommt in allen Channels vor)
prothit12.setMetaValue("description", "test sequence 12");
prothit12.setAccession("ACC5");
prothit12.setMetaValue("intensity", 115.0);
ProteinIdentification protIdent1;
protIdent1.insertHit(prothit1);
protIdent1.insertHit(prothit2);
protIdent1.insertHit(prothit3);
protIdent1.insertHit(prothit12);
vector<ProteinIdentification> protIdents_vec1;
protIdents_vec1.push_back(protIdent1);
fm1.setProteinIdentifications(protIdents_vec1);
// create labeled map
prothit4.setSequence("AAAAAAAKAAAAA"); // Ergbeniss: AAAAAAAK(Label Medium_K) , AAAAA ( einmal kommt in allen Channels vor)
prothit4.setMetaValue("description", "test sequence 4");
prothit4.setAccession("ACC4");
prothit4.setMetaValue("intensity", 50.0);
prothit5.setSequence("CNARCNCNCN"); // Ergebniss: CNAR(Label Medium_R) , CNCNCN (einmal kommt in allen Channels vor)
prothit5.setMetaValue("description", "test sequence 5");
prothit5.setAccession("ACC5");
prothit5.setMetaValue("intensity", 100.0);
prothit6.setSequence("LDRCEL"); // Ergbeniss : LDR(label Medium_R) , CEL (einmal kommt in channel 2 und 3 vor)
prothit6.setMetaValue("description", "test sequence 6");
prothit6.setAccession("ACC6");
prothit6.setMetaValue("intensity", 120.0);
prothit11.setSequence("VNAAAAAARVNCNCNAAAA"); // Ergebniss: CNAAAAAAR(Label Medium_R) , CNCNCNAAAA (einmal kommt in allen Channels vor)
prothit11.setMetaValue("description", "test sequence 11");
prothit11.setAccession("ACC5");
prothit11.setMetaValue("intensity", 110.0);
ProteinIdentification protIdent2;
protIdent2.insertHit(prothit4);
protIdent2.insertHit(prothit5);
protIdent2.insertHit(prothit6);
protIdent2.insertHit(prothit11);
vector<ProteinIdentification> protIdents_vec2;
protIdents_vec2.push_back(protIdent2);
fm2.setProteinIdentifications(protIdents_vec2);
feature_maps.push_back(fm1);
feature_maps.push_back(fm2);
if (add3rd)
{
prothit7.setSequence("AAAAAAAKAAAAA"); // Ergebniss : AAAAAAAK(Label Heavy_K) , AAAAA ( einmal kommt in allen Channels vor )
prothit7.setMetaValue("description", "test sequence 7");
prothit7.setAccession("ACC7");
prothit7.setMetaValue("intensity", 30.0);
prothit8.setSequence("CNARCNCNCN"); // Ergebniss: CNAR(Label Heavy_R) , CNCNCN (einmal kommt in allen Channels vor)
prothit8.setMetaValue("description", "test sequence 8");
prothit8.setAccession("ACC8");
prothit8.setMetaValue("intensity", 130.0);
prothit9.setSequence("LDRCEL"); //Ergebniss: LDR(label Heavy_R) , CEL (einmal kommt in channel 2 und 3 vor)
prothit9.setMetaValue("description", "test sequence 9");
prothit9.setAccession("ACC9");
prothit9.setMetaValue("intensity", 70.0);
prothit10.setSequence("YCYCY"); //Ergebniss: YCYCY kommt nur in diesem Channel vor
prothit10.setMetaValue("description", "test sequence 10");
prothit10.setAccession("ACC10");
prothit10.setMetaValue("intensity", 80.0);
ProteinIdentification protIdent3;
protIdent3.insertHit(prothit7);
protIdent3.insertHit(prothit8);
protIdent3.insertHit(prothit9);
protIdent3.insertHit(prothit10);
vector<ProteinIdentification> protIdents_vec3;
protIdents_vec3.push_back(protIdent3);
fm3.setProteinIdentifications(protIdents_vec3);
feature_maps.push_back(fm3);
}
}
void digestFeaturesMapSimVector_(FeatureMapSimVector& feature_maps)
{
// digest here
DigestSimulation digest_sim;
Param p;
p.setValue("model", "naive");
p.setValue("model_naive:missed_cleavages", 0);
digest_sim.setParameters(p);
std::cout << digest_sim.getParameters() << std::endl;
for(FeatureMapSimVector::iterator iter = feature_maps.begin() ; iter != feature_maps.end() ; ++iter)
{
digest_sim.digest((*iter));
}
}
START_TEST(SILACLabeler, "$Id: SILACLabeler_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
SILACLabeler* ptr = 0;
SILACLabeler* nullPtr = 0;
START_SECTION(SILACLabeler())
{
ptr = new SILACLabeler();
TEST_NOT_EQUAL(ptr, nullPtr)
}
END_SECTION
START_SECTION(~SILACLabeler())
{
delete ptr;
}
END_SECTION
START_SECTION((void preCheck(Param &) const))
{
SILACLabeler labeler;
Param p;
labeler.preCheck(p);
}
END_SECTION
START_SECTION((void setUpHook(FeatureMapSimVector & )))
{
SILACLabeler labeler;
FeatureMapSimVector feature_maps;
FeatureMapSim fm1,fm2,fm3,fm4;
feature_maps.push_back(fm1);
TEST_EXCEPTION_WITH_MESSAGE(Exception::IllegalArgument, labeler.setUpHook(feature_maps),"1 channel(s) given. We currently support only 2-channel SILAC. Please provide two FASTA files!")
feature_maps.push_back(fm2);
labeler.setUpHook(feature_maps);
feature_maps.push_back(fm3);
labeler.setUpHook(feature_maps);
feature_maps.push_back(fm4);
TEST_EXCEPTION_WITH_MESSAGE(Exception::IllegalArgument, labeler.setUpHook(feature_maps),"4 channel(s) given. We currently support only 2-channel SILAC. Please provide two FASTA files!")
}
END_SECTION
START_SECTION((void postDigestHook(FeatureMapSimVector & )))
{
FeatureMapSimVector feature_maps;
createTestFeatureMapSimVector_(feature_maps, false);
SILACLabeler labeler;
labeler.setUpHook(feature_maps);
digestFeaturesMapSimVector_(feature_maps);
// maps are digested by now
labeler.postDigestHook(feature_maps);
TEST_EQUAL(feature_maps.size(), 1)
ABORT_IF(feature_maps.size() != 1)
TEST_EQUAL(feature_maps[0].size(), 12)
ABORT_IF(feature_maps[0].size() != 12)
TEST_EQUAL(feature_maps[0][0].getIntensity(), 250)
TEST_EQUAL(feature_maps[0][0].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAA")
TEST_EQUAL(feature_maps[0][1].getIntensity(), 50)
TEST_EQUAL(feature_maps[0][1].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAAAAK(Label:2H(4))")
TEST_EQUAL(feature_maps[0][2].getIntensity(), 200)
TEST_EQUAL(feature_maps[0][2].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAAAAK")
TEST_EQUAL(feature_maps[0][3].getIntensity(), 120)
TEST_EQUAL(feature_maps[0][3].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CEL")
TEST_EQUAL(feature_maps[0][4].getIntensity(), 100)
TEST_EQUAL(feature_maps[0][4].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNAR(Label:13C(6))")
TEST_EQUAL(feature_maps[0][5].getIntensity(), 80)
TEST_EQUAL(feature_maps[0][5].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNAR")
TEST_EQUAL(feature_maps[0][6].getIntensity(), 180)
TEST_EQUAL(feature_maps[0][6].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNCNCN")
TEST_EQUAL(feature_maps[0][7].getIntensity(), 120)
TEST_EQUAL(feature_maps[0][7].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "LDR(Label:13C(6))")
TEST_EQUAL(feature_maps[0][8].getIntensity(), 110)
TEST_EQUAL(feature_maps[0][8].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "VNAAAAAAR(Label:13C(6))")
TEST_EQUAL(feature_maps[0][9].getIntensity(), 115)
TEST_EQUAL(feature_maps[0][9].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "VNAAAAAAR")
TEST_EQUAL(feature_maps[0][10].getIntensity(), 225)
TEST_EQUAL(feature_maps[0][10].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "VNCNCNAAAA")
TEST_EQUAL(feature_maps[0][11].getIntensity(), 100)
TEST_EQUAL(feature_maps[0][11].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNHAADDAAAAA")
createTestFeatureMapSimVector_(feature_maps, true);
SILACLabeler three_channel_labeler;
three_channel_labeler.setUpHook(feature_maps);
digestFeaturesMapSimVector_(feature_maps);
// maps are digested by now
three_channel_labeler.postDigestHook(feature_maps);
TEST_EQUAL(feature_maps.size(), 1)
ABORT_IF(feature_maps.size() != 1)
TEST_EQUAL(feature_maps[0].size(), 16)
ABORT_IF(feature_maps[0].size() != 16)
TEST_EQUAL(feature_maps[0][0].getIntensity(), 280)
TEST_EQUAL(feature_maps[0][0].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAA")
TEST_EQUAL(feature_maps[0][1].getIntensity(), 30)
TEST_EQUAL(feature_maps[0][1].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAAAAK(Label:13C(6)15N(2))")
TEST_EQUAL(feature_maps[0][2].getIntensity(), 50)
TEST_EQUAL(feature_maps[0][2].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAAAAK(Label:2H(4))")
TEST_EQUAL(feature_maps[0][3].getIntensity(), 200)
TEST_EQUAL(feature_maps[0][3].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAAAAK")
TEST_EQUAL(feature_maps[0][4].getIntensity(), 190)
TEST_EQUAL(feature_maps[0][4].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CEL")
TEST_EQUAL(feature_maps[0][5].getIntensity(), 130)
TEST_EQUAL(feature_maps[0][5].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNAR(Label:13C(6)15N(4))")
TEST_EQUAL(feature_maps[0][6].getIntensity(), 100)
TEST_EQUAL(feature_maps[0][6].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNAR(Label:13C(6))")
TEST_EQUAL(feature_maps[0][7].getIntensity(), 80)
TEST_EQUAL(feature_maps[0][7].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNAR")
TEST_EQUAL(feature_maps[0][8].getIntensity(), 310)
TEST_EQUAL(feature_maps[0][8].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNCNCN")
TEST_EQUAL(feature_maps[0][9].getIntensity(), 70)
TEST_EQUAL(feature_maps[0][9].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "LDR(Label:13C(6)15N(4))")
TEST_EQUAL(feature_maps[0][10].getIntensity(), 120)
TEST_EQUAL(feature_maps[0][10].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "LDR(Label:13C(6))")
TEST_EQUAL(feature_maps[0][11].getIntensity(), 80)
TEST_EQUAL(feature_maps[0][11].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "YCYCY")
TEST_EQUAL(feature_maps[0][12].getIntensity(), 110)
TEST_EQUAL(feature_maps[0][12].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "VNAAAAAAR(Label:13C(6))")
TEST_EQUAL(feature_maps[0][13].getIntensity(), 115)
TEST_EQUAL(feature_maps[0][13].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "VNAAAAAAR")
TEST_EQUAL(feature_maps[0][14].getIntensity(), 225)
TEST_EQUAL(feature_maps[0][14].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "VNCNCNAAAA")
TEST_EQUAL(feature_maps[0][15].getIntensity(), 100)
TEST_EQUAL(feature_maps[0][15].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "CNHAADDAAAAA")
}
END_SECTION
START_SECTION((void postRawMSHook(FeatureMapSimVector &)))
{
// TODO
}
END_SECTION
START_SECTION((void postRTHook(FeatureMapSimVector &)))
{
// we do not modify the map in this step
NOT_TESTABLE
}
END_SECTION
START_SECTION((void postDetectabilityHook(FeatureMapSimVector &)))
{
// we do not modify the map in this step
NOT_TESTABLE
}
END_SECTION
START_SECTION((void postIonizationHook(FeatureMapSimVector &)))
{
// we do not modify the map in this step
NOT_TESTABLE
}
END_SECTION
START_SECTION((void postRawTandemMSHook(FeatureMapSimVector &, MSSimExperiment &)))
{
// we do not modify the map in this step
NOT_TESTABLE
}
END_SECTION
START_SECTION((static BaseLabeler* create()))
{
BaseLabeler* labeler = SILACLabeler::create();
BaseLabeler* nullPointer = 0;
TEST_NOT_EQUAL(labeler, nullPointer)
delete labeler;
}
END_SECTION
START_SECTION((static const String getProductName()))
{
TEST_EQUAL(SILACLabeler::getProductName(), "SILAC")
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
