From 863d97f18802f3796ab485fbb6f34b5f5bbb02aa Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sat, 29 Apr 2017 16:12:01 +0200
Subject: [PATCH] replacing X amino acid by nothing to compute mass and valid
tryptic peptide number
---
src/CMakeLists.txt | 8 ++++----
src/core/proteinmatch.cpp | 7 +++++++
src/core/proteinxtp.cpp | 19 ++++++++++++++++---
src/output/ods/proteinsheet.cpp | 11 ++++++++++-
src/output/ods/spectrasheet.cpp | 10 +++++-----
5 files changed, 42 insertions(+), 13 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c08b83a5..a16ae686 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -27,11 +27,11 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
-FIND_PACKAGE( Pappsomspp REQUIRED )
+#FIND_PACKAGE( Pappsomspp REQUIRED )
# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
-# SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
-# SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
+ SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+ SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake_modules)
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index f0c4cdd8..a03347af 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -23,6 +23,7 @@
#include "proteinmatch.h"
#include <pappsomspp/grouping/grpprotein.h>
+#include <pappsomspp/pappsoexception.h>
#include <set>
#include <cmath>
@@ -308,8 +309,14 @@ pappso::pappso_double ProteinMatch::getEvalue(const MsRun * sp_msrun_id) const {
}
pappso::pappso_double ProteinMatch::getPAI(const MsRun * sp_msrun_id) const {
+ try {
pappso::pappso_double PAI = (pappso::pappso_double) countPeptideMassCharge(ValidationState::validAndChecked ,sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->countTrypticPeptidesForPAI();
return PAI;
+
+ }
+ catch (pappso::PappsoException error) {
+ throw pappso::PappsoException(QObject::tr("Error computing PAI for protein %1 :\n%2").arg(this->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ }
}
pappso::pappso_double ProteinMatch::getEmPAI(const MsRun * sp_msrun_id) const {
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 0b593577..3f468ea4 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -23,6 +23,7 @@
#include "proteinxtp.h"
#include <pappsomspp/protein/enzyme.h>
+#include <pappsomspp/pappsoexception.h>
ProteinXtp::ProteinXtp():pappso::Protein()
{
@@ -74,8 +75,14 @@ QString ProteinXtp::getOnlyAminoAcidSequence() const {
}
pappso::pappso_double ProteinXtp::getMass() const {
- pappso::Peptide peptide(getOnlyAminoAcidSequence());
+ try {
+ pappso::Peptide peptide(getOnlyAminoAcidSequence().replace("X",""));
return peptide.getMass();
+
+ }
+ catch (pappso::PappsoException error) {
+ throw pappso::PappsoException(QObject::tr("Error computing mass for protein %1 :\n%2").arg(getAccession()).arg(error.qwhat()));
+ }
}
class DigestionHandler: public pappso::EnzymeProductInterface {
@@ -89,11 +96,12 @@ public:
unsigned int ProteinXtp::countTrypticPeptidesForPAI() const {
qDebug() << "ProteinXtp::countTrypticPeptidesForPAI begin";
+ try {
pappso::Enzyme kinase;
kinase.setMiscleavage(0);
DigestionHandler digestion;
- pappso::ProteinSp protein = std::make_shared<const pappso::Protein>(this->getDescription(),this->getOnlyAminoAcidSequence());
+ pappso::ProteinSp protein = std::make_shared<const pappso::Protein>(this->getDescription(),this->getOnlyAminoAcidSequence().replace("X",""));
kinase.eat(0,protein,false,digestion);
unsigned int count = 0;
@@ -105,6 +113,11 @@ unsigned int ProteinXtp::countTrypticPeptidesForPAI() const {
}
}
- return count;
qDebug() << "ProteinXtp::countTrypticPeptidesForPAI end";
+ return count;
+
+ }
+ catch (pappso::PappsoException error) {
+ throw pappso::PappsoException(QObject::tr("Error in countTrypticPeptidesForPAI for protein %1 :\n%2").arg(getAccession()).arg(error.qwhat()));
+ }
}
diff --git a/src/output/ods/proteinsheet.cpp b/src/output/ods/proteinsheet.cpp
index a16bbff3..150bc996 100644
--- a/src/output/ods/proteinsheet.cpp
+++ b/src/output/ods/proteinsheet.cpp
@@ -30,6 +30,7 @@
#include "proteinsheet.h"
#include "../../core/identificationgroup.h"
#include <pappsomspp/utils.h>
+#include <pappsomspp/pappsoexception.h>
ProteinSheet::ProteinSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
_p_writer = p_writer;
@@ -102,8 +103,10 @@ void ProteinSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinMatch * p_protein_match) {
+ try {
_p_writer->writeLine();
+ qDebug() << "ProteinSheet::writeOneProtein begin" ;
ValidationState validation_state = ValidationState::validAndChecked;
pappso::GrpProtein * p_grp_protein = p_protein_match->getGrpProteinSp().get();
@@ -140,6 +143,7 @@ void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinM
_p_writer->writeCell(p_protein_match->countPeptideMassCharge(validation_state));
+ qDebug() << "ProteinSheet::writeOneProtein tryptic" ;
_p_writer->writeCell(p_protein->countTrypticPeptidesForPAI());
// _p_writer->writeCell("PAI");
// _p_writer->writeCell(new Double((float) hashProt
@@ -160,5 +164,10 @@ void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinM
//number of MS sample
_p_writer->writeCell(p_protein_match->countDistinctMsSamples(validation_state));
-
+
+ qDebug() << "ProteinSheet::writeOneProtein end" ;
+ }
+ catch (pappso::PappsoException error) {
+ throw pappso::PappsoException(QObject::tr("Error writing protein %1 :\n%2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ }
}
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index feec26b6..90f179fe 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -35,7 +35,7 @@
SpectraSheet::SpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
_p_ods_export = p_ods_export;
_p_writer = p_writer;
- p_writer->writeSheet("peptides");
+ p_writer->writeSheet("spectra");
std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
for (IdentificationGroup * p_ident:identification_list) {
@@ -90,12 +90,12 @@ void SpectraSheet::writeBestPeptideMatch(const GroupingGroup * p_group,const Pep
_p_writer->writeCell(p_peptide_match->getGrpPeptideSp().get()->getGroupingId());
_p_writer->clearTableCellStyleRef();
_p_writer->writeCell(p_peptide_match->getMsRunP()->getSampleName());
- _p_writer->writeCell(QString("%1").arg(p_peptide_match->getScan()));
- _p_writer->writeCell(QString::number(p_peptide_match->getRetentionTime(), 'f', 2));
+ _p_writer->writeCell(p_peptide_match->getScan());
+ _p_writer->writeCell(p_peptide_match->getRetentionTime());
_p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getSequence());
_p_writer->writeCell(p_peptide_match->getPeptideXtpSp().get()->getModifString());
- _p_writer->writeCell(QString::number(p_peptide_match->getEvalue(), 'f', 2));
- _p_writer->writeCell(QString::number(p_peptide_match->getParam(PeptideMatchParam::tandem_hyperscore).toDouble(), 'f', 2));
+ _p_writer->writeCell(p_peptide_match->getEvalue());
+ _p_writer->writeCell(p_peptide_match->getParam(PeptideMatchParam::tandem_hyperscore).toDouble());
}
--
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