From 0d7a761a852f4b6462918ea3b87f72de7e437b2b Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 20 Apr 2017 11:07:28 +0200
Subject: [PATCH] make protein sequence resistant to unknown amino acid
---
src/core/proteinxtp.cpp | 16 ++++++++++++++--
src/core/proteinxtp.h | 10 ++++++++++
src/gui/protein_view/proteinwindow.cpp | 3 +--
src/input/xtandemsaxhandler.cpp | 3 ++-
4 files changed, 27 insertions(+), 5 deletions(-)
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index a010608a..0b593577 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -53,7 +53,7 @@ ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
void ProteinXtp::setCompleteDescription(const QString & full_description) {
setAccession (full_description.simplified().section(" ", 0,0));
setDescription (full_description.simplified().section(" ", 1));
-
+
}
void ProteinXtp::setIsContaminant(bool conta) {
_is_contaminant = conta;
@@ -68,6 +68,16 @@ bool ProteinXtp::isDecoy() const {
return _is_decoy;
}
+QString ProteinXtp::getOnlyAminoAcidSequence() const {
+ QString sequence(this->getSequence());
+ return sequence.replace(QRegExp("\\*"), "");
+}
+
+pappso::pappso_double ProteinXtp::getMass() const {
+ pappso::Peptide peptide(getOnlyAminoAcidSequence());
+ return peptide.getMass();
+}
+
class DigestionHandler: public pappso::EnzymeProductInterface {
public:
void setPeptide(std::int8_t sequence_database_id, const pappso::ProteinSp & protein_sp, bool is_decoy, const QString& peptide, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override {
@@ -82,7 +92,9 @@ unsigned int ProteinXtp::countTrypticPeptidesForPAI() const {
pappso::Enzyme kinase;
kinase.setMiscleavage(0);
DigestionHandler digestion;
- kinase.eat(0,this->makeProteinSp(),false,digestion);
+
+ pappso::ProteinSp protein = std::make_shared<const pappso::Protein>(this->getDescription(),this->getOnlyAminoAcidSequence());
+ kinase.eat(0,protein,false,digestion);
unsigned int count = 0;
for (const QString & peptide_str: digestion._peptide_list) {
diff --git a/src/core/proteinxtp.h b/src/core/proteinxtp.h
index b9831814..9356fdc6 100644
--- a/src/core/proteinxtp.h
+++ b/src/core/proteinxtp.h
@@ -22,6 +22,7 @@
******************************************************************************/
#include <pappsomspp/protein/protein.h>
+#include <pappsomspp/types.h>
#include "sequencedatabase.h"
#ifndef PROTEIN_XTP_H
@@ -51,6 +52,15 @@ public:
bool isContaminant() const;
bool isDecoy() const;
unsigned int countTrypticPeptidesForPAI() const;
+
+ /** @brief get only amino acid sequence
+ * clean sequence of other characters : * _ ...
+ */
+ QString getOnlyAminoAcidSequence() const;
+
+ /** @brief get protein mass in dalton
+ */
+ pappso::pappso_double getMass() const;
private:
SequenceDatabase * _p_sequence_database;
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 7f04c882..9b9a2baf 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -77,8 +77,7 @@ void ProteinWindow::updateDisplay() {
ui->description_label->setText(_p_protein_match->getProteinXtpSp().get()->getDescription());
ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
ui->coverage_label->setText(QString("%1 %").arg(_p_protein_match->getCoverage()*100));
- pappso::Peptide peptide(_p_protein_match->getProteinXtpSp().get()->getSequence());
- ui->mw_label->setText(QString("%1 kDa").arg(peptide.getMass()/1000));
+ ui->mw_label->setText(QString("%1 kDa").arg(_p_protein_match->getProteinXtpSp().get()->getMass()/1000));
ui->evalue_label->setText(QString("%1 (log10: %2)").arg(_p_protein_match->getEvalue()).arg(std::log10(_p_protein_match->getEvalue())));
}
catch (pappso::PappsoException exception_pappso) {
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 23b4862b..e1649cf2 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -195,7 +195,8 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
_current_text = _current_text.simplified().replace(" ", "");
if (!_current_text.isEmpty()) {
//._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
- _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text.replace(QRegExp("\\*"), ""));
+ //_p_protein_match->getProteinXtpSp().get()->setSequence(_current_text.replace(QRegExp("\\*"), ""));
+ _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text);
}
// <domain id="4017.1.1" start="21" end="31" expect="2.0e-06"
--
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