From 02099c63144217844325beb099ebc9ed84590526 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 10 Mar 2017 16:47:27 +0100
Subject: [PATCH] parsing xpip WIP
---
src/CMakeLists.txt | 3 +-
src/input/xpipsaxhandler.cpp | 125 ++++++++++++++++++++++++++++++++---
src/input/xpipsaxhandler.h | 28 +++++---
src/utils/peptidestore.cpp | 52 +++++++++++++++
src/utils/peptidestore.h | 50 ++++++++++++++
5 files changed, 237 insertions(+), 21 deletions(-)
create mode 100644 src/utils/peptidestore.cpp
create mode 100644 src/utils/peptidestore.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 1db1f3d7..63f81e5d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -53,13 +53,14 @@ configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/c
# File list
SET(CPP_FILES
- utils/readspectrum.cpp
core/project.cpp
core/match.cpp
core/identification_sources/identificationdatasource.cpp
core/identification_sources/identificationxtandemfile.cpp
files/xpipfile.cpp
input/xpipsaxhandler.cpp
+ utils/peptidestore.cpp
+ utils/readspectrum.cpp
)
set(QTLIBS ${Qt5Xml_LIBRARIES} ${Qt5Gui_LIBRARIES} ${Qt5Svg_LIBRARIES})
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 520c02a7..5b797e3b 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -22,6 +22,7 @@
#include "xpipsaxhandler.h"
#include <pappsomspp/msrun/msrunid.h>
+#include <pappsomspp/exception/exceptionnotfound.h>
XpipSaxHandler::XpipSaxHandler(Project * p_project):_p_project(p_project)
{
@@ -49,10 +50,14 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
//<sample value="P6_08_10"/>
else if (qName == "sample") {
is_ok = startElement_sample(attributes);
+ } else if (qName == "peptide") {
+ is_ok = startElement_peptide(attributes);
+ } else if (qName == "modifs_mass") {
+ is_ok = startElement_modifs_mass(attributes);
}
_current_text.clear();
}
- catch (PappsoException exception_pappso) {
+ catch (pappso::PappsoException exception_pappso) {
_errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
return false;
}
@@ -73,6 +78,9 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
{
is_ok = endElement_protein();
}
+ else if (qName == "peptide") {
+ is_ok = endElement_peptide();
+ }
else if (qName == "sequence") {
is_ok = endElement_sequence();
}
@@ -81,7 +89,7 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
// else if ((_tag_stack.size() > 1) &&
// (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
}
- catch (PappsoException exception_pappso) {
+ catch (pappso::PappsoException exception_pappso) {
_errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
return false;
}
@@ -96,34 +104,78 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
return is_ok;
}
+bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
+
+ /*
+ <modifs_list_mass><modifs_mass modvalue="-18.01056"/>
+ <modifs_mass modvalue="-17.02655"/>
+ <modifs_mass modvalue="15.99491"/>
+ <modifs_mass modvalue="42.01057"/>
+ <modifs_mass modvalue="42.01056"/>
+ <modifs_mass modvalue="57.02146"/>
+ </modifs_list_mass>
+ */
+ qDebug() << "startElement_modifs_mass ";
+ QString mass_str(attributes.value("modvalue").simplified());
+ pappso::mz mass = mass_str.toDouble();
+
+ pappso::AaModificationP mod = getAaModificationP(mass);
+
+ _map_massstr_aamod[mass_str] = mod;
+ qDebug() << "startElement_modifs_mass end" ;
+ return true;
+}
+
//<sample value="P6_21_23"/>
bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
qDebug() << "startElement_sample ";
- MsRunId ms_run;
+ pappso::MsRunId ms_run;
ms_run.setXmlId(attributes.value("value").simplified());
ms_run.setFilename(attributes.value("value").simplified());
-
+
_p_project->addMsRunIdSp(ms_run.makeMsRunIdSp());
qDebug() << "startElement_sample end" ;
return true;
}
-/*
- * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta" description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
- <protein_evalue evalue="-399.36093" sample="20120906_balliau_extract_1_A02_urzb-1"/>
- <protein_evalue evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
- <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
- </protein>
- */
bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
+ /*
+ * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta" description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
+ <protein_evalue evalue="-399.36093" sample="20120906_balliau_extract_1_A02_urzb-1"/>
+ <protein_evalue evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
+ <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
+ </protein>
+ */
qDebug() << "startElement_protein ";
_current_protein.setDescription(attributes.value("description").simplified());
_current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
qDebug() << "startElement_protein end" ;
return true;
}
+bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
+
+//<peptide sample="20120208_Blein_rep4_1_B03_DW21-4-26-328"
+ //sample_file="/gorgone/pappso/moulon/users/Melisande/test-param-masschroq/20120208_Blein_rep4_1_B03_DW21-4-26-328.xml"
+ //scan="2589" scan_in_xtandem="2589" RT="603" mhplus_obser="873.5401" mhplus_theo="873.5408" deltamass="-7.0E-4"
+ //sequence="IATAIEKK" pre="NPAR" post="AADA" start="331" stop="338" charge="2" evalue="9.2E-4" hypercorr="35.2" validate="true">
+//<modifs></modifs></peptide>
+
+ //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
+//</modifs>
+ qDebug() << "startElement_peptide ";
+ _current_peptide_sp = pappso::Peptide(attributes.value("sequence").simplified()).makePeptideSp();
+ qDebug() << "startElement_peptide end" ;
+ return true;
+}
+
+bool XpipSaxHandler::endElement_peptide() {
+ qDebug() << "endElement_peptide ";
+
+ _current_peptide_sp = peptide_store.getInstance(_current_peptide_sp);
+ return true;
+}
bool XpipSaxHandler::endElement_sequence() {
if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
@@ -175,3 +227,54 @@ bool XpipSaxHandler::characters(const QString &str) {
return true;
}
+
+pappso::AaModificationP XpipSaxHandler::getAaModificationP(pappso::mz mass) const {
+ pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
+
+ pappso::AaModificationP oxidation = pappso::AaModification::getInstance("MOD:00719");
+ if (pappso::MassRange(oxidation->getMass(),precision).contains(mass)) {
+ return oxidation;
+ }
+ pappso::AaModificationP iodoacetamide = pappso::AaModification::getInstance("MOD:00397");
+ if (pappso::MassRange(iodoacetamide->getMass(),precision).contains(mass)) {
+ return iodoacetamide;
+ }
+ pappso::AaModificationP acetylated = pappso::AaModification::getInstance("MOD:00408");
+ if (pappso::MassRange(acetylated->getMass(),precision).contains(mass)) {
+ return acetylated;
+ }
+ pappso::AaModificationP phosphorylated = pappso::AaModification::getInstance("MOD:00696");
+ if (pappso::MassRange(phosphorylated->getMass(),precision).contains(mass)) {
+ return phosphorylated;
+ }
+ pappso::AaModificationP ammonia = pappso::AaModification::getInstance("MOD:01160");
+ if (pappso::MassRange(ammonia->getMass(),precision).contains(mass)) {
+ return ammonia;
+ }
+ pappso::AaModificationP dehydrated = pappso::AaModification::getInstance("MOD:00704");
+ if (pappso::MassRange(dehydrated->getMass(),precision).contains(mass)) {
+ return dehydrated;
+ }
+ pappso::AaModificationP dimethylated = pappso::AaModification::getInstance("MOD:00429");
+ if (pappso::MassRange(dimethylated->getMass(),precision).contains(mass)) {
+ return dimethylated;
+ }
+
+ pappso::AaModificationP dimethylated_medium = pappso::AaModification::getInstance("MOD:00552");
+ if (pappso::MassRange(dimethylated_medium->getMass(),precision).contains(mass)) {
+ return dimethylated_medium;
+ }
+
+ pappso::AaModificationP dimethylated_heavy = pappso::AaModification::getInstance("MOD:00638");
+ if (pappso::MassRange(dimethylated_heavy->getMass(),precision).contains(mass)) {
+ return dimethylated_heavy;
+ }
+ pappso::AaModificationP DimethylpyrroleAdduct = pappso::AaModification::getInstance("MOD:00628");
+ if (pappso::MassRange(DimethylpyrroleAdduct->getMass(),precision).contains(mass)) {
+ return DimethylpyrroleAdduct;
+ }
+
+
+ throw pappso::ExceptionNotFound(QObject::tr("XpipSaxHandler::getAaModificationP => modification not found for mass %1").arg(mass));
+}
+
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index e8b2dc45..5eca4cad 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -26,9 +26,10 @@
#include <QXmlDefaultHandler>
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/protein/protein.h>
+#include <pappsomspp/peptide/peptide.h>
+#include <pappsomspp/amino_acid/aamodification.h>
#include "../core/project.h"
-
-using namespace pappso;
+#include "../utils/peptidestore.h"
class XpipSaxHandler: public QXmlDefaultHandler
{
@@ -53,20 +54,29 @@ public:
QString errorString() const;
-
+
private:
- bool startElement_protein(QXmlAttributes attributes);
- bool startElement_sample(QXmlAttributes attributes);
- bool endElement_sequence();
- bool endElement_protein();
+ bool startElement_peptide(QXmlAttributes attributes);
+ bool startElement_protein(QXmlAttributes attributes);
+ bool startElement_sample(QXmlAttributes attributes);
+ bool startElement_modifs_mass(QXmlAttributes attributes);
+ bool endElement_sequence();
+ bool endElement_protein();
+ bool endElement_peptide();
+
+ pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
private:
std::vector<QString> _tag_stack;
QString _errorStr;
QString _current_text;
-
+
Project * _p_project;
- Protein _current_protein;
+ pappso::Protein _current_protein;
+ pappso::PeptideSp _current_peptide_sp;
+
+ PeptideStore peptide_store;
+ QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
};
#endif // XTANDEMRESULTSHANDLER_H
diff --git a/src/utils/peptidestore.cpp b/src/utils/peptidestore.cpp
new file mode 100644
index 00000000..5da496c7
--- /dev/null
+++ b/src/utils/peptidestore.cpp
@@ -0,0 +1,52 @@
+/**
+ * \file utils/peptidestore.h
+ * \date 7/10/2016
+ * \author Olivier Langella
+ * \brief store unique version of peptides
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of peptider.
+ *
+ * peptider 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.
+ *
+ * peptider 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 peptider. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+ ******************************************************************************/
+
+#include "peptidestore.h"
+
+PeptideStore::PeptideStore()
+{
+
+}
+
+PeptideStore::~PeptideStore()
+{
+
+}
+
+pappso::PeptideSp & PeptideStore::getInstance(pappso::PeptideSp & peptide_in) {
+ std::size_t sequence_li_crc = _hash_fn ( peptide_in.get()->getLiAbsoluteString().toStdString());
+
+ //QByteArray source = peptide_in.get()->getLiAbsoluteString().toUtf8();
+ //quint16 sequence_li_crc = qChecksum(source.data(), source.length());
+
+ std::pair<std::unordered_map< std::size_t, pappso::PeptideSp>::iterator,bool> ret = _map_crc_peptide_list.insert(std::pair<std::size_t, pappso::PeptideSp>(sequence_li_crc,peptide_in));
+
+ return ret.first->second;
+
+}
diff --git a/src/utils/peptidestore.h b/src/utils/peptidestore.h
new file mode 100644
index 00000000..d6f88ea1
--- /dev/null
+++ b/src/utils/peptidestore.h
@@ -0,0 +1,50 @@
+/**
+ * \file utils/peptidestore.h
+ * \date 7/10/2016
+ * \author Olivier Langella
+ * \brief store unique version of peptides
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of peptider.
+ *
+ * peptider 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.
+ *
+ * peptider 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 peptider. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+ ******************************************************************************/
+
+#ifndef PEPTIDESTORE_H
+#define PEPTIDESTORE_H
+
+#include <pappsomspp/peptide/peptide.h>
+#include <unordered_map>
+
+class PeptideStore
+{
+public:
+ PeptideStore();
+ ~PeptideStore();
+
+ pappso::PeptideSp & getInstance(pappso::PeptideSp & peptide_in);
+
+private :
+
+ std::hash<std::string> _hash_fn;
+ std::unordered_map<std::size_t, pappso::PeptideSp> _map_crc_peptide_list;
+};
+
+#endif // PEPTIDESTORE_H
--
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