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Commit 4d6eaacc authored by Langella Olivier's avatar Langella Olivier
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proticdbML output debug

parent f32440b7
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src/output/proticdbml.cpp
+ 61
− 27
View file @ 4d6eaacc
......@@ -151,7 +151,7 @@ void ProticdbMl::writeSequence(ProteinMatch * p_protein_match) {
}
void ProticdbMl::writeProject() {
qDebug() << "ProticdbMl::writeProject begin";
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeStartElement("project");
_output_stream->writeAttribute("name", "");
_output_stream->writeAttribute("id", "p1");
......@@ -179,9 +179,11 @@ void ProticdbMl::writeProject() {
_output_stream->writeEndDocument();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writeIdentMethod() {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// Ajout des méthodes
_output_stream->writeStartElement("identMeth");
_output_stream->writeAttribute("name", "");
......@@ -193,11 +195,13 @@ void ProticdbMl::writeIdentMethod() {
_output_stream->writeAttribute("name", "");
_output_stream->writeAttribute("id", "customdb0");
_output_stream->writeEndElement();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writeSamples() {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeStartElement("samples");
for (MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
_output_stream->writeStartElement("sample");
......@@ -218,10 +222,12 @@ void ProticdbMl::writeSamples() {
}
_output_stream->writeEndElement();// samples
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writeMsRuns() {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeStartElement("msRuns");
for (MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
......@@ -267,11 +273,13 @@ void ProticdbMl::writeMsRuns() {
}
_output_stream->writeEndElement();// msRuns
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source) {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeStartElement("dataProcessing");
_output_stream->writeStartElement("software");
_output_stream->writeStartElement("name");
......@@ -315,9 +323,11 @@ void ProticdbMl::writeIdentificationDataSource(IdentificationDataSource * p_iden
_output_stream->writeEndElement();// processingMethod
_output_stream->writeEndElement();// dataProcessing
*/
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification) {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeAttribute("ident_method_id", "m1");
_output_stream->writeAttribute("customdb_id", "customdb0");
......@@ -357,6 +367,7 @@ void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification)
for (IdentificationDataSource * p_identification_data_source : p_identification->getIdentificationDataSourceList()) {
writeIdentificationDataSource(p_identification_data_source);
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// id: PROTICdbO:0000316
// name: X!TandemPipeline
......@@ -407,15 +418,18 @@ void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification)
_output_stream->writeEndElement();// dataProcessing
_output_stream->writeEndElement();// description
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writepeptideHits(IdentificationGroup * p_identification) {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeStartElement("peptideHits");
for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
writepeptideHitsbyGroup(group_pair.second.get());
}
_output_stream->writeEndElement();// "peptideHits");
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
QString getProticPeptideHitKey(const PeptideEvidence * p_peptide_evidence) {
......@@ -429,16 +443,17 @@ struct ProticPeptideHit {
/** key = getProticPeptideHitKey
* */
QString key;
const PeptideMatch * peptide_match;
PeptideMatch peptide_match;
};
void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
std::vector <ProticPeptideHit> protic_peptide_hit_list;
for (const ProteinMatch* p_protein_match : p_group->getProteinMatchList()) {
for (const PeptideMatch & peptide_match : p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
ProticPeptideHit protic_peptide_hit = {getProticPeptideHitKey(peptide_match.getPeptideEvidence()), &peptide_match};
ProticPeptideHit protic_peptide_hit = {getProticPeptideHitKey(peptide_match.getPeptideEvidence()), peptide_match};
protic_peptide_hit_list.push_back(protic_peptide_hit);
}
}
......@@ -453,24 +468,39 @@ void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
writePeptideHit(xml_id, protic_peptide_hit);
_peptidekey_to_id.insert(std::pair<QString, QString>(protic_peptide_hit.key, xml_id));
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit) {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if (protic_peptide_hit.peptide_match.getPeptideEvidence() == nullptr) {
throw pappso::PappsoException(QObject::tr("Error protic_peptide_hit.peptide_match->getPeptideEvidence() == nullptr : \n%1 %2 %3").arg(__FILE__)
.arg(__FUNCTION__)
.arg(__LINE__)
);
}
if (protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get() == nullptr) {
throw pappso::PappsoException(QObject::tr("Error protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get() == nullptr : \n%1 %2 %3").arg(__FILE__)
.arg(__FUNCTION__)
.arg(__LINE__)
);
}
// param par default
_output_stream->writeStartElement("peptideHit");
_output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->getMass()));
_output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getExperimentalMz()));
_output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getDeltaMass()));
_output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getExperimentalMz()- pappso::MHPLUS));
_output_stream->writeAttribute("acq_number", QString ("%1").arg(protic_peptide_hit.peptide_match->getPeptideEvidence()->getScan()));
_output_stream->writeAttribute("ms_run_id", protic_peptide_hit.peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId());
_output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMass()));
_output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getExperimentalMz()));
_output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getDeltaMass()));
_output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getExperimentalMass()));
_output_stream->writeAttribute("acq_number", QString ("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()->getScan()));
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeAttribute("ms_run_id", protic_peptide_hit.peptide_match.getPeptideEvidence()->getMsRunP()->getXmlId());
_output_stream->writeAttribute("id", xml_id);
_output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match->getPeptideEvidence()->getCharge()));
_output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()->getCharge()));
writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match->getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId(),
writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match.getPeptideEvidence()->getGrpPeptideSp().get()->getGroupingId(),
"peptide mass id");
/*
if (xtpExperimentType.equals("phospho")) {
......@@ -479,32 +509,34 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
"phosphopeptide mass id");
}
*/
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// pep.getMsRun().
IdentificationEngine identification_engine = protic_peptide_hit.peptide_match->getPeptideEvidence()->getIdentificationDataSource()->getIdentificationEngine();
IdentificationEngine identification_engine = protic_peptide_hit.peptide_match.getPeptideEvidence()->getIdentificationDataSource()->getIdentificationEngine();
if (identification_engine == IdentificationEngine::XTandem) {
// cvparam specifique xtandem
writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getEvalue()),
writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getEvalue()),
"xtandem peptide evalue");
writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble()),
writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match.getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore).toDouble()),
"xtandem peptide hyperscore");
}
writeCvParam("PROTICdbO:0000289",QString ("%1").arg(protic_peptide_hit.peptide_match->getPeptideEvidence()->getRetentionTime()),
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
writeCvParam("PROTICdbO:0000289",QString ("%1").arg(protic_peptide_hit.peptide_match.getPeptideEvidence()->getRetentionTime()),
"xtandem peptide retention time");
// sequences avec les modifs
_output_stream->writeStartElement("pepSeq");
_output_stream->writeStartElement("peptide");
_output_stream->writeCharacters(protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
_output_stream->writeCharacters(protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getSequence());
_output_stream->writeEndElement();// peptide
if (!protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->getModifString().isEmpty()) {
writePtms(protic_peptide_hit.peptide_match->getPeptideEvidence()->getPeptideXtpSp().get());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if (!protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getModifString().isEmpty()) {
writePtms(protic_peptide_hit.peptide_match.getPeptideEvidence()->getPeptideXtpSp().get());
}
_output_stream->writeEndElement();// pepSeq
_output_stream->writeEndElement();// peptideHit
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
......@@ -532,6 +564,7 @@ void ProticdbMl::writePtms(PeptideXtp * p_peptide) {
}
void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeStartElement("matchs");
for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
......@@ -563,6 +596,7 @@ void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
writeMatch(protein_match_subgroup_list);
}
_output_stream->writeEndElement();// "matchs");
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
const QString & ProticdbMl::getPeptideXmlId(const PeptideMatch* p_peptide_match) const {
......@@ -570,11 +604,11 @@ const QString & ProticdbMl::getPeptideXmlId(const PeptideMatch* p_peptide_match)
auto it = _peptidekey_to_id.find(peptide_key);
if (it == _peptidekey_to_id.end()) {
throw pappso::PappsoException(QObject::tr("Error peptide key %1 not found for peptide match %2 sample=%3 scan=%4 start=%5").arg(peptide_key)
.arg(p_peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->toString())
.arg(p_peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId())
.arg(p_peptide_match->getPeptideEvidence()->getScan())
.arg(p_peptide_match->getStart())
);
.arg(p_peptide_match->getPeptideEvidence()->getPeptideXtpSp().get()->toString())
.arg(p_peptide_match->getPeptideEvidence()->getMsRunP()->getXmlId())
.arg(p_peptide_match->getPeptideEvidence()->getScan())
.arg(p_peptide_match->getStart())
);
}
return it->second;
......@@ -583,8 +617,8 @@ const QString & ProticdbMl::getProteinXmlId(const ProteinMatch* p_protein_match)
auto it = _map_accession2xmlid.find(p_protein_match->getProteinXtpSp().get()->getAccession());
if (it == _map_accession2xmlid.end()) {
throw pappso::PappsoException(QObject::tr("Error protein accession %1 not found for protein %2")
.arg(p_protein_match->getProteinXtpSp().get()->getAccession())
.arg(p_protein_match->getProteinXtpSp().get()->getAccession()));
.arg(p_protein_match->getProteinXtpSp().get()->getAccession())
.arg(p_protein_match->getProteinXtpSp().get()->getAccession()));
}
return it->second;
}
......
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