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Commit 1fb321a2 authored by Olivier Langella's avatar Olivier Langella
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better proticdbml check

parent 1d4e8f2e
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src/output/proticdbml.cpp
+ 106
− 76
View file @ 1fb321a2
...@@ -68,7 +68,7 @@ ProticdbMl::~ProticdbMl() ...@@ -68,7 +68,7 @@ ProticdbMl::~ProticdbMl()
void ProticdbMl::close() { void ProticdbMl::close() {
_output_stream->writeEndDocument(); _output_stream->writeEndDocument();
_output_file->close(); _output_file->close();
qDebug() << "ProticdbMl::close end duration = " << _duracel.elapsed() << "ms"; qDebug() << "ProticdbMl::close end duration = " << _duracel.elapsed() << "ms";
} }
...@@ -563,91 +563,121 @@ void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) { ...@@ -563,91 +563,121 @@ void ProticdbMl::writeMatchs(IdentificationGroup * p_identification) {
_output_stream->writeEndElement();// "matchs"); _output_stream->writeEndElement();// "matchs");
} }
const QString & ProticdbMl::getPeptideXmlId(const PeptideMatch* p_peptide_match) const {
void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list) { QString peptide_key = getProticPeptideHitKey(p_peptide_match);
auto it = _peptidekey_to_id.find(peptide_key);
if (protein_match_sg_list.size() == 0) return; if (it == _peptidekey_to_id.end()) {
//for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) { throw pappso::PappsoException(QObject::tr("Error peptide key %1 not found for peptide match %2 sample=%3 scan=%4 start=%5").arg(peptide_key)
_output_stream->writeStartElement("match"); .arg(p_peptide_match->getPeptideXtpSp().get()->toString())
.arg(p_peptide_match->getMsRunP()->getXmlId())
// samples .arg(p_peptide_match->getScan())
QStringList sample_name_list; .arg(p_peptide_match->getStart())
for (const PeptideMatch * p_peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) { );
sample_name_list << p_peptide_match->getMsRunP()->getSampleName();
}
sample_name_list = sample_name_list.toSet().toList();
for (QString sample_name :sample_name_list) {
_output_stream->writeStartElement("matchSample");
_output_stream->writeAttribute(
"sample_id",_sample_to_id[sample_name]);
_output_stream->writeAttribute("name", sample_name);
_output_stream->writeEndElement();// "matchSample");
} }
return it->second;
// proteins }
for (const ProteinMatch * p_protein_match: protein_match_sg_list) { const QString & ProticdbMl::getProteinXmlId(const ProteinMatch* p_protein_match) const {
_output_stream->writeStartElement("proteinHit"); auto it = _map_accession2xmlid.find(p_protein_match->getProteinXtpSp().get()->getAccession());
_output_stream->writeAttribute("sequence_id",QString("%1 %2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(p_protein_match->getProteinXtpSp().get()->getDescription())); if (it == _map_accession2xmlid.end()) {
// proteinHit.setAttribute("score", ""); throw pappso::PappsoException(QObject::tr("Error protein accession %1 not found for protein %2")
_output_stream->writeAttribute("rank", QString("%1").arg(p_protein_match->getGrpProteinSp().get()->getRank())); .arg(p_protein_match->getProteinXtpSp().get()->getAccession())
.arg(p_protein_match->getProteinXtpSp().get()->getAccession()));
// //cvparam
writeCvParam("PROTICdbO:0000284",QString("%1").arg(p_protein_match->getProteinXtpSp().get()->getMass()),
"MW computation");
// evalue
writeCvParam("PROTICdbO:0000291", Utils::getXmlDouble(p_protein_match->getLogEvalue())
, "Xtandem log evalue");
// coverage
writeCvParam(
"PROTICdbO:0000285", Utils::getXmlDouble(p_protein_match->getCoverage()),
"protein coverage");
// [Term]
// id: PROTICdbO:0000335
// name: X!TandemPipeline PAI
writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
// [Term]
// id: PROTICdbO:0000337
// name: protein group number
writeCvParam("PROTICdbO:0000337",p_protein_match->getGrpProteinSp().get()->getGroupingId(), "grouping number");
_output_stream->writeEndElement();// "proteinHit");
} }
return it->second;
}
void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list) {
try {
if (protein_match_sg_list.size() == 0) return;
//for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
_output_stream->writeStartElement("match");
// samples
QStringList sample_name_list;
for (const PeptideMatch * p_peptide_match: protein_match_sg_list[0]->getPeptideMatchList(ValidationState::grouped)) {
sample_name_list << p_peptide_match->getMsRunP()->getSampleName();
}
sample_name_list = sample_name_list.toSet().toList();
for (QString sample_name :sample_name_list) {
_output_stream->writeStartElement("matchSample");
_output_stream->writeAttribute(
"sample_id",_sample_to_id[sample_name]);
_output_stream->writeAttribute("name", sample_name);
_output_stream->writeEndElement();// "matchSample");
}
for (const ProteinMatch * p_protein_match: protein_match_sg_list) { // proteins
//peptides for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
for (const PeptideMatch * p_peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) { _output_stream->writeStartElement("proteinHit");
// peptidesHitRef _output_stream->writeAttribute("sequence_id",QString("%1 %2").arg(p_protein_match->getProteinXtpSp().get()->getAccession()).arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
QString peptide_key = getProticPeptideHitKey(p_peptide_match); // proteinHit.setAttribute("score", "");
QString peptide_xml_id = _peptidekey_to_id.at(peptide_key); _output_stream->writeAttribute("rank", QString("%1").arg(p_protein_match->getGrpProteinSp().get()->getRank()));
// //cvparam
writeCvParam("PROTICdbO:0000284",QString("%1").arg(p_protein_match->getProteinXtpSp().get()->getMass()),
"MW computation");
// evalue
writeCvParam("PROTICdbO:0000291", Utils::getXmlDouble(p_protein_match->getLogEvalue())
, "Xtandem log evalue");
// coverage
writeCvParam(
"PROTICdbO:0000285", Utils::getXmlDouble(p_protein_match->getCoverage()),
"protein coverage");
// [Term]
// id: PROTICdbO:0000335
// name: X!TandemPipeline PAI
writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
// [Term]
// id: PROTICdbO:0000337
// name: protein group number
writeCvParam("PROTICdbO:0000337",p_protein_match->getGrpProteinSp().get()->getGroupingId(), "grouping number");
_output_stream->writeEndElement();// "proteinHit");
}
_output_stream->writeStartElement("peptideHitRef"); for (const ProteinMatch * p_protein_match: protein_match_sg_list) {
_output_stream->writeAttribute("peptide_hit_id", peptide_xml_id); //peptides
for (const PeptideMatch * p_peptide_match: p_protein_match->getPeptideMatchList(ValidationState::grouped)) {
// peptidesHitRef
QString peptide_xml_id = getPeptideXmlId(p_peptide_match);
_output_stream->writeStartElement("peptideHitRef");
_output_stream->writeAttribute("peptide_hit_id", peptide_xml_id);
_output_stream->writeStartElement("fromSeq");
_output_stream->writeAttribute(
"seq_id", getProteinXmlId(p_protein_match));
_output_stream->writeAttribute("start", QString("%1").arg(p_peptide_match->getStart()+1));
_output_stream->writeAttribute("stop", QString("%1").arg(p_peptide_match->getStop()+1));
QString residue_before_nter = "-";
if (p_peptide_match->getStart() > 0) {
residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStart()-1,1);
}
_output_stream->writeAttribute("residue_before_nter", residue_before_nter);
QString residue_after_cter = "-";
if (p_peptide_match->getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStop(),1);
}
_output_stream->writeAttribute("residue_after_cter", residue_after_cter);
_output_stream->writeStartElement("fromSeq"); _output_stream->writeEndElement();// fromSeq
_output_stream->writeAttribute( _output_stream->writeEndElement();// peptideHitRef
"seq_id",_map_accession2xmlid.at(p_protein_match->getProteinXtpSp().get()->getAccession()));
_output_stream->writeAttribute("start", QString("%1").arg(p_peptide_match->getStart()+1));
_output_stream->writeAttribute("stop", QString("%1").arg(p_peptide_match->getStop()+1));
QString residue_before_nter = "-";
if (p_peptide_match->getStart() > 0) {
residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStart()-1,1);
}
_output_stream->writeAttribute("residue_before_nter", residue_before_nter);
QString residue_after_cter = "-";
if (p_peptide_match->getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
residue_after_cter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStop(),1);
} }
_output_stream->writeAttribute("residue_after_cter", residue_after_cter);
_output_stream->writeEndElement();// fromSeq
_output_stream->writeEndElement();// peptideHitRef
} }
_output_stream->writeEndElement();// "match");
}
catch (pappso::PappsoException &error)
{
throw pappso::PappsoException(QObject::tr("Error in ProticdbMl::writeMatch :\n%1").arg(error.qwhat()));
}
catch (std::exception &error)
{
throw pappso::PappsoException(QObject::tr("Error in ProticdbMl::writeMatch stdex :\n%1").arg(error.what()));
} }
_output_stream->writeEndElement();// "match");
} }
void ProticdbMl::writeOboModif(pappso::AaModificationP mod) { void ProticdbMl::writeOboModif(pappso::AaModificationP mod) {
_output_stream->writeStartElement("cvParam"); _output_stream->writeStartElement("cvParam");
......
src/output/proticdbml.h
+ 3
− 0
View file @ 1fb321a2
...@@ -66,6 +66,9 @@ private : ...@@ -66,6 +66,9 @@ private :
void writeMatchs(IdentificationGroup * p_identification); void writeMatchs(IdentificationGroup * p_identification);
void writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list); void writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list);
const QString & getPeptideXmlId(const PeptideMatch* p_peptide_match) const;
const QString & getProteinXmlId(const ProteinMatch* p_protein_match) const;
private : private :
QFile * _output_file; QFile * _output_file;
QXmlStreamWriter * _output_stream; QXmlStreamWriter * _output_stream;
......
src/resources/catalog_label.xml
+ 0
− 1
View file @ 1fb321a2
...@@ -12,5 +12,4 @@ ...@@ -12,5 +12,4 @@
<mod at="Nter" value="36.0" acc="MOD:00638"/> <mod at="Nter" value="36.0" acc="MOD:00638"/>
<mod at="K" value="36.0" acc="MOD:00638"/> <mod at="K" value="36.0" acc="MOD:00638"/>
</isotope_label> </isotope_label>
</isotope_label_list>
</catalog> </catalog>
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