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Commit 32e92c77 authored by Langella Olivier's avatar Langella Olivier
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read decoy peptide in mascot dat file

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src/input/mascot/mascotdatparser.cpp
+ 80
− 61
View file @ 32e92c77
......@@ -395,90 +395,109 @@ void MascotDatParser::saveQuery() {
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
if (_current_query.query_index > 0) {
std::vector< PeptideLine> peptide_list = _query_peptide_results[_current_query.query_index-1];
savePeptideList(peptide_list, false);
peptide_list = _decoy_query_peptide_results[_current_query.query_index-1];
savePeptideList(peptide_list, true);
}
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
}
void MascotDatParser::savePeptideList(std::vector< PeptideLine> & peptide_list, bool is_decoy) {
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
PeptideEvidence peptide_evidence(_p_identification_data_source->getMsRunSp().get(),_current_query.query_index);
peptide_evidence.setCharge(_current_query.charge);
peptide_evidence.setChecked(true);
peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
peptide_evidence.setRetentionTime(_current_query.rt);
PeptideEvidence peptide_evidence(_p_identification_data_source->getMsRunSp().get(),_current_query.query_index);
peptide_evidence.setCharge(_current_query.charge);
peptide_evidence.setChecked(true);
peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
peptide_evidence.setRetentionTime(_current_query.rt);
peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
//parse and save
for(PeptideLine & peptide_line:peptide_list) {
peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
//parse and save
for(PeptideLine & peptide_line:peptide_list) {
pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
peptide_evidence.setParam(PeptideEvidenceParam::mascot_score, QVariant(ion_score));
peptide_evidence.setEvalue(getEvalue(ion_score, _current_query.query_index, 0.05));
if (is_decoy) {
peptide_evidence.setEvalue(getEvalue(ion_score, _decoy_summary_list.at(_current_query.query_index-1), 0.05));
}
else {
peptide_evidence.setEvalue(getEvalue(ion_score, _summary_list.at(_current_query.query_index-1), 0.05));
}
peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value, QVariant(peptide_evidence.getEvalue()));
peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value, QVariant(peptide_evidence.getEvalue()));
QString peptide_str =peptide_line.peptide_string_list.at(4);
if (!peptide_line.subst.isEmpty()) {
//q856_p9_subst=1,X,W
//q24379_p2_subst=1,B,D,8,B,D
QStringList subst_list = peptide_line.subst.split(",");
for (unsigned int i=0; i < subst_list.size(); i+=3) {
peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
}
QString peptide_str =peptide_line.peptide_string_list.at(4);
if (!peptide_line.subst.isEmpty()) {
//q856_p9_subst=1,X,W
//q24379_p2_subst=1,B,D,8,B,D
QStringList subst_list = peptide_line.subst.split(",");
for (unsigned int i=0; i < subst_list.size(); i+=3) {
peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
}
PeptideXtpSp peptide_sp;
peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
}
PeptideXtpSp peptide_sp;
peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
peptide_evidence.setPeptideXtpSp(_p_project->getPeptideStore().getInstance(peptide_sp));
//qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" << peptide_str << " evalue=" << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
//qDebug() << __FILE__ << " " << __FUNCTION__<< " peptide=" << peptide_str << " evalue=" << peptide_evidence.getEvalue() << " ionscore=" << ion_score;
if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
}
if (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) {
throw pappso::PappsoException(QObject::tr("ERROR (peptide_line.protein_string_list.size() != peptide_line.fasta_file_list.size()) %1").arg(peptide_line.protein_string_list.join(",\"")));
unsigned int i=0;
foreach (const QString &str, peptide_line.protein_string_list) {
//sp|O95006|OR2F2_HUMAN":0:299:303:1
int position = str.indexOf("\"", 0);
QString accession = str.mid(0, position);
if (is_decoy) {
accession = QString("%1|reversed").arg(accession);
}
qDebug() << "accession=" << accession;
QStringList position_list = str.mid(position+2).split(":");
if (position_list.size() != 4) {
throw pappso::PappsoException(QObject::tr("ERROR position_list.size() != 4 %1").arg(str));
}
unsigned int start = position_list.at(1).toUInt()-1;
unsigned int stop = position_list.at(2).toUInt()-1;
//qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
ProteinXtp protein;
protein.setAccession(accession);
protein.setFastaFileP(peptide_line.fasta_file_list[i].get());
if (is_decoy) {
protein.setIsDecoy(true);
}
unsigned int i=0;
foreach (const QString &str, peptide_line.protein_string_list) {
//sp|O95006|OR2F2_HUMAN":0:299:303:1
int position = str.indexOf("\"", 0);
QString accession = str.mid(0, position);
qDebug() << "accession=" << accession;
QStringList position_list = str.mid(position+2).split(":");
if (position_list.size() != 4) {
throw pappso::PappsoException(QObject::tr("ERROR position_list.size() != 4 %1").arg(str));
}
unsigned int start = position_list.at(1).toUInt()-1;
unsigned int stop = position_list.at(2).toUInt()-1;
//qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
ProteinXtp protein;
protein.setAccession(accession);
protein.setFastaFileP(peptide_line.fasta_file_list[i].get());
ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(accession);
if (p_protein_match == nullptr) {
throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
}
//qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
p_protein_match->setChecked(true);
ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(accession);
if (p_protein_match == nullptr) {
throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
}
//qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
p_protein_match->setChecked(true);
PeptideMatch peptide_match;
peptide_match.setStart(start);
peptide_match.setPeptideEvidenceSp(_p_identification_data_source->getPeptideEvidenceStore().getInstance(&peptide_evidence));
PeptideMatch peptide_match;
peptide_match.setStart(start);
peptide_match.setPeptideEvidenceSp(_p_identification_data_source->getPeptideEvidenceStore().getInstance(&peptide_evidence));
p_protein_match->addPeptideMatch(peptide_match);
i++;
}
p_protein_match->addPeptideMatch(peptide_match);
i++;
}
}
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
}
pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval) const {
pappso::pappso_double identity_threshold = (pappso::pappso_double)10.0 * std::log(_summary_list.at(query_index-1).match / (confidence_interval * (pappso::pappso_double)20.0)) / log((pappso::pappso_double)10);;
pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval) const {
pappso::pappso_double identity_threshold = (pappso::pappso_double)10.0 * std::log(summary_line.match / (confidence_interval * (pappso::pappso_double)20.0)) / log((pappso::pappso_double)10);;
return (confidence_interval * pow((pappso::pappso_double)10, ((identity_threshold - ion_score) / (pappso::pappso_double)10)));
}
pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval) const {
pappso::pappso_double MascotDatParser::getEvalueExperimental(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval) const {
// Evalue experimental Homology threshold (QPlughole value from .dat file).
pappso::pappso_double eval = (ion_score - _summary_list.at(query_index-1).plug_hole) / (pappso::pappso_double)10;
pappso::pappso_double eval = (ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
eval = confidence_interval / pow((pappso::pappso_double)10, eval);
}
src/input/mascot/mascotdatparser.h
+ 4
− 2
View file @ 32e92c77
......@@ -49,8 +49,6 @@ private:
void saveAndClearPeptide();
pappso::pappso_double getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
pappso::pappso_double getEvalueExperimental(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
......@@ -74,6 +72,10 @@ private:
pappso::pappso_double exp_mass=0;
pappso::pappso_double plug_hole=0; //qplughole, homology threshold
};
void savePeptideList(std::vector< PeptideLine> & peptide_list, bool is_decoy);
pappso::pappso_double getEvalue(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval = 0.05) const;
pappso::pappso_double getEvalueExperimental(pappso::pappso_double ion_score, SummaryLine & summary_line, pappso::pappso_double confidence_interval = 0.05) const;
private:
Project * _p_project;
IdentificationGroup * _p_identification_group;
......
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