From a7057bfd68e1e01d726c803f5d4e860e3c0162c0 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 19 Jun 2018 17:09:16 +0200
Subject: [PATCH] WIP: better pep xml support
---
src/input/pepxmlsaxhandler.cpp | 117 ++++++++++++++++++++++++++-------
src/input/pepxmlsaxhandler.h | 3 +
src/utils/types.h | 6 +-
3 files changed, 101 insertions(+), 25 deletions(-)
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index 05090d158..809b68575 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -120,7 +120,10 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
{
is_ok = startElement_mod_aminoacid_mass(attributes);
}
-
+ else if(qName == "modification_info")
+ {
+ is_ok = startElement_modification_info(attributes);
+ }
_current_text.clear();
}
catch(pappso::PappsoException exception_pappso)
@@ -211,10 +214,29 @@ PepXmlSaxHandler::startElement_msms_pipeline_analysis(QXmlAttributes attributes)
bool
PepXmlSaxHandler::startElement_msms_run_summary(QXmlAttributes attributes)
{
- bool is_ok = true;
- QString mz_datafile = QString("%1%2")
- .arg(attributes.value("base_name"))
- .arg(attributes.value("raw_data"));
+ bool is_ok = true;
+ QString old_file;
+ if(!_current_complete_msrun_file_path.isEmpty())
+ {
+ old_file = _current_complete_msrun_file_path;
+ }
+ _current_complete_msrun_file_path = QString("%1%2")
+ .arg(attributes.value("base_name"))
+ .arg(attributes.value("raw_data"));
+ if((!old_file.isEmpty()) &&
+ (QFileInfo(_current_complete_msrun_file_path).baseName() !=
+ QFileInfo(old_file).baseName()))
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR reading pepxml file :\nX!TandemPipeline does not "
+ "support identification source files containing results "
+ "from multiple MS runs (%1 != %2)")
+ .arg(old_file)
+ .arg(_current_complete_msrun_file_path));
+ }
+ _sp_msrun.get()->setFilename(attributes.value("base_name"));
+ _sp_msrun.get()->setSampleName(
+ QFileInfo(_current_complete_msrun_file_path).baseName());
return is_ok;
}
@@ -259,7 +281,12 @@ PepXmlSaxHandler::startElement_search_summary(QXmlAttributes attributes)
bool
PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
{
- bool is_ok = true;
+ bool is_ok = true;
+ QString spectrum_ref = attributes.value("spectrum");
+ if(_current_complete_msrun_file_path.isEmpty())
+ {
+ _sp_msrun.get()->setFilename(QFileInfo(spectrum_ref).baseName());
+ }
unsigned int start_scan = attributes.value("start_scan").toUInt();
unsigned int end_scan = attributes.value("end_scan").toUInt();
if(start_scan != end_scan)
@@ -272,6 +299,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
.arg(start_scan)
.arg(end_scan));
}
+ _scan = start_scan;
_current_charge = attributes.value("assumed_charge").toUInt();
if(attributes.value("retention_time_sec").isEmpty())
{
@@ -297,7 +325,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
@@ -482,37 +510,78 @@ PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
if(name == "expect")
{
_p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
- if(_p_peptide_evidence->getIdentificationEngine() ==
- IdentificationEngine::OMSSA)
- {
- _p_peptide_evidence->setParam(PeptideEvidenceParam::omssa_evalue,
- valueStr.simplified().toDouble());
- }
}
else if(name == "EValue")
{
_p_peptide_evidence->setEvalue(valueStr.simplified().toDouble());
}
- // <search_score name="hyperscore" value="232"/>
- else if(name == "hyperscore")
- {
- _p_peptide_evidence->setParam(
- PeptideEvidenceParam::tandem_hyperscore,
- QVariant(attributes.value("hyperscore").toDouble()));
- }
- else if(name == "pvalue")
+
+ IdentificationEngine identification_engine =
+ _p_peptide_evidence->getIdentificationEngine();
+ if(identification_engine == IdentificationEngine::OMSSA)
{
- if(_p_peptide_evidence->getIdentificationEngine() ==
- IdentificationEngine::OMSSA)
+ if(name == "pvalue")
{
_p_peptide_evidence->setParam(PeptideEvidenceParam::omssa_pvalue,
valueStr.simplified().toDouble());
}
+ else if(name == "expect")
+ {
+ _p_peptide_evidence->setParam(PeptideEvidenceParam::omssa_evalue,
+ valueStr.simplified().toDouble());
+ }
+ }
+ else if(identification_engine == IdentificationEngine::XTandem)
+ {
+ if(name == "hyperscore")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::tandem_hyperscore,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ }
+ else if(identification_engine == IdentificationEngine::MSGFplus)
+ {
+ if(name == "raw")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_raw,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ else if(name == "SpecEValue")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_SpecEValue,
+ QVariant(valueStr.simplified().toDouble()));
+ }
+ else if(name == "EValue")
+ {
+ _p_peptide_evidence->setParam(
+ PeptideEvidenceParam::msgfplus_EValue,
+ QVariant(valueStr.simplified().toDouble()));
+ }
}
}
return is_ok;
}
+
+// <modification_info mod_nterm_mass="43.018389" modified_peptide="SQRDCR">
+bool
+PepXmlSaxHandler::startElement_modification_info(QXmlAttributes attributes)
+{
+ bool is_ok = true;
+
+ if(!attributes.value("mod_nterm_mass").isEmpty())
+ {
+ pappso::AaModificationP modif =
+ Utils::guessAaModificationPbyMonoisotopicMassDelta(
+ attributes.value("mod_nterm_mass").toDouble());
+
+ _current_peptide_sp.get()->addAaModification(modif, 0);
+ }
+ return is_ok;
+}
// <modification_info modified_peptide="SQRDCR"> <mod_aminoacid_mass
// position="5" mass="160.030649"/> </modification_info>
bool
@@ -521,7 +590,7 @@ PepXmlSaxHandler::startElement_mod_aminoacid_mass(QXmlAttributes attributes)
bool is_ok = true;
double mass = attributes.value("mass").toDouble();
unsigned int position = attributes.value("position").toUInt() - 1;
- const pappso::Aa &aa = _current_peptide_sp.get()->getConstAa(position);
+ const pappso::Aa aa(_current_peptide_sp.get()->getSequence()[position].toLatin1());
double mass_modif = mass - aa.getMass();
pappso::AaModificationP modif =
diff --git a/src/input/pepxmlsaxhandler.h b/src/input/pepxmlsaxhandler.h
index ed38bc289..40a44ecc0 100644
--- a/src/input/pepxmlsaxhandler.h
+++ b/src/input/pepxmlsaxhandler.h
@@ -76,6 +76,8 @@ class PepXmlSaxHandler : public QXmlDefaultHandler
bool startElement_interprophet_result(QXmlAttributes attributes);
bool startElement_search_score(QXmlAttributes attributes);
bool startElement_mod_aminoacid_mass(QXmlAttributes attributes);
+ bool startElement_modification_info(QXmlAttributes attributes);
+
bool endElement_search_hit();
bool endElement_modification_info();
@@ -100,6 +102,7 @@ class PepXmlSaxHandler : public QXmlDefaultHandler
QString _current_group_type;
QString _current_note_label;
QString _current_note_type;
+ QString _current_complete_msrun_file_path;
unsigned int _scan;
unsigned int _current_charge;
pappso::pappso_double _current_retention_time;
diff --git a/src/utils/types.h b/src/utils/types.h
index 9c7ed47c5..df9423e49 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -75,7 +75,11 @@ enum class PeptideEvidenceParam : std::int8_t
peptide_inter_prophet_probability = 5, ///< no PSI MS description
omssa_evalue = 6, ///< MS:1001328 "OMSSA E-value." [PSI:PI]
omssa_pvalue = 7, ///< MS:1001329 "OMSSA p-value." [PSI:PI]
-
+ msgfplus_raw = 8, ///< MS:1002049 "MS-GF raw score." [PSI:PI]
+ msgfplus_denovo = 9, ///< MS:1002050 "MS-GF de novo score." [PSI:PI]
+ msgfplus_energy = 10, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
+ msgfplus_SpecEValue = 11, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
+ msgfplus_EValue = 12, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
};
--
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