From 01a1fa8e339bdbac0a109e2d35d6f136a87522f9 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 9 Jul 2018 12:05:40 +0200
Subject: [PATCH] mzidentml : circumvent buggy spectrum id
---
src/input/identificationpwizreader.cpp | 65 ++++++++++++++++++++++----
1 file changed, 56 insertions(+), 9 deletions(-)
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 4cfb8bfe..45492efd 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -35,11 +35,13 @@
#include <QFileInfo>
#include <QDir>
#include <QString>
+#include <QRegularExpression>
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/exception/exceptionoutofrange.h>
#include <pwiz/data/common/ParamTypes.hpp>
#include <pwiz/data/identdata/IdentData.hpp>
+#include <pwiz/data/msdata/MSData.hpp>
#include <pwiz/data/identdata/IdentDataFile.hpp>
#include "../core/peptidematch.h"
#include <locale>
@@ -138,11 +140,11 @@ IdentificationPwizReader::getIdentificationEngine() const
</AnalysisSoftware>
</AnalysisSoftwareList>
*/
- IdentificationEngine identification_engine = IdentificationEngine::peptider;
+ IdentificationEngine identification_engine = IdentificationEngine::unknown;
for(pwiz::identdata::AnalysisSoftwarePtr software_ptr :
_pwiz_ident_data_file->analysisSoftwareList)
{
- return getIdentificationEngine(software_ptr);
+ identification_engine = getIdentificationEngine(software_ptr);
}
return identification_engine;
}
@@ -166,9 +168,17 @@ IdentificationPwizReader::getIdentificationEngine(const QString &xml_id) const
{
if(software_ptr.get()->id == xml_id.toStdString())
{
- return getIdentificationEngine(software_ptr);
+ identification_engine = getIdentificationEngine(software_ptr);
}
}
+
+ /*
+ throw pappso::PappsoException(
+ QObject::tr("Analysis software (%1 %2) not known to XTPcpp")
+ .arg(analysis_software_p->id.c_str())
+ .arg(analysis_software_p->name.c_str()));
+ */
+
return identification_engine;
}
@@ -192,10 +202,7 @@ IdentificationPwizReader::getIdentificationEngine(
}
else
{
- throw pappso::PappsoException(
- QObject::tr("Analysis software (%1 %2) not known to XTPcpp")
- .arg(analysis_software_p->id.c_str())
- .arg(analysis_software_p->name.c_str()));
+ return IdentificationEngine::unknown;
}
return identification_engine;
@@ -364,8 +371,48 @@ IdentificationPwizReader::read(
}
else
{
- throw pappso::PappsoException(
- QObject::tr("Scan number not found"));
+ // spectrumID="20170616_test_digestion_liquide_2_2_1_1H4.mzXML
+ // scan 2271 (charge 2)"
+ QRegularExpression re("^.* scan (\\d+) .*$");
+ QRegularExpressionMatch match =
+ re.match(spectrum_ptr.get()->spectrumID.c_str());
+ if(match.hasMatch())
+ {
+ // this is a bad hack to circumvent buggy spectrum id...
+ scan = match.captured(1).toULong();
+ }
+ else
+ {
+ // last try : regular proteowizard spectrum id
+ try
+ {
+ scan =
+ QString(pwiz::msdata::id::value(
+ spectrum_ptr.get()->spectrumID, "scan")
+ .c_str())
+ .toULong();
+ }
+ catch(runtime_error &pwiz_error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("Pwiz runtime error :\n%1\n parsing "
+ "spectrum ID :\n%2")
+ .arg(pwiz_error.what())
+ .arg(spectrum_ptr.get()->spectrumID.c_str()));
+ }
+ }
+ /* QString(pwiz::msdata::id::translateNativeIDToScanNumber(
+ pwiz::cv::CVID::MS_mzIdentML_format,
+ spectrum_ptr.get()->spectrumID)
+ .c_str())
+ .toULong();*/
+ if(scan == 0)
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Failure parsing spectrumID %1 to find scan number")
+ .arg(spectrum_ptr.get()->spectrumID.c_str()));
+ }
}
//<cvParam accession="MS:1001115" cvRef="PSI-MS" value="4925"
// name="scan number(s)"/>
--
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