diff --git a/CMakeLists.txt b/CMakeLists.txt
index e7e0d57ec4a426e53c36f8b55929f7229099de2e..477412052e10a64c2b9ba6f9b8fb0e2e75132294 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,7 +41,7 @@ SET(SOFTWARE_NAME "XTPcpp")
SET(XTPCPP_VERSION_MAJOR "0")
SET(XTPCPP_VERSION_MINOR "1")
-SET(XTPCPP_VERSION_PATCH "17")
+SET(XTPCPP_VERSION_PATCH "18")
SET(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}")
# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
diff --git a/debian/changelog b/debian/changelog
index 117859fb62b43b134d3437df03ba00eca1ac54af..0d790e1aba003cd0a703b8e7fae67b28b79b17cf 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+xtpcpp (0.1.18-1) stretch; urgency=medium
+
+ * MS run and identification statistics
+
+ -- Olivier Langella <olivier.langella@u-psud.fr> Tue, 26 Sep 2017 10:07:10 +0200
+
xtpcpp (0.1.17-2) stretch; urgency=medium
* fix desktop file
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index af74978257dd3ec2664ddf549e3f92f8a5533152..a435cd3596971e549534e16713203bed078b71b2 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -78,6 +78,20 @@ void SampleSheet::writeHeaders() {
_p_writer->writeCell("Total unique assigned");
+ if (_msrun_statistics) {
+ _p_writer->setCellAnnotation("total number of scans during the MS run (from mz file)");
+ _p_writer->writeCell("Total scans");
+
+ _p_writer->setCellAnnotation("total number of MS level 1 during the MS run (from mz file)");
+ _p_writer->writeCell("Total MS1");
+
+ _p_writer->setCellAnnotation("total number of MS level 2 during the MS run (from mz file)");
+ _p_writer->writeCell("Total MS2");
+
+ _p_writer->setCellAnnotation("total number of MS level 3 during the MS run (from mz file)");
+ _p_writer->writeCell("Total MS3");
+
+ }
/*
total_peptide_used=3,///< total number of peptides generated and used in identification
@@ -93,7 +107,7 @@ void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ide
if (_msrun_statistics) {
SpectrumStore::checkMsRunStatistics(msrun_sp);
}
-
+
_p_writer->writeCell(msrun_sp.get()->getXmlId());
_p_writer->writeCell(msrun_sp.get()->getSampleName());
_p_writer->writeCell(msrun_sp.get()->getFilename());
@@ -140,7 +154,32 @@ void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ide
} else {
_p_writer->writeCell(var_sample.toInt());
}
-
-
+
+ if (_msrun_statistics) {
+ var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
+ if (var_sample.isNull()) {
+ _p_writer->writeEmptyCell();
+ } else {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms1);
+ if (var_sample.isNull()) {
+ _p_writer->writeEmptyCell();
+ } else {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms2);
+ if (var_sample.isNull()) {
+ _p_writer->writeEmptyCell();
+ } else {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ var_sample = msrun_sp.get()->getMsRunStatistics(MsRunStatistics::total_spectra_ms3);
+ if (var_sample.isNull()) {
+ _p_writer->writeEmptyCell();
+ } else {
+ _p_writer->writeCell(var_sample.toInt());
+ }
+ }
}
diff --git a/src/output/ods/samplesheet.h b/src/output/ods/samplesheet.h
index 9c1fc7c435ed2e77c014d4aa51de3db333b8866d..345d1629e356d9b77134489f4fcc51c71dd846a9 100644
--- a/src/output/ods/samplesheet.h
+++ b/src/output/ods/samplesheet.h
@@ -46,7 +46,7 @@ private :
OdsExport * _p_ods_export;
const Project * _p_project;
CalcWriterInterface * _p_writer;
- bool _msrun_statistics = false;
+ bool _msrun_statistics = true;
};
#endif // SAMPLESHEET_H
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index 67c8579ceac160f43115a5d3cf6e8780e3ebf930..7b9f599774262ff8cdf8d32807ae1ef8aa4d1dbe 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -133,17 +133,17 @@ pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::M
try {
simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(spectrum_index, getBinaryData);
} catch (std::runtime_error & error) {
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile error " << error.what() << " " << typeid(error).name();
+ qDebug() << "getQualifiedSpectrumFromPwizMSDataFile error " << error.what() << " " << typeid(error).name();
throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file std::runtime_error :\n%2").arg(scan_num).arg(error.what()));
- }
+ }
catch (std::exception & error) {
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile error " << error.what() << " " << typeid(error).name();
+ qDebug() << "getQualifiedSpectrumFromPwizMSDataFile error " << error.what() << " " << typeid(error).name();
throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file :\n%2").arg(scan_num).arg(error.what()));
- }
+ }
if (simple_spectrum_pwiz.get() == nullptr) {
throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file : null pointer").arg(scan_num));
}
-
+
qDebug() << "getQualifiedSpectrumFromPwizMSDataFile precursors.size() " << simple_spectrum_pwiz.get()->precursors.size();
if (simple_spectrum_pwiz.get()->precursors.size() > 0) {
pwiz::msdata::Precursor & precursor = *(simple_spectrum_pwiz.get()->precursors.begin());
@@ -173,8 +173,8 @@ pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::M
}
}
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile msLevel" ;
- unsigned int msLevel(QString(simple_spectrum_pwiz->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
+ qDebug() << "getQualifiedSpectrumFromPwizMSDataFile msLevel" ;
+ unsigned int msLevel(QString(simple_spectrum_pwiz->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
pappso_double retentionTime = QString(simple_spectrum_pwiz->scanList.scans[0].cvParam(pwiz::msdata::MS_scan_start_time).value.c_str()).toDouble();
qspectrum.setRtInSeconds(retentionTime);
@@ -263,7 +263,21 @@ void SpectrumStore::checkMsRunStatistics(MsRunSp msrun) {
if (msrun_var.isNull()) {
try {
pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
- msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) p_msdatafile->run.spectrumListPtr.get()->size());
+ const pwiz::msdata::SpectrumList * p_spectrum_list = p_msdatafile->run.spectrumListPtr.get();
+ std::size_t spectrum_list_size = p_spectrum_list->size();
+ msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
+
+ unsigned int count_mslevel[50] = {0};
+ for (std::size_t i=0; i < spectrum_list_size; i++) {
+ pwiz::msdata::SpectrumPtr spectrum = p_spectrum_list->spectrum(i, false);
+ unsigned int msLevel(QString(spectrum->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
+ count_mslevel[msLevel]++;
+ }
+
+ msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
+ msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra_ms1, (unsigned int) count_mslevel[1]);
+ msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra_ms2, (unsigned int) count_mslevel[2]);
+ msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra_ms3, (unsigned int) count_mslevel[3]);
}
catch (pappso::ExceptionNotFound& error) {
//no file found, no statistics
@@ -297,7 +311,7 @@ pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(MsRunSp msrun) {
pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num) {
pappso::QualifiedSpectrum spectrum;
pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
-
+
if (p_msdatafile == nullptr) {
return spectrum.getOriginalSpectrumSp();
}