From c25fa15b914a665e2212dca4cacea0fe64fdb457 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Tue, 12 Dec 2023 18:18:42 -0500 Subject: [PATCH] BiblioSpec pepXML check base_name parent path (#2809) * - fixed BiblioSpec pepXML reader to check for spectrum files in the base_name's parent path (if present) --- pwiz_tools/BiblioSpec/src/BuildParser.cpp | 23 +- pwiz_tools/BiblioSpec/src/PepXMLreader.cpp | 8 - pwiz_tools/BiblioSpec/tests/Jamfile.jam | 4 + ...parent-path-first-with-missing-file.pepXML | 202 +++ .../msfragger-check-parent-path-first.pepXML | 202 +++ .../Hela%20QC_PASEF_42_uncalibrated.mgf | 1416 +++++++++++++++++ .../msfragger-check-parent-path-first.check | 37 + 7 files changed, 1878 insertions(+), 14 deletions(-) create mode 100644 pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first-with-missing-file.pepXML create mode 100644 pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first.pepXML create mode 100644 pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first/Hela%20QC_PASEF_42_uncalibrated.mgf create mode 100644 pwiz_tools/BiblioSpec/tests/reference/msfragger-check-parent-path-first.check diff --git a/pwiz_tools/BiblioSpec/src/BuildParser.cpp b/pwiz_tools/BiblioSpec/src/BuildParser.cpp index 64215da522..520c99903b 100644 --- a/pwiz_tools/BiblioSpec/src/BuildParser.cpp +++ b/pwiz_tools/BiblioSpec/src/BuildParser.cpp @@ -92,15 +92,26 @@ void BuildParser::setSpecFileName( curSpecFileName_.clear(); - string fileroot = specfileroot; - Verbosity::debug("checking for basename: %s", fileroot); + auto localDirectories = directories; + bal::replace_all(specfileroot, "\\", "/"); // attempt to make Windows paths parseable on POSIX + + // if specfileroot has a parent path, try that directory first + bfs::path specfilepath(specfileroot); + if (specfilepath.has_parent_path() && bfs::exists(bfs::complete(specfilepath.parent_path(), filepath_))) + localDirectories.insert(localDirectories.begin(), specfilepath.parent_path().string()); + + string fileroot = specfilepath.filename().string(); + Verbosity::debug("checking for basename: %s", fileroot.c_str()); do { // try the location of the result file, then all dirs in the list - for(int i=-1; i<(int)directories.size(); i++) { + for(int i=-1; i<(int)localDirectories.size(); i++) { string path = filepath_.c_str(); if( i >= 0 ) { - path += directories.at(i); + if (bfs::path(localDirectories[i]).is_absolute()) + path = localDirectories[i]; + else + path += localDirectories[i]; } if (path.empty()) path = "."; @@ -151,7 +162,7 @@ void BuildParser::setSpecFileName( if( curSpecFileName_.empty() ) { string extString = fileNotFoundMessage(specfileroot, - extensions, directories); + extensions, localDirectories); throw BlibException(true, extString.c_str()); }// else we found a file and set the name @@ -223,7 +234,7 @@ string BuildParser::filesNotFoundMessage( messageString += "\n\nIn any of the following directories:\n" + bfs::canonical(deepestPath).make_preferred().string(); set parentPaths; for (const auto& dir : directories) - parentPaths.insert(bfs::canonical(deepestPath / dir).make_preferred().string()); + parentPaths.insert((bfs::path(dir).is_absolute() ? dir : bfs::canonical(deepestPath / dir)).make_preferred().string()); for (const auto& dir : boost::make_iterator_range(parentPaths.rbegin(), parentPaths.rend())) messageString += "\n" + dir; diff --git a/pwiz_tools/BiblioSpec/src/PepXMLreader.cpp b/pwiz_tools/BiblioSpec/src/PepXMLreader.cpp index d48916a335..3d0c9ecd78 100644 --- a/pwiz_tools/BiblioSpec/src/PepXMLreader.cpp +++ b/pwiz_tools/BiblioSpec/src/PepXMLreader.cpp @@ -146,14 +146,6 @@ void PepXMLreader::startElement(const XML_Char* name, const XML_Char** attr) } else if(isElement("msms_run_summary",name)) { fileroot_ = getRequiredAttrValue("base_name",attr); Verbosity::comment(V_DEBUG, "PepXML base_name is %s", fileroot_.c_str()); - // Because Mascot2XML uses the full path for the base_name, - // only the part beyond the last "\" or "/" is taken. - size_t slash = fileroot_.rfind('/'); - size_t bslash = fileroot_.rfind('\\'); - if (slash == string::npos || (bslash != string::npos && bslash > slash)) - slash = bslash; - if (slash != string::npos) - fileroot_.erase(0, slash + 1); // Check if this pepXML file is from Proteome Discoverer string rawType = getAttrValue("raw_data_type", attr); diff --git a/pwiz_tools/BiblioSpec/tests/Jamfile.jam b/pwiz_tools/BiblioSpec/tests/Jamfile.jam index 6779e76eaf..2c9fc6e7d2 100644 --- a/pwiz_tools/BiblioSpec/tests/Jamfile.jam +++ b/pwiz_tools/BiblioSpec/tests/Jamfile.jam @@ -183,10 +183,12 @@ rule blib-test-search ( name : args * : output-name : reference-names + : inputs if NT = $(.os) { .percent = "%%" ; + .slash = "\\" ; } else { .percent = "%" ; + .slash = "/" ; } # Add --unicode to optional arguments section to test that a format supports Unicode input paths @@ -242,6 +244,8 @@ blib-test-build msfragger-tims : -o : output/msfragger-tims.blib : msfragger-tim blib-test-build msfragger-thermo : -o : output/msfragger-thermo.blib : msfragger-thermo.check : $(TEST_INPUTS_PATH)/BSA_min_21.pepXML ; blib-test-build peptideprophet-msfragger-thermo-mzml : -o : output/peptideprophet-msfragger-thermo-mzml.blib : peptideprophet-msfragger-thermo-mzml.check : $(TEST_INPUTS_PATH)/peptideprophet-msfragger-thermo-mzml.pep.xml ; blib-test-build peptideprophet-msfragger-bruker-mgf : -o : output/peptideprophet-msfragger-bruker-mgf.blib : peptideprophet-msfragger-bruker-mgf.check : $(TEST_INPUTS_PATH)/peptideprophet-msfragger-bruker-mgf.pep.xml ; +blib-test-build-basic msfragger-check-parent-path-first : -o : $(TEST_INPUTS_PATH)/msfragger-check-parent-path-first.pepXML ; +blib-test-build-basic msfragger-check-parent-path-first-with-missing-file : -o -e@inputs$(.slash)msfragger-check-parent-path-first : $(TEST_INPUTS_PATH)/msfragger-check-parent-path-first-with-missing-file.pepXML ; # Test other xml formats (idpicker, xtandem) diff --git a/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first-with-missing-file.pepXML b/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first-with-missing-file.pepXML new file mode 100644 index 0000000000..7986d77066 --- /dev/null +++ b/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first-with-missing-file.pepXML @@ -0,0 +1,202 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first.pepXML b/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first.pepXML new file mode 100644 index 0000000000..f62fc42cd2 --- /dev/null +++ b/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first.pepXML @@ -0,0 +1,202 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first/Hela%20QC_PASEF_42_uncalibrated.mgf b/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first/Hela%20QC_PASEF_42_uncalibrated.mgf new file mode 100644 index 0000000000..8c968cdf26 --- /dev/null +++ b/pwiz_tools/BiblioSpec/tests/inputs/msfragger-check-parent-path-first/Hela%20QC_PASEF_42_uncalibrated.mgf @@ -0,0 +1,1416 @@ +BEGIN IONS 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/dev/null +++ b/pwiz_tools/BiblioSpec/tests/reference/msfragger-check-parent-path-first.check @@ -0,0 +1,37 @@ +libLSID numSpecs majorVersion minorVersion +urn:lsid:proteome.gs.washington.edu:spectral_library:bibliospec:redundant:msfragger-check-parent-path-first.blib 5 1 10 +id RefSpectraID position mass +1 1 7 57.0215 +2 1 15 57.0215 +3 1 18 57.0215 +4 2 5 57.0215 +5 3 13 57.0215 +id peptideSeq precursorMZ precursorCharge peptideModSeq prevAA nextAA copies numPeaks ionMobility collisionalCrossSectionSqA ionMobilityHighEnergyOffset ionMobilityType retentionTime startTime endTime totalIonCurrent moleculeName chemicalFormula precursorAdduct inchiKey otherKeys fileID SpecIDinFile score scoreType +1 NTAAMVCSLENRDECLMCGS 1159.978345 2 NTAAMVC[+57.0]SLENRDEC[+57.0]LMC[+57.0]GS - - 1 154 1.2009081 0.0 0.0 2 60.01123809 N/A N/A 875.10499799 N/A N/A N/A N/A N/A 1 Hela_QC_PASEF_Slot1-5_01_57_cutout_2min.1.1.2 0.000361 6 +2 EYTACELMNIYK 767.84817 2 EYTAC[+57.0]ELMNIYK - - 1 152 1.0267171 0.0 0.0 2 60.01123809 N/A N/A 2811.76187801 N/A N/A N/A N/A N/A 1 Hela_QC_PASEF_Slot1-5_01_57_cutout_2min.2.2.2 0.00169 6 +3 MLHFLTAVVGSTCDVK 593.28488 3 MLHFLTAVVGSTC[+57.0]DVK - - 1 96 0.85685045 0.0 0.0 2 60.01123809 N/A N/A 3102.44897747 N/A N/A N/A N/A N/A 1 Hela_QC_PASEF_Slot1-5_01_57_cutout_2min.3.3.3 0.009354 6 +4 YQLEIPENFTTR 755.87887 2 YQLEIPENFTTR - - 1 150 1.0246093 0.0 0.0 2 60.01123809 N/A N/A 1057.74871420 N/A N/A N/A N/A N/A 1 Hela_QC_PASEF_Slot1-5_01_57_cutout_2min.7.7.2 4.377e-05 6 +5 LQQTQNQVDEVVDIMR 958.489305 2 LQQTQNQVDEVVDIMR - - 1 150 1.1342232 0.0 0.0 2 60.01123809 N/A N/A 1255.91934108 N/A N/A N/A N/A N/A 1 Hela_QC_PASEF_Slot1-5_01_57_cutout_2min.8.8.2 8.699e-07 6 +id fileName idFileName cutoffScore +1 /BiblioSpec/tests/inputs/msfragger-check-parent-path-first/Hela%20QC_PASEF_42_uncalibrated.mgf /BiblioSpec/tests/inputs/msfragger-check-parent-path-first.pepXML -1.0 +id scoreType probabilityType +0 UNKNOWN NOT_A_PROBABILITY_VALUE +1 PERCOLATOR QVALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +2 PEPTIDE PROPHET SOMETHING PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT +3 SPECTRUM MILL NOT_A_PROBABILITY_VALUE +4 IDPICKER FDR PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +5 MASCOT IONS SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +6 TANDEM EXPECTATION VALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +7 PROTEIN PILOT CONFIDENCE PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT +8 SCAFFOLD SOMETHING PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT +9 WATERS MSE PEPTIDE SCORE NOT_A_PROBABILITY_VALUE +10 OMSSA EXPECTATION SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +11 PROTEIN PROSPECTOR EXPECTATION SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +12 SEQUEST XCORR PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +13 MAXQUANT SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +14 MORPHEUS SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +15 MSGF+ SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +16 PEAKS CONFIDENCE SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +17 BYONIC SCORE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT +18 PEPTIDE SHAKER CONFIDENCE PROBABILITY_THAT_IDENTIFICATION_IS_CORRECT +19 GENERIC Q-VALUE PROBABILITY_THAT_IDENTIFICATION_IS_INCORRECT