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[proteowizard-commit] SF.net SVN: proteowizard:[1961] trunk/pwiz/pwiz/data/mziddata
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From: <br...@us...> - 2010-04-22 22:25:18
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Revision: 1961
http://proteowizard.svn.sourceforge.net/proteowizard/?rev=1961&view=rev
Author: broter
Date: 2010-04-22 22:25:12 +0000 (Thu, 22 Apr 2010)
Log Message:
-----------
Correct CV assignments for Pep2Mzident
Modified Paths:
--------------
trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp
trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.hpp
Modified: trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp
===================================================================
--- trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp 2010-04-21 23:07:58 UTC (rev 1960)
+++ trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp 2010-04-22 22:25:12 UTC (rev 1961)
@@ -66,6 +66,8 @@
size_t pdp;
};
+namespace {
+
struct sequence_p
{
const string seq;
@@ -151,7 +153,6 @@
}
};
-
AnalysisSoftwarePtr findSoftware(const vector<AnalysisSoftwarePtr>& software,
CVID cvid)
{
@@ -168,17 +169,21 @@
CVParam guessThreshold(const vector<AnalysisSoftwarePtr>& software)
{
- static const CVID cvids[] = {MS_Mascot, MS_Sequest,
- MS_Phenyx, CVID_Unknown};
+ static const CVID cvids[][2] = {
+ {MS_Mascot, MS_mascot_score},
+ {MS_Sequest, MS_sequest_probability},
+ {MS_Phenyx, MS_Phenyx_Score},
+ {CVID_Unknown, CVID_Unknown}
+ };
CVParam cvparam;
- for (size_t idx = 0; cvids[idx] != CVID_Unknown; idx++)
+ for (size_t idx = 0; cvids[idx][0] != CVID_Unknown; idx++)
{
- AnalysisSoftwarePtr as = findSoftware(software, cvids[idx]);
+ AnalysisSoftwarePtr as = findSoftware(software, cvids[idx][0]);
if (!as.get())
{
- cvparam = CVParam(cvids[idx], "0.5");
+ cvparam = CVParam(cvids[idx][1], "0.5");
break;
}
}
@@ -186,7 +191,7 @@
// TODO put a reasonable default here and a reasonable way to set it.
if (cvparam.cvid == CVID_Unknown)
{
- cvparam.cvid = MS_Mascot;
+ cvparam.cvid = MS_mascot_score;
cvparam.value = "0.05";
}
@@ -214,6 +219,8 @@
return asp;
}
+} // namespace
+
//
// Pep2MzIdent
//
@@ -307,7 +314,7 @@
SpectraDataPtr sd(new SpectraData(
"SD_"+lexical_cast<string>(indices->sd++)));
- // TODO verify that both of these valules are legit.
+ // TODO verify that both of these cvid values are legit.
sd->location = msmsRunSummary.base_name;
if (iequals(msmsRunSummary.raw_data, ".mzml"))
@@ -343,10 +350,17 @@
// Cross fingers and pray that the name enzyme matches a cv name.
// TODO create a more flexable conversion.
- enzyme->enzymeName.set(getCVID(sampleEnzyme.name));
- enzyme->enzymeName.userParams.
- push_back(UserParam("description", sampleEnzyme.description));
+ CVID seCVID = getCVID(sampleEnzyme.name);
+ if (seCVID != CVID_Unknown)
+ enzyme->enzymeName.set(seCVID);
+ else
+ enzyme->enzymeName.userParams.
+ push_back(UserParam("name", sampleEnzyme.name));
+ if (sampleEnzyme.description.size()>0)
+ enzyme->enzymeName.userParams.
+ push_back(UserParam("description", sampleEnzyme.description));
+
if (sampleEnzyme.fidelity == "Semispecific")
enzyme->semiSpecific = true;
else if (sampleEnzyme.fidelity == "Nonspecific")
@@ -422,16 +436,35 @@
// push SourceFilePtr onto sourceFile
// in Inputs in DataCollection
+ //
+ // Removed because sourcefiles are for intermediate file formats,
+ // not the source of the data.
+
+ /*
SourceFilePtr sourceFile(new SourceFile());
sourceFile->id = "SF_1";
sourceFile->location = summary->baseName;
sourceFile->fileFormat.set(MS_ISB_mzXML_file);
result->dataCollection.inputs.sourceFile.push_back(sourceFile);
-
+ */
+
AnalysisSoftwarePtr as(new AnalysisSoftware());
as->id = "AS";
- as->softwareName.set(getCVID(summary->searchEngine));
+ CVID cvid = getCVID(summary->searchEngine);
+ if (cvid != CVID_Unknown)
+ as->softwareName.set(cvid);
+ else
+ {
+ cvid = mapToNearestSoftware(summary->searchEngine);
+ if (cvid == CVID_Unknown)
+ throw invalid_argument(("Unknown search software name "+
+ summary->searchEngine).c_str());
+
+ as->softwareName.set(cvid);
+ as->softwareName.userParams.push_back(
+ UserParam("search_engine full name", summary->searchEngine));
+ }
result->analysisSoftwareList.push_back(as);
// handle precursorMassType/fragmentMassType
@@ -461,10 +494,11 @@
{
fs::path localPath(summary->searchDatabase.localPath);
searchDatabase->DatabaseName.userParams.push_back(
- UserParam(localPath.filename()));
+ UserParam("local_path", localPath.filename()));
}
- // TODO make this more elegant
+ // TODO this goes in the analysis software section, I think.
+ /*
if (iends_with(summary->baseName, ".dat") &&
iequals(summary->searchEngine, "mascot"))
searchDatabase->fileFormat.set(MS_Mascot_DAT_file);
@@ -472,7 +506,8 @@
searchDatabase->fileFormat.set(MS_Sequest_out_file);
else if (iequals(summary->searchEngine, "xtandem"))
searchDatabase->fileFormat.set(MS_xtandem_xml_file);
-
+ */
+
mzid->dataCollection.inputs.searchDatabase.push_back(searchDatabase);
// Save for later.
@@ -480,6 +515,23 @@
}
+CVID Pep2MzIdent::mapToNearestSoftware(const string& softwareName)
+{
+ CVID cvid = getCVID(softwareName);
+
+ if (cvid == CVID_Unknown)
+ {
+ if (istarts_with(softwareName, "X! Tandem") ||
+ istarts_with(softwareName, "X!Tandem"))
+ {
+ cvid = MS_xtandem;
+ }
+ }
+
+ return cvid;
+}
+
+
void Pep2MzIdent::addModifications(
const vector<AminoAcidModification>& aminoAcidModifications,
PeptidePtr peptide, MzIdentMLPtr result)
@@ -591,28 +643,50 @@
// TODO find out if this is right.
sii->chargeState = query->assumedCharge;
- // TODO get search_score
+ // TODO get search_score(s)
+ for (vector<SearchScorePtr>::const_iterator ssit=(*shit)->searchScore.begin();
+ ssit != (*shit)->searchScore.end(); ssit++)
+ {
+ CVParam cvp;
+ cvp = getParamForSearchScore(*ssit);
+ if (cvp.cvid != CVID_Unknown)
+ sii->paramGroup.set(cvp.cvid, cvp.value);
+ else
+ sii->paramGroup.userParams.
+ push_back(UserParam((*ssit)->name, (*ssit)->value));
+
+ }
+ /*
CVParam cvp = translateSearchScore("ionscore",
(*shit)->searchScore);
+ std::cerr << "ionscore=" << cvp.cvid << "\n";
if (cvp.cvid != CVID_Unknown)
sii->paramGroup.set(cvp.cvid, cvp.value);
+
cvp = translateSearchScore("expect", (*shit)->searchScore);
+ std::cerr << "expect=" << cvp.cvid << "\n";
if (cvp.cvid != CVID_Unknown)
sii->paramGroup.set(cvp.cvid, cvp.value);
+
sii->peptideEvidence.push_back(pepEv);
// TODO handle precursorNeutralMass
// TODO handle index/retentionTimeSec fields
-
+
+ */
SpectrumIdentificationResultPtr sirp(
new SpectrumIdentificationResult());
sirp->id = "SIR_"+lexical_cast<string>(indices->sir++);
+ /*
cvp = translateSearchScore("identityscore", (*shit)->searchScore);
- sirp->paramGroup.set(cvp.cvid, cvp.value);
-
+ std::cerr << "identityscore=" << cvp.cvid << "\n";
+ if (cvp.cvid != CVID_Unknown)
+ sirp->paramGroup.set(cvp.cvid, cvp.value);
+ */
+
sirp->spectrumID = query->spectrum;
sirp->spectrumIdentificationItem.push_back(sii);
if (mzid->dataCollection.inputs.spectraData.size()>0)
Modified: trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.hpp
===================================================================
--- trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.hpp 2010-04-21 23:07:58 UTC (rev 1960)
+++ trunk/pwiz/pwiz/data/mziddata/Pep2MzIdent.hpp 2010-04-22 22:25:12 UTC (rev 1961)
@@ -130,6 +130,10 @@
// found in pepXML.
CVID getCVID(const std::string& name);
+ /// Maps known odd software names to the most applicable CVID.
+ /// TODO make this loadable from a file.
+ CVID mapToNearestSoftware(const std::string& softwareName);
+
/// Translates the search_score with the given name into a CVParam
/// object using getParamForSearchScore.
CVParam translateSearchScore(const std::string& name,
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