public override IEnumerable <string> Process(string filename)
{
string msLevelFilename = filename + ".msLevel";
using (IRawFile rawFile = new RawFileImpl(filename))
{
using (var sw = new StreamWriter(msLevelFilename))
{
int firstScan = rawFile.GetFirstSpectrumNumber();
int lastScan = rawFile.GetLastSpectrumNumber();
Progress.SetRange(rawFile.GetFirstSpectrumNumber(), rawFile.GetLastSpectrumNumber());
Progress.SetMessage("Processing " + filename + "...");
sw.WriteLine("Scan\tMsLevel");
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
sw.WriteLine(scan + "\t" + rawFile.GetMsLevel(scan));
Progress.SetPosition(scan);
}
Progress.SetPosition(lastScan);
Progress.SetMessage("Processing " + filename + " finished.");
}
}
return(new[] { msLevelFilename });
}
public void TestSetup()
{
this.fullRawFile = new RawFileImpl();
this.fullRawFile.Open(@"../../../data/Standard_Protein_FT2_Lock_Re5.RAW");
this.ms2OnlyRawFile = new RawFileImpl();
this.ms2OnlyRawFile.Open(@"../../../data/Full_scan_apiginin_ms2.RAW");
}
public Raw2MzXmlMultipleProcessor(RawFileImpl rawFile, bool fullMsOnly, bool doCentroid, string targetDirectoryName,
string dataProcessingSoftware, string dataProcessingSoftwareVersion,
Dictionary <string, string> dataProcessingOperations)
{
this.processor = new Raw2MzXmlProcessor(rawFile, fullMsOnly, doCentroid, targetDirectoryName,
dataProcessingSoftware, dataProcessingSoftwareVersion,
dataProcessingOperations);
}
public override IEnumerable <string> Process(string fileName)
{
string resultFilename = fileName + ".tic";
if (ignoreWhenResultExist && File.Exists(resultFilename))
{
return(new string[] { resultFilename });
}
using (IRawFile reader = new RawFileImpl(fileName))
{
Progress.SetMessage(MyConvert.Format("Processing {0} ...", new FileInfo(fileName).Name));
using (StreamWriter sw = new StreamWriter(resultFilename))
{
sw.WriteLine("Scan\tMode\tPrecursor\tTIC");
int firstScan = reader.GetFirstSpectrumNumber();
int lastScan = reader.GetLastSpectrumNumber();
Progress.SetRange(firstScan, lastScan);
for (int i = firstScan; i <= lastScan; i++)
{
if (Progress.IsCancellationPending())
{
sw.Close();
File.Delete(resultFilename);
throw new UserTerminatedException();
}
if (1 == reader.GetMsLevel(i))
{
continue;
}
PeakList <Peak> pkl = reader.GetPeakList(i);
Peak precursor = reader.GetPrecursorPeak(i);
double tic = (from p in pkl
select p.Intensity).Sum();
string mode = reader.GetScanMode(i);
sw.WriteLine("{0}\t{1}\t{2:0.0000}\t{3:0.0}", i, mode.ToUpper(), precursor.Mz, tic);
Progress.SetPosition(i);
}
Progress.End();
}
Progress.SetMessage(MyConvert.Format("Processing {0} finished.", new FileInfo(fileName).Name));
}
return(new string[] { resultFilename });
}
public MzXmlFormat(RawFileImpl rawFile, bool fullMsOnly, bool doCentroid, string targetDirectoryName,
string dataProcessingSoftware, string dataProcessingSoftwareVersion,
Dictionary <string, string> dataProcessingOperations)
{
this.rawFile = rawFile;
this.fullMsOnly = fullMsOnly;
this.doCentroid = doCentroid;
if (null == targetDirectoryName || 0 == targetDirectoryName.Length)
{
this.saveToSourceDirectory = true;
}
else
{
this.saveToSourceDirectory = false;
this.targetDirectory = new DirectoryInfo(targetDirectoryName);
if (!this.targetDirectory.Exists)
{
this.targetDirectory.Create();
}
}
this.dataProcessingSoftware = dataProcessingSoftware;
this.dataProcessingSoftwareVersion = dataProcessingSoftwareVersion;
this.dataProcessingOperations = dataProcessingOperations;
}
public override IEnumerable <string> Process(string fileName)
{
SequestResultTextFormat format = new SequestResultTextFormat();
IIdentifiedResult sr = format.ReadFromFile(fileName);
Dictionary <string, HashSet <IIdentifiedSpectrum> > peptideMap = sr.GetExperimentalPeptideMap();
Dictionary <IIdentifiedSpectrum, int> confused = new Dictionary <IIdentifiedSpectrum, int>();
List <IIdentifiedSpectrum> wrongMs2 = new List <IIdentifiedSpectrum>();
List <IIdentifiedSpectrum> wrongMs3 = new List <IIdentifiedSpectrum>();
int pepcount = 0;
List <string> exps = new List <string>(peptideMap.Keys);
exps.Sort();
foreach (string exp in exps)
{
Console.Out.WriteLine(exp);
HashSet <IIdentifiedSpectrum> peps = peptideMap[exp];
pepcount += peps.Count;
using (IRawFile rawFile = new RawFileImpl(expRawMap[exp]))
{
foreach (IIdentifiedSpectrum pep in peps)
{
int msLevel = rawFile.GetMsLevel(pep.Query.FileScan.FirstScan);
bool bMs2 = ms2seqPattern.Match(pep.Sequence).Success;
bool bMs3 = ms3seqPattern.Match(pep.Sequence).Success;
if (bMs2 && bMs3)
{
confused[pep] = msLevel;
continue;
}
if (bMs3)
{
if (msLevel != 3)
{
wrongMs3.Add(pep);
continue;
}
}
else if (bMs2)
{
if (msLevel != 2)
{
wrongMs2.Add(pep);
continue;
}
}
}
}
}
string incorrectFilename = FileUtils.ChangeExtension(fileName, ".incorrect.peptides.txt");
using (StreamWriter sw = new StreamWriter(incorrectFilename))
{
sw.WriteLine("Type\tFilename\tSequence\tScore\tDeltaScore\tmsLevel");
foreach (IIdentifiedSpectrum pep in confused.Keys)
{
sw.WriteLine(MyConvert.Format("Confused\t{0}\t{1}\t{2:0.00}\t{3:0.00}\t{4}",
pep.Query.FileScan.LongFileName,
pep.Sequence,
pep.Score,
pep.DeltaScore,
confused[pep]));
}
foreach (IIdentifiedSpectrum pep in wrongMs2)
{
sw.WriteLine(MyConvert.Format("WrongMS2\t{0}\t{1}\t{2:0.00}\t{3:0.00}\t3",
pep.Query.FileScan.LongFileName,
pep.Sequence,
pep.Score,
pep.DeltaScore));
}
foreach (IIdentifiedSpectrum pep in wrongMs3)
{
sw.WriteLine(MyConvert.Format("WrongMS3\t{0}\t{1}\t{2:0.00}\t{3:0.00}\t2",
pep.Query.FileScan.LongFileName,
pep.Sequence,
pep.Score,
pep.DeltaScore));
}
sw.WriteLine();
sw.WriteLine("Total\t" + pepcount);
sw.WriteLine("Confused\t" + confused.Count);
sw.WriteLine("WrongMs2\t" + wrongMs2.Count);
sw.WriteLine("WrongMs3\t" + wrongMs3.Count);
}
List <string> incorrectDtafilenames = new List <string>();
foreach (IIdentifiedSpectrum pep in confused.Keys)
{
incorrectDtafilenames.Add(pep.Query.FileScan.LongFileName);
}
foreach (IIdentifiedSpectrum pep in wrongMs2)
{
incorrectDtafilenames.Add(pep.Query.FileScan.LongFileName);
}
foreach (IIdentifiedSpectrum pep in wrongMs3)
{
incorrectDtafilenames.Add(pep.Query.FileScan.LongFileName);
}
for (int i = sr.Count - 1; i >= 0; i--)
{
foreach (IIdentifiedProtein sp in sr[i])
{
for (int j = sp.Peptides.Count - 1; j >= 0; j--)
{
if (incorrectDtafilenames.Contains(sp.Peptides[j].Spectrum.Query.FileScan.Experimental))
{
sp.Peptides.RemoveAt(j);
}
}
}
if (sr[i][0].Peptides.Count == 0)
{
sr.RemoveAt(i);
}
}
string correctFilename = FileUtils.ChangeExtension(fileName, ".correct.txt");
//BuildSummaryResultUtils.Write(correctFilename, cr);
return(new[] { correctFilename });
}
