public static void WritePepXml()
{
string filePath = Path.Combine(Examples.BASE_DIRECTORY, "example.pepXML");
Console.WriteLine("Writting to " + filePath);
using (PepXmlWriter writer = new PepXmlWriter(filePath))
{
writer.WriteSampleProtease(Protease.GetProtease("Trypsin"));
writer.StartSearchSummary("OMSSA", true, true);
writer.WriteProteinDatabase("Resources/yeast_uniprot_120226.fasta");
writer.WriteSearchProtease(Protease.GetProtease("Trypsin"), 3);
writer.WriteModification(ModificationDictionary.GetModification("Acetyl"), ModificationSites.K | ModificationSites.NPep);
writer.WriteModification(ModificationDictionary.GetModification("CAM"), ModificationSites.C);
writer.WriteModification(ModificationDictionary.GetModification("Phospho"), ModificationSites.S | ModificationSites.T | ModificationSites.Y, false);
writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);
writer.StartSpectrum(15, 1.234, 523.4324, 3);
PeptideSpectralMatch psm = new PeptideSpectralMatch(PeptideSpectralMatchScoreType.OmssaEvalue);
psm.Score = 1.5e-5;
Protein protein = new Protein("", "Test Protein");
psm.Peptide = new Peptide("DEREK", protein);
psm.Charge = 3;
writer.WritePSM(psm);
writer.EndSpectrum();
}
}
public override IEnumerable <string> Process(string filename)
{
var parser = new OutParser();
string resultFilename;
if (null == this.targetDir)
{
resultFilename = FileUtils.ChangeExtension(filename, ".xml");
}
else
{
resultFilename = targetDir + "/" + FileUtils.ChangeExtension(new FileInfo(filename).Name, ".xml");
}
using (PepXmlWriter writer = new PepXmlWriter("out"))
{
writer.Open(resultFilename);
writer.OpenMsmsRunSummary(filename);
SequestParam sp = new SequestParamFile().ReadFromFile(filename);
writer.WriteSequestParam(sp);
using (var reader = new OutsReader(filename))
{
int totalCount = reader.FileCount;
Progress.SetRange(0, totalCount);
int currentCount = 0;
while (reader.HasNext)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
List <string> contents = reader.NextContent();
IIdentifiedSpectrum sph = parser.Parse(contents);
if (sph == null)
{
continue;
}
writer.WriteSequestPeptideHit(sph);
currentCount++;
Progress.SetPosition(currentCount);
}
Progress.SetPosition(totalCount);
}
writer.CloseMsmsRunSummary();
}
return(new[] { resultFilename });
}
public void Convert(string omssaCSV, MSDataFile dataFile)
{
string filePath = Path.ChangeExtension(omssaCSV, ".pepxml");
using (PepXmlWriter writer = new PepXmlWriter(filePath))
{
writer.WriteSampleProtease(Protease);
writer.StartSearchSummary("OMSSA", true, true);
writer.WriteProteinDatabase(FastaDatabaseFile);
writer.WriteSearchProtease(Protease, MissedClevages);
foreach (int modNumber in FixedMods)
{
OmssaModification mod;
if (OmssaModification.TryGetModification(modNumber, out mod))
{
writer.WriteModification(mod, mod.Sites, true);
}
}
foreach (int modNumber in VariableMods)
{
OmssaModification mod;
if (OmssaModification.TryGetModification(modNumber, out mod))
{
writer.WriteModification(mod, mod.Sites, false);
}
}
writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);
using (OmssaCsvPsmReader reader = new OmssaCsvPsmReader(omssaCSV, UserModFile))
{
reader.AddMSDataFile(dataFile);
reader.LoadProteins(FastaDatabaseFile);
foreach (PeptideSpectralMatch psm in reader.ReadNextPsm())
{
writer.StartSpectrum(psm.SpectrumNumber, psm.Spectrum.RetentionTime, psm.Spectrum.PrecursorMz, psm.Spectrum.PrecursorCharge);
writer.WritePSM(psm);
writer.EndSpectrum();
}
}
}
}
