public static void Start()
{
Console.WriteLine("**Start OMSSA Reader**");
long startMem = System.Environment.WorkingSet;
Stopwatch watch = new Stopwatch();
watch.Start();
List<PeptideSpectralMatch> psms;
using (PsmReader reader = new OmssaCsvPsmReader("Resources/Omssa_yeast.csv"))
{
reader.LoadProteins("Resources/yeast_uniprot_120226.fasta");
reader.AddFixedModification(ModificationDictionary.GetModification("CAM"));
reader.AddVariableModification(ModificationDictionary.GetModification("Oxidation"),"oxdiation of M");
psms = reader.ReadNextPsm().OrderBy(psm => psm.Score).ToList();
}
watch.Stop();
Console.WriteLine("{0:N0} psms were read in", psms.Count);
Console.WriteLine("Time elapsed: {0}", watch.Elapsed);
Console.WriteLine("Memory used: {0:N0} MB", (System.Environment.WorkingSet - startMem) / (1024 * 1024));
Console.WriteLine("**End OMSSA Reader**");
}
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();
}
}
}
}