Beispiel #1
0
        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**");
        }
Beispiel #2
0
        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();
                    }

                }

            }
        }