WriteSearchProtease() public méthode

public WriteSearchProtease ( Protease protease, int maxMissedClevages, bool semiDigested = false ) : void
protease CSMSL.Proteomics.Protease
maxMissedClevages int
semiDigested bool
Résultat void
PepXmlWriter Class Documentation
Exemple #1
0
        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.Trypsin);

                writer.StartSearchSummary("OMSSA", true, true);

                writer.WriteProteinDatabase("Resources/yeast_uniprot_120226.fasta");

                writer.WriteSearchProtease(Protease.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();
            }
        }
Exemple #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();
                    }

                }

            }
        }