CSMSL.IO.PepXML.PepXmlWriter.WriteProteinDatabase C# (CSharp) Метод

        public void WriteProteinDatabase(string fastaFilePath, string name = "", string releaseDate = "")
        {
            if (CurrentStage != Stage.SearchSummary)
                throw new ArgumentException("You must be in the Search Summary stage to write protein databases");

            _writer.WriteStartElement("search_database");
            _writer.WriteAttributeString("seq_type", "AA");
            _writer.WriteAttributeString("local_path", fastaFilePath);

            name = (string.IsNullOrEmpty(name)) ? Path.GetFileNameWithoutExtension(fastaFilePath) : name;
            _writer.WriteAttributeString("database_name", name);

            if (!string.IsNullOrEmpty(releaseDate))
                _writer.WriteAttributeString("database_release_date", releaseDate);

            int entries = FastaReader.NumberOfEntries(fastaFilePath);
            _writer.WriteAttributeString("size_in_db_entries", entries.ToString());

            _writer.WriteEndElement(); // search_database
        }

        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();
            }
        }