public override IEnumerable <string> Process()
{
var result = new List <string>();
var titleParser = options.GetTitleParser();
var parser = new MascotDatSpectrumParser(titleParser);
foreach (var datFile in options.InputFiles)
{
Progress.SetMessage("Parsing the data file : " + datFile + " ...");
var spectra = parser.ReadFromFile(datFile).Where(m => m.Peptide.PureSequence.Length >= options.MinPeptideLength).ToList();
var targetFile = options.GetOutputFile(datFile);
var pars = new PepXmlWriterParameters();
pars.Protease = parser.CurrentProtease;
pars.Modifications = new PepXmlModifications(parser.CurrentModifications);
pars.Parameters = parser.CurrentParameters;
pars.SourceFile = parser.CurrentParameters["FILE"].StringAfter("File Name:").Trim();
pars.SearchDatabase = parser.CurrentParameters["DB"];
pars.SearchEngine = "MASCOT";
pars.NotCombineRank1PSMs = this.options.NotCombine;
Progress.SetMessage("Writing {0} spectra to file : {1}", spectra.Count, targetFile);
new MascotPepXmlWriter(pars).WriteToFile(targetFile, spectra);
result.Add(targetFile);
}
return(result);
}
public override IEnumerable <string> Process()
{
var result = new List <string>();
var titleParser = options.GetTitleParser();
var parser = new MascotDatSpectrumParser(titleParser);
foreach (var datFile in options.InputFiles)
{
Progress.SetMessage("Parsing the data file : " + datFile + " ...");
var spectra = parser.ReadFromFile(datFile);
var proteins = parser.ParseSection(datFile, "proteins");
var targetFile = options.GetOutputFile(datFile);
var dbName = "mascot_db";
using (var sw = new StreamWriter(targetFile, false, System.Text.Encoding.UTF8))
{
sw.Write(@"<?xml version=""1.0"" encoding=""utf-8""?>
<MzIdentML id=""report"" version=""1.1.0""
xsi:schemaLocation=""http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd""
xmlns=""http://psidev.info/psi/pi/mzIdentML/1.1""
xmlns:xsi=""http://www.w3.org/2001/XMLSchema-instance""
creationDate=""{0:yyyy-MM-dd}T{0:hh:mm:ss}"">
<cvList xmlns=""http://psidev.info/psi/pi/mzIdentML/1.1"">
<cv id=""PSI-MS"" uri=""http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"" version=""3.30.0"" fullName=""PSI-MS"" />
<cv id=""UNIMOD"" uri=""http://www.unimod.org/obo/unimod.obo"" fullName=""UNIMOD"" />
<cv id=""UO"" uri=""http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"" fullName=""UNIT-ONTOLOGY"" />
</cvList>
<AnalysisSoftwareList>
<AnalysisSoftware id=""AS_mascot_server"" name=""Mascot Server"" version=""2.4.1"" uri=""http://www.matrixscience.com/search_form_select.html"">
<SoftwareName>
<cvParam accession=""MS:1001207"" cvRef=""PSI-MS"" name=""Mascot"" />
</SoftwareName>
</AnalysisSoftware>
</AnalysisSoftwareList>
", DateTime.Now);
foreach (var seqName in proteins.Keys.OrderBy(m => m))
{
var description = proteins[seqName].StringAfter(",");
sw.Write(@" <DBSequence id={0} searchDatabase_ref=""{1}"" accession={0}>
<cvParam accession=""MS:1001088"" name=""protein description"" cvRef=""PSI-MS"" value={2} />
</DBSequence>
", seqName, dbName, description);
}
}
result.Add(targetFile);
}
return(result);
}
public void TestGetSourceFile()
{
Assert.AreEqual("dyckall.asc", MascotDatSpectrumParser.GetSourceFile(@TestContext.CurrentContext.TestDirectory + "/../../../data//F001264.dat"));
}
