public void TestUpdatePrecursor()
{
var pkl = new PeakList <Peak>();
pkl.Precursor = new PrecursorPeak(new Peak(1000.0, 1.0, 4));
pkl.FirstScan = 620;
pkl.Annotations["TITLE"] = "TCGA-AA-A01F-01A-23_W_VU_20120727_A0218_1B_R_FR04.620.620.4.dta";
var titleFormat = TitleParserUtils.FindByName("DTA");
MascotGenericFormatShiftPrecursorProcessor.UpdatePrecursor(titleFormat, pkl, -10.0, 10000);
Assert.AreEqual(10620, pkl.FirstScan);
Assert.AreEqual("TCGA-AA-A01F-01A-23_W_VU_20120727_A0218_1B_R_FR04.10620.10620.4.dta", pkl.Annotations["TITLE"]);
Assert.AreEqual(997.5, pkl.PrecursorMZ, 0.1);
}
public void Test()
{
var spectra = new CometXmlRank2Parser()
{
TitleParser = TitleParserUtils.FindByName("DTA")
}.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/comet.pep.xml");
Assert.AreEqual(2, spectra.Count);
Assert.AreEqual("K.M*REGPAK.N", spectra[0].Sequence);
Assert.AreEqual(3, spectra[0].Rank);
Assert.AreEqual(0.743, spectra[0].Score, 0.001);
Assert.AreEqual(0.035, spectra[0].DeltaScore, 0.001);
Assert.AreEqual(66.0, spectra[0].SpScore, 0.01);
Assert.AreEqual(13, spectra[0].SpRank);
Assert.AreEqual(2.47E+01, spectra[0].ExpectValue, 0.01);
Assert.AreEqual(1077, spectra[0].Query.MatchCount);
Assert.AreEqual("Elite_CIDIT_Human.minus10dalton.2.2.2.dta", spectra[0].Query.FileScan.LongFileName);
}
public override bool PrepareOptions()
{
if (!File.Exists(this.InputFile))
{
ParsingErrors.Add(string.Format("Input file not exists {0}.", this.InputFile));
}
if (TitleParserUtils.FindByName(TitleType) == null)
{
if (!string.IsNullOrEmpty(this.TitleType) && !this.TitleType.ToLower().Equals("help"))
{
ParsingErrors.Add(string.Format("Unknown title type {0}.", this.TitleType));
}
ParsingErrors.Add(" Those titles are valid:");
(from t in TitleParserUtils.GetTitleParsers()
select t.FormatName).ToList().ForEach(m => ParsingErrors.Add(" " + m));
}
return(ParsingErrors.Count == 0);
}
public override IEnumerable <string> Process()
{
var titleParser = TitleParserUtils.FindByName(options.TitleType);
Progress.SetMessage("Parsing " + options.InputFile + "...");
var outputFile = options.OutputFile + ".tmp";
new Mgf2Ms2Processor(outputFile, titleParser)
{
Progress = this.Progress
}.Process(options.InputFile);
if (File.Exists(outputFile))
{
File.Move(outputFile, options.OutputFile);
}
return(new[] { options.OutputFile });
}
public void Test()
{
var spectra = new CometXmlParser()
{
TitleParser = TitleParserUtils.FindByName("DTA")
}.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/comet.pep.xml");
Assert.AreEqual(2, spectra.Count);
Assert.AreEqual("R.HFM*LEMK.S", spectra[0].Sequence);
Assert.AreEqual(1, spectra[0].Rank);
Assert.AreEqual(0.778, spectra[0].Score, 0.001);
Assert.AreEqual(0.001, spectra[0].DeltaScore, 0.001);
Assert.AreEqual(80.2, spectra[0].SpScore, 0.01);
Assert.AreEqual(7, spectra[0].SpRank);
Assert.AreEqual(1.91E+01, spectra[0].ExpectValue, 0.01);
Assert.AreEqual("sp|Q9BV73|CP250_HUMAN", spectra[0].Proteins[0]);
Assert.AreEqual(4, spectra[0].MatchedIonCount);
Assert.AreEqual(10, spectra[0].TheoreticalIonCount);
Assert.AreEqual(803.399995, spectra[0].TheoreticalMass, 0.000001);
Assert.AreEqual(2, spectra[0].Query.FileScan.Charge);
Assert.AreEqual(1077, spectra[0].Query.MatchCount);
Assert.AreEqual("Elite_CIDIT_Human.minus10dalton.2.2.2.dta", spectra[0].Query.FileScan.LongFileName);
}
public ITitleParser GetTitleParser()
{
return(TitleParserUtils.FindByName(this.TitleFormat));
}