public void LoadData(string dtaFile, string outFile)
{
ExperimentalPeakList = DtaIO.ReadFromDta <MatchedPeak>(dtaFile);
SequestOutHeaderParser parser = new SequestOutHeaderParser();
string[] lines = FileUtils.ReadFile(outFile).ToArray();
int index = ParseMassType(lines, 0, parser);
index = ParseModification(lines, index, parser);
IIdentifiedSpectrum spectrum = new OutParser().ParseFromFile(outFile);
ScoreMap = new Dictionary <string, string>();
if (spectrum != null)
{
Peptide = spectrum.Sequence;
ScoreMap["Xcorr"] = MyConvert.Format("{0:0.0000}", spectrum.Score);
ScoreMap["DeltaCn"] = MyConvert.Format("{0:0.0000}", spectrum.DeltaScore);
InitTheoreticalPeaks();
}
}
public override IEnumerable <string> Process(string filename)
{
var parser = new OutParser();
string resultFilename;
if (null == this.targetDir)
{
resultFilename = FileUtils.ChangeExtension(filename, ".xml");
}
else
{
resultFilename = targetDir + "/" + FileUtils.ChangeExtension(new FileInfo(filename).Name, ".xml");
}
using (PepXmlWriter writer = new PepXmlWriter("out"))
{
writer.Open(resultFilename);
writer.OpenMsmsRunSummary(filename);
SequestParam sp = new SequestParamFile().ReadFromFile(filename);
writer.WriteSequestParam(sp);
using (var reader = new OutsReader(filename))
{
int totalCount = reader.FileCount;
Progress.SetRange(0, totalCount);
int currentCount = 0;
while (reader.HasNext)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
List <string> contents = reader.NextContent();
IIdentifiedSpectrum sph = parser.Parse(contents);
if (sph == null)
{
continue;
}
writer.WriteSequestPeptideHit(sph);
currentCount++;
Progress.SetPosition(currentCount);
}
Progress.SetPosition(totalCount);
}
writer.CloseMsmsRunSummary();
}
return(new[] { resultFilename });
}
public void TestParseFromVersion_27_12_WithoutDuplicatedReferencesCheck()
{
var parser = new OutParser(false);
IIdentifiedSpectrum peptide = parser.ParseFromFile(@"../../../data/mouseliver.4587.4587.2.out");
Assert.IsNotNull(peptide);
Assert.AreEqual("20030714_MouseLiver_2,4587", peptide.Query.FileScan.ShortFileName);
Assert.AreEqual("-.S*AILS*NTPS*LLALR.-", peptide.Peptides[0].Sequence);
Assert.AreEqual("Q8VI59", peptide.Peptides[0].Proteins[0]);
Assert.AreEqual(1696.6531, peptide.TheoreticalMH, 0.0001);
Assert.AreEqual(1695.9512, peptide.ExperimentalMH, 0.0001);
}
public void TestParseFromVersion_27_12_WithDuplicatedReferencesCheck()
{
var parser = new OutParser(true);
parser.ParseFromFile(@"../../../data/mouseliver.4587.4587.2.out");
}
