public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ProteinQuantificationResult();
pqr.Items["D1"] = new QuantificationItem()
{
Enabled = true,
Ratio = 1.5,
SampleIntensity = 150,
ReferenceIntensity = 100,
Correlation = 0.9,
ScanCount = 55,
Filename = "test1.silac"
};
pqr.Items["D2"] = new QuantificationItem()
{
Enabled = false,
Ratio = 3,
SampleIntensity = 250,
ReferenceIntensity = 200,
Correlation = 0.8,
ScanCount = 77,
Filename = "test2.silac"
};
ann.Annotations[SilacQuantificationConstants.SILAC_KEY] = pqr;
var converter = new SilacProteinQuantificationResultConverter2 <IAnnotation>();
List <IPropertyConverter <IAnnotation> > converters = new List <IPropertyConverter <IAnnotation> >();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter <IAnnotation> finalConverter = new CompositePropertyConverter <IAnnotation>(converters, ',');
Assert.AreEqual("S_COUNT,SE_D1,SR_D1,SRC_D1,SSI_D1,SRI_D1,SE_D2,SR_D2,SRC_D2,SSI_D2,SRI_D2", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
Assert.AreEqual("2,True,1.5000,0.9000,150.0,100.0,False,3.0000,0.8000,250.0,200.0", line1);
var protein2 = new IdentifiedProtein();
var finalC = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ProteinQuantificationResult();
pqr.Items["D1"] = new QuantificationItem()
{
Enabled = true,
Ratio = 1.5,
SampleIntensity = 150,
ReferenceIntensity = 100,
Correlation = 0.9,
ScanCount = 55,
Filename = "test1.silac"
};
pqr.Items["D2"] = new QuantificationItem()
{
Enabled = false,
Ratio = 3,
SampleIntensity = 250,
ReferenceIntensity = 200,
Correlation = 0.8,
ScanCount = 77,
Filename = "test2.silac"
};
ann.Annotations[SilacQuantificationConstants.SILAC_KEY] = pqr;
var converter = new SilacProteinQuantificationResultConverter2<IAnnotation>();
List<IPropertyConverter<IAnnotation>> converters = new List<IPropertyConverter<IAnnotation>>();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter<IAnnotation> finalConverter = new CompositePropertyConverter<IAnnotation>(converters, ',');
Assert.AreEqual("S_COUNT,SE_D1,SR_D1,SRC_D1,SSI_D1,SRI_D1,SE_D2,SR_D2,SRC_D2,SSI_D2,SRI_D2", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
Assert.AreEqual("2,True,1.5000,0.9000,150.0,100.0,False,3.0000,0.8000,250.0,200.0", line1);
var protein2 = new IdentifiedProtein();
var finalC = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
public override IEnumerable <string> Process(string filename)
{
string resultFile = filename + ".SILACsummary";
FileInfo resultFI = new FileInfo(resultFile);
DirectoryInfo detailDir = new DirectoryInfo(resultFI.DirectoryName + "\\" + resultFI.Name + ".details");
if (!detailDir.Exists)
{
detailDir.Create();
}
builder.Progress = this.Progress;
IIdentifiedResult sr = resultFormat.ReadFromFile(filename);
var spectra = sr.GetSpectra();
builder.Quantify(spectra, detailDir.FullName);
SilacQuantificationSummaryOption option = new SilacQuantificationSummaryOption()
{
MinimumPeptideRSquare = this.MinPeptideRegressionCorrelation
};
spectra.ForEach(m =>
{
m.SetEnabled(option.IsPeptideRatioValid(m) && !option.IsPeptideOutlier(m));
var dupSpectra = m.GetDuplicatedSpectra();
dupSpectra.ForEach(n => n.SetEnabled(option.IsPeptideRatioValid(n) && !option.IsPeptideOutlier(n)));
});
var calc = new ExtendSilacProteinRatioCalculator();
Dictionary <string, string> datasetMap = new Dictionary <string, string>();
foreach (var ds in datasets)
{
var lst = ds.Value;
lst.ForEach(m => datasetMap[m] = ds.Key);
}
foreach (IIdentifiedProteinGroup mpg in sr)
{
var realSpectra = new List <IIdentifiedSpectrum>(mpg.GetPeptides());
foreach (var spectrum in realSpectra)
{
var dupSpectra = spectrum.GetDuplicatedSpectra();
mpg.AddIdentifiedSpectra(dupSpectra);
}
ProteinQuantificationResult pr = new ProteinQuantificationResult();
foreach (var ds in datasets)
{
var lst = ds.Value;
pr.Items[ds.Key] = calc.Calculate(mpg, m => lst.Contains(m.Query.FileScan.Experimental));
}
bool valid = pr.Items.Values.FirstOrDefault(m => m.Enabled) != null;
foreach (IIdentifiedProtein protein in mpg)
{
protein.SetEnabled(valid);
protein.Annotations[SilacQuantificationConstants.SILAC_KEY] = pr;
}
}
var finalSpectra = sr.GetSpectra();
finalSpectra.ForEach(m => m.SetDataset(datasetMap[m.Query.FileScan.Experimental]));
resultFormat.InitializeByResult(sr);
resultFormat.WriteToFile(resultFile, sr);
return(new[] { resultFile });
}
