public void WriteToFile(string proteinFile, IIdentifiedResult mr)
{
if (this.proteinConverter == null)
{
this.proteinConverter =
IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(
"Locus\tSequence Count\tSpectrum Count\tSequence Coverage\tLength\tMolWt\tpI\tValidation Status\tDescriptive Name",
'\t', "Dtaselect");
this.peptideConverter =
IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(
"Unique\tFileName\tScore\tDeltCN\tM+H+\tCalcM+H+\tTotalIntensity\tSpRank\tSpScore\tIonProportion\tRedundancy\tSequence",
'\t', "Dtaselect");
}
using (var sw = new StreamWriter(proteinFile))
{
sw.WriteLine("DTASelect v1.9");
sw.WriteLine();
sw.WriteLine("true Use criteria");
sw.WriteLine();
sw.WriteLine(this.proteinConverter.Name);
sw.WriteLine(this.peptideConverter.Name);
foreach (IdentifiedProteinGroup mpg in mr)
{
for (int proteinIndex = 0; proteinIndex < mpg.Count; proteinIndex++)
{
IIdentifiedProtein mpro = mpg[proteinIndex];
sw.WriteLine(this.proteinConverter.GetProperty(mpro));
}
mpg.GetSortedPeptides().ForEach(m => sw.WriteLine(this.peptideConverter.GetProperty(m)));
}
}
}
public List <IIdentifiedProtein> ReadFromFile(string filename)
{
if (!File.Exists(filename))
{
throw new FileNotFoundException("File not exist : " + filename);
}
var result = new List <IIdentifiedProtein>();
long fileSize = new FileInfo(filename).Length;
Progress.SetRange(0, fileSize);
using (var br = new StreamReader(filename))
{
String line = br.ReadLine();
ProteinFormat = new LineFormat <IIdentifiedProtein>(IdentifiedProteinPropertyConverterFactory.GetInstance(), line, engineName);
while ((line = br.ReadLine()) != null)
{
if (0 == line.Trim().Length)
{
break;
}
Progress.SetPosition(br.BaseStream.Position);
result.Add(ProteinFormat.ParseString(line));
}
}
return(result);
}
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 IIdentifiedResult ReadFromFile(string proteinFile)
{
if (!File.Exists(proteinFile))
{
throw new FileNotFoundException("File not exist : " + proteinFile);
}
var result = new MascotResult();
var peptideMap = new Dictionary <string, IIdentifiedSpectrum>();
using (var filein = new StreamReader(proteinFile))
{
string lastLine;
while ((lastLine = filein.ReadLine()) != null)
{
if (lastLine.StartsWith("Locus"))
{
this.proteinConverter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(lastLine, '\t',
"Dtaselect");
}
if (lastLine.StartsWith("Unique"))
{
this.peptideConverter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(lastLine,
'\t',
"Dtaselect");
break;
}
}
IIdentifiedProteinGroup group;
lastLine = null;
while ((group = ReadNextProteinGroup(filein, peptideMap, ref lastLine)) != null)
{
result.Add(group);
}
}
return(result);
}
public void TestReadWrite()
{
var ann = new IdentifiedProtein();
var pqr = new ITraqQuantificationResult();
pqr.DatasetMap["D1"] = new ITraqQuantificationDatasetItem()
{
DatasetName = "D1"
};
pqr.DatasetMap["D1"].RatioMap["R114/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R114/REF",
Ratio = 1.5
};
pqr.DatasetMap["D1"].RatioMap["R115/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R115/REF",
Ratio = 1.8
};
pqr.DatasetMap["D2"] = new ITraqQuantificationDatasetItem()
{
DatasetName = "D2"
};
pqr.DatasetMap["D2"].RatioMap["R116/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R116/REF",
Ratio = 2.5
};
pqr.DatasetMap["D2"].RatioMap["R117/REF"] = new ITraqQuantificationChannelItem()
{
ChannelName = "R117/REF",
Ratio = 3.8
};
ann.Annotations[ITraqConsts.ITRAQ_KEY] = pqr;
var converter = new ITraqQuantificationResultConverter <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, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual("ITRAQ_COUNT,IR_D1_R114/REF,IR_D1_R115/REF,IR_D2_R116/REF,IR_D2_R117/REF", finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual("2,1.5000,1.8000,2.5000,3.8000", 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 MascotProteinTextReader2(string headers)
{
this.converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(headers, '\t');
}