public override IEnumerable <string> Process(string fileName)
{
MaxQuantPeptideTextFormat format = new MaxQuantPeptideTextFormat();
var spectra = format.ReadFromFile(fileName);
var ratioResult = fileName + ".ratio";
var ratioNormResult = fileName + ".norm.ratio";
ExtractRatio(spectra, ratioResult, m => m.Ratio);
ExtractRatio(spectra, ratioNormResult, m => m.Ratio_Norm);
return(new[] { ratioResult, ratioNormResult });
}
public void TestReadPeptideFile()
{
MaxQuantPeptideTextFormat reader = new MaxQuantPeptideTextFormat();
var spectra = reader.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/maxquant.peptides.txt");
for (int i = 0; i < spectra.Count; i++)
{
var s = spectra[i];
if (s.Query.FileScan.Experimental == "exp3_T_SAX_091215_02")
{
Console.WriteLine("{0}, {1}", i, s.Query.FileScan.LongFileName);
//break;
}
}
}
public void TestRead()
{
MaxQuantPeptideTextFormat reader = new MaxQuantPeptideTextFormat();
var spectra = reader.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/All_Phospho (STY)Sites.txt");
Assert.AreEqual(1, spectra.Count);
var m = spectra[0].GetMaxQuantItemList();
Assert.IsNotNull(m);
Assert.AreEqual(6, m.Count);
var dsNames = m.GetDatasetNames();
Assert.IsTrue(dsNames.Contains("0min"));
Assert.IsTrue(dsNames.Contains("5min"));
Assert.IsTrue(dsNames.Contains("15min"));
Assert.IsTrue(dsNames.Contains("30min"));
Assert.IsTrue(dsNames.Contains("60min"));
Assert.IsTrue(dsNames.Contains("120min"));
reader.ResetBySpectra(spectra);
reader.WriteToFile(@TestContext.CurrentContext.TestDirectory + "/../../../data//All_Phospho (STY)Sites.txt.copy", spectra);
}