/// <summary>
/// Generates decoys for a list of proteins
/// </summary>
/// <param name="proteins"></param>
/// <param name="decoyType"></param>
/// <param name="digestionParams"></param>
/// <param name="randomSeed">Used when decoy type is shuffle for shuffling the peptides</param>
/// <returns></returns>
public static List <Protein> GenerateDecoys(List <Protein> proteins, DecoyType decoyType, int maxThreads = -1)
{
if (decoyType == DecoyType.None)
{
return(new List <Protein>());
}
else if (decoyType == DecoyType.Reverse)
{
return(GenerateReverseDecoys(proteins, maxThreads));
}
else if (decoyType == DecoyType.Slide)
{
return(GenerateSlideDecoys(proteins, maxThreads));
}
else
{
throw new ArgumentException("Decoy type " + decoyType.ToString() + " is not implemented.");
}
}
public void MoreTests(string filename, DecoyType decoyType = DecoyType.None)
{
string xmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", filename);
var proteins = ProteinDbLoader.LoadProteinXML(xmlName, decoyType == DecoyType.None, decoyType, null, false, null, out var un);
var peps = proteins[1].Digest(CommonParameters.DigestionParams, null, null).ToList();
PeptideWithSetModifications pep = peps[peps.Count - 2];
string mzmlName = $"ajgdiv{filename}{decoyType.ToString()}.mzML";
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pep
});
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, $"TestSearchWithVariants{filename}{decoyType.ToString()}");
Directory.CreateDirectory(outputFolder);
SearchTask st = new SearchTask
{
SearchParameters = new SearchParameters
{
DoParsimony = true,
DecoyType = decoyType,
SearchTarget = decoyType == DecoyType.None,
ModPeptidesAreDifferent = false
},
CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(minPeptideLength: 2), precursorMassTolerance: new PpmTolerance(20)),
};
st.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(xmlName, false)
}, new List <string> {
mzmlName
}, "");
var psms = File.ReadAllLines(Path.Combine(outputFolder, "AllPSMs.psmtsv"));
//Assert.IsTrue(psms.Any(line => line.Contains($"\t{variantPsmShort}\t" + (containsVariant ? variantPsmShort : "\t"))));
Directory.Delete(outputFolder, true);
File.Delete(mzmlName);
//Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}