/// <summary>
/// Create the decoy version of this databse
/// </summary>
/// <param name="enzyme"></param>
/// <param name="shuffle"></param>
public void CreateDecoyDatabase(Enzyme enzyme, bool shuffle)
{
var reader = new FastaFileReader();
if (!reader.OpenFile(_databaseFilePath))
{
return;
}
var decoyDatabaseFileName = GetDecoyDatabasePath(enzyme, shuffle);
Console.WriteLine("Creating " + decoyDatabaseFileName);
using (var decoyWriter = new StreamWriter(decoyDatabaseFileName))
{
while (reader.ReadNextProteinEntry())
{
var name = reader.ProteinName;
var description = reader.ProteinDescription;
var sequence = reader.ProteinSequence;
decoyWriter.WriteLine(">{0}_{1} {2}", FastaDatabaseConstants.DecoyProteinPrefix, name, description);
if (!shuffle)
{
// Reversed protein sequence
var decoySequence = new StringBuilder();
for (var i = sequence.Length - 1; i >= 0; i--)
{
var residue = sequence[i];
if (enzyme != null && enzyme.Residues.Length > 0 && enzyme.IsCleavable(residue) && decoySequence.Length > 0)
{
var residueToBeReplaced = decoySequence[decoySequence.Length - 1];
decoySequence.Remove(decoySequence.Length - 1, 1);
decoySequence.Append((char)residue);
decoySequence.Append(residueToBeReplaced);
}
else
{
decoySequence.Append((char)residue);
}
}
decoyWriter.WriteLine(decoySequence);
}
else
{
// Shuffled protein sequences
decoyWriter.WriteLine(SimpleStringProcessing.Mutate(SimpleStringProcessing.Shuffle(sequence), NumMutations));
}
}
reader.CloseFile();
}
}
public void TestStringShuffling()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string str = "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG"; // Histone H4
var shuffled = SimpleStringProcessing.Shuffle(str);
var strSorted = String.Concat(str.OrderBy(c => c));
var shuffledSorted = String.Concat(shuffled.OrderBy(c => c));
Assert.IsTrue(strSorted.Equals(shuffledSorted));
}