/// <summary>
/// Get the Decoy version of this database (create it if missing)
/// </summary>
/// <param name="enzyme"></param>
/// <param name="shuffle"></param>
/// <returns></returns>
public FastaDatabase Decoy(Enzyme enzyme, bool shuffle = false)
{
if (IsDecoy)
{
throw new InvalidOperationException("Already a decoy database");
}
var decoyDatabasePath = GetDecoyDatabasePath(enzyme, shuffle);
if (!File.Exists(decoyDatabasePath))
CreateDecoyDatabase(enzyme, shuffle);
return new FastaDatabase(decoyDatabasePath, true);
}
public RankScore(ActivationMethod activationMethod, Ms2DetectorType ms2DetectorType, Enzyme enzyme, Protocol protocol)
{
if (activationMethod == ActivationMethod.HCD && enzyme == Enzyme.Trypsin)
{
var paramFile = Properties.Resources.HCD_Trypsin;
var stream = new MemoryStream();
var writer = new StreamWriter(stream);
writer.Write(paramFile);
writer.Flush();
stream.Position = 0;
_trainingParameters = new TrainingParameters(stream);
}
else
{
throw new ArgumentException("No parameter file available for selected arguments.");
}
}
public IcBottomUpLauncher(
string specFilePath,
string dbFilePath,
string outputDir,
AminoAcidSet aaSet,
Enzyme enzyme)
{
ErrorMessage = string.Empty;
SpecFilePath = specFilePath;
DatabaseFilePath = dbFilePath;
AminoAcidSet = aaSet;
Enzyme = enzyme;
if (outputDir == null)
{
OutputDir = Path.GetDirectoryName(SpecFilePath);
}
else
{
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
throw new Exception(outputDir + " is not a directory!");
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
}
OutputDir = outputDir;
MinSequenceLength = 6;
MaxSequenceLength = 30;
MinPrecursorIonCharge = 1;
MaxPrecursorIonCharge = 4;
MinProductIonCharge = 1;
MaxProductIonCharge = 3;
PrecursorIonTolerance = new Tolerance(10);
ProductIonTolerance = new Tolerance(10);
RunTargetDecoyAnalysis = DatabaseSearchMode.Both;
NumTolerableTermini = 1;
NumMatchesPerSpectrum = 10;
}
public PeptideEnumerator(Enzyme enzyme, int ntt)
{
_enzyme = enzyme;
_ntt = ntt;
}
public IEnumerable<AnnotationAndOffset> AnnotationsAndOffsetsParallel(int minLength, int maxLength, int numTolerableTermini,
int numMissedCleavages, Enzyme enzyme, int threads, CancellationToken? cancellationToken = null)
{
return AnnotationsAndOffsetsParallel(minLength, maxLength, numTolerableTermini, numMissedCleavages, enzyme.Residues,
enzyme.IsNTerm, threads, cancellationToken);
}
public IEnumerable<AnnotationAndOffset> AnnotationsAndOffsets(int minLength, int maxLength, int numTolerableTermini,
int numMissedCleavages, Enzyme enzyme)
{
return AnnotationsAndOffsets(minLength, maxLength, numTolerableTermini, numMissedCleavages, enzyme.Residues,
enzyme.IsNTerm);
}
/// <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}", 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(residue);
decoySequence.Append(residueToBeReplaced);
}
else
{
decoySequence.Append(residue);
}
}
decoyWriter.WriteLine(decoySequence);
}
else
{
// Shuffled protein sequences
decoyWriter.WriteLine(SimpleStringProcessing.Mutate(SimpleStringProcessing.Shuffle(sequence), NumMutations));
}
}
reader.CloseFile();
}
}
public string GetDecoyDatabasePath(Enzyme enzyme, bool shuffle = false)
{
string newExtension;
if (!shuffle)
{
// Reverse the sequences
if (enzyme != null && enzyme.Residues.Length > 0)
newExtension = ".icdecoy." + new string(enzyme.Residues) + ".fasta";
else
newExtension = DecoyDatabaseFileExtension;
}
else
{
// Shuffle the sequences
newExtension = ShuffleDecoyFileExtension;
}
return Path.ChangeExtension(_databaseFilePath, newExtension);
}
