private void CreateDecoy()
{
Sequence.Reverse();
var sequence = Sequence.Aggregate("", (current, aa) => current + aa.Residue);
sequence = SimpleStringProcessing.Mutate(sequence, sequence.Length / 2);
Peptide = sequence;
Sequence = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequence);
}
public void DiaRankScore()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataFile =
@"\\protoapps\UserData\Wilkins\BottomUp\HCD_QCShew\raw\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
const string tsvFile =
@"\\protoapps\UserData\Wilkins\BottomUp\HCD_QCShew\tsv\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.tsv";
if (!File.Exists(dataFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dataFile);
}
if (!File.Exists(tsvFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tsvFile);
}
var parser = new TsvFileParser(tsvFile);
var sequences = parser.GetData("Peptide");
var charges = parser.GetData("Charge");
var scans = parser.GetData("ScanNum");
var lcms = InMemoryLcMsRun.GetLcMsRun(dataFile, 0, 0);
var rankScorer =
new DiaRankScore(
@"C:\Users\wilk011\Documents\DataFiles\TestFolder\HCD_QExactive_Tryp.txt");
using (
var outFile = new StreamWriter(@"C:\Users\wilk011\Documents\DataFiles\TestFolder\HCD_QCShew_Score_2.txt"))
{
outFile.WriteLine("Target\tDecoy");
for (int i = 0; i < sequences.Count; i++)
{
string sequenceStr = sequences[i];
int charge = Convert.ToInt32(charges[i]);
int scan = Convert.ToInt32(scans[i]);
var sequence = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequenceStr);
var decoySeq = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequenceStr);
decoySeq.Reverse();
var decoyStr = decoySeq.Aggregate("", (current, aa) => current + aa);
decoyStr = SimpleStringProcessing.Mutate(decoyStr, sequence.Count / 2);
decoySeq = Sequence.GetSequenceFromMsGfPlusPeptideStr(decoyStr);
var sequenceScore = rankScorer.GetScore(sequence, charge, scan, lcms);
var decoyScore = rankScorer.GetScore(decoySeq, charge, scan, lcms);
outFile.WriteLine("{0}\t{1}", sequenceScore, decoyScore);
}
}
}
/// <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 TestStringMutation()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string str = "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG"; // Histone H4
const int numMutations = 3;
var mutated = SimpleStringProcessing.Mutate(str, numMutations);
Console.WriteLine(mutated);
Assert.IsTrue(str.Length == mutated.Length);
var numDiff = str.Where((t, i) => t != mutated[i]).Count();
Console.WriteLine("Mutations: {0}", numDiff);
//var strSorted = String.Concat(str.OrderBy(c => c));
//var shuffledSorted = String.Concat(mutated.OrderBy(c => c));
//Assert.IsTrue(strSorted.Equals(shuffledSorted));
}