public bool RunSearch(double corrThreshold)
{
var sw = new Stopwatch();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
sw.Start();
_run = InMemoryLcMsRun.GetLcMsRun(SpecFilePath, 1.4826, 1.4826);
_bottomUpScorer = new InformedBottomUpScorer(_run, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Determining precursor masses...");
sw.Start();
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(_run, PrecursorIonTolerance, MinPrecursorIonCharge, MaxPrecursorIonCharge,
400, 5000, corrThreshold, 0, 0);
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Deconvoluting MS2 spectra...");
sw.Start();
_ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(
_run,
MinProductIonCharge, MaxProductIonCharge,
new Tolerance(10),
0
);
_ms2ScorerFactory.DeconvoluteAllProductSpectra();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
// string dirName = OutputDir ?? Path.GetDirectoryName(SpecFilePath);
var baseName = Path.GetFileNameWithoutExtension(SpecFilePath);
var targetOutputFilePath = Path.Combine(OutputDir, baseName + TargetFileExtension);
var decoyOutputFilePath = Path.Combine(OutputDir, baseName + DecoyFileExtension);
var tdaOutputFilePath = Path.Combine(OutputDir, baseName + TdaFileExtension);
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
var targetMatches = RunSearch(GetAnnotationsAndOffsets(targetDb), ms1Filter, false);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Target database search elapsed time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing target results...");
sw.Start();
WriteResultsToFile(targetMatches, targetOutputFilePath, targetDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
Console.Write(@"Reading the decoy database...");
sw.Start();
var decoyDb = targetDb.Decoy(Enzyme);
decoyDb.Read();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
var decoyMatches = RunSearch(GetAnnotationsAndOffsets(decoyDb), ms1Filter, true);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Decoy database search elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing decoy results...");
sw.Start();
WriteResultsToFile(decoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return false;
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
Console.WriteLine(@"Done");
return true;
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.7, 0.7, 0.7, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
//const string prot =
// "ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKKTEVSAVSIVVAAAKKLLA";
//var protMass = (new AminoAcidSet().GetComposition(prot) + Composition.H2O).Mass;
//Console.WriteLine("************ScanNums: " + string.Join("\t", ms1Filter.GetMatchingMs2ScanNums(protMass)));
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\MSAlign\NoMod.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var scanNums = tsvReader.GetData("Scan(s)");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("E-value");
var sequences = tsvReader.GetData("Peptide");
//const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_N30_C30.tsv";
//var tsvReader = new TsvFileParser(resultFilePath);
//var scanNums = tsvReader.GetData("ScanNum");
//var charges = tsvReader.GetData("Charge");
//var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Sequence");
var aaSet = new AminoAcidSet();
var seqSet = new HashSet<string>();
var allSeqSet = new HashSet<string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < scores.Count; i++)
{
var score = Convert.ToDouble(scores[i]);
if (score > 1E-4) continue;
//if (score < 10) continue;
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var sequence = SimpleStringProcessing.GetStringBetweenDots(sequences[i]);
if (sequence == null || sequence.Contains("(")) continue;
//var sequence = sequences[i];
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void FilteringEfficiency()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
//var ms1BasedFilter = new Ms1BasedFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm);
//
//var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//var ms1BasedFilter = new ProductScorerBasedOnDeconvolutedSpectra(run,
// minPrecursorCharge, maxPrecursorCharge,
// 0, 0,
// 600.0, 1800.0, new Tolerance(tolerancePpm), null);
//ms1BasedFilter.CachePrecursorMatchesBinCentric();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.5, 0.5, 0.5, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon_4PTMs.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("Score");
var qvalues = tsvReader.GetData("QValue");
var sequences = tsvReader.GetData("Sequence");
var sequenceCount = new Dictionary<string, int>();
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01) continue;
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13) continue;
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
var sequence = sequences[i];
int count;
if (sequenceCount.TryGetValue(sequence, out count)) sequenceCount[sequence] = count + 1;
else sequenceCount[sequence] = 1;
}
//var sequences = tsvReader.GetData("Annotation");
var seqSet = new HashSet<string>();
var allSeqSet = new HashSet<string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01) continue;
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13) continue;
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
//var xic = run.GetFullPrecursorIonExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance);
////xic.Display();
//var apexScanNum = xic.GetNearestApexScanNum(run.GetPrecursorScanNum(scanNum), false);
//var apexSpec = run.GetSpectrum(apexScanNum);
//var corr3 = apexSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax, sequenceCount[sequences[i]]);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons/(double)(maxBinNum-minBinNum+1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs/(double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count/(double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestPossibleSequenceMasses()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\DataFiles\SBEP_STM_001_02272012_Aragon.raw";
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, 3, 30, 15, 0.7, 1000);
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10));
//var masses = ms1BasedFilter.GetPossibleSequenceMasses(1113);
//var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, 3, 30, 15);
//var masses = ms1BasedFilter.GetPossibleSequenceMasses(2819, 20);
//foreach (var m in masses)
//{
// Console.WriteLine(m);
//}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestMs1Filter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string msgfPlusResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod.tsv";
if (!File.Exists(msgfPlusResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, msgfPlusResultPath);
}
var msgfPlusResults = new MsGfResults(msgfPlusResultPath);
const string specFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0);
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10), 1, 4,
400, 5000, 0.3, 0, 0);
var matches = msgfPlusResults.GetMatchesAtPsmFdr(0.01);
var aminoAcidSet = new AminoAcidSet();
var numPsms = 0;
var numSurvived = 0;
Console.WriteLine("ScanNum\tPeptide\tSpecEValue\tFilter");
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var peptide = match.Peptide;
var specEValue = match.SpecEValue;
var peptideMass = (new Sequence(peptide, aminoAcidSet).Composition + Composition.H2O).Mass;
var survive = ms1Filter.GetMatchingMs2ScanNums(peptideMass).Contains(scanNum) ? 1 : 0;
++numPsms;
numSurvived += survive;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", scanNum, peptide, specEValue, survive);
}
Console.WriteLine("SuccessRage: {0}, {1}/{2}", numSurvived/(float)numPsms, numSurvived, numPsms);
}
