public void TestMs2Caching()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\DataFiles\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);
//const int minPrecursorIonCharge = 3; // 3
//const int maxPrecursorIonCharge = 30;// 67
//const int minProductIonCharge = 1;
//const int maxProductIonCharge = 10;
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var runCache = new ProductScorerBasedOnDeconvolutedSpectra(run);
runCache.DeconvoluteAllProductSpectra();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestPossibleSequenceMasses()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 TestFitScoreCalculationEtd()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(FilePaths.TestTopDownRawFilePathEtd))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + FilePaths.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(FilePaths.TestTopDownRawFilePathEtd, 810, 810);
var spec = run.GetSpectrum(810) as ProductSpectrum;
Assert.True(spec != null);
const string suf54 = "ENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK";
var suf54Comp = new AminoAcidSet().GetComposition(suf54);
Assert.True(suf54Comp != null);
var ionType = new IonTypeFactory(10).GetIonType("z6");
var ion = ionType.GetIon(suf54Comp);
//ion.Composition.ComputeApproximateIsotopomerEnvelop();
Console.WriteLine("MonoMz: {0}, MonoMass: {1}", ion.GetMonoIsotopicMz(), ion.Composition.Mass);
var fitScore = spec.GetFitScore(ion, new Tolerance(15), 0.1);
Console.WriteLine("FitScore: {0}", fitScore);
Assert.True(fitScore < 0.15);
}
public void TestGeneratingProductXic()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath);
// const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
const string rafFilePath = @"H:\Research\Jarret\10mz\raw\Q_2014_0523_50_10_fmol_uL_10mz.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping raf portion of test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
const double precursorIonMz = 815.16;
const double productIonMz = 902.445;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullProductExtractedIonChromatogram(productIonMz, tolerance, precursorIonMz);
// xic1.Display();
var xic2 = rafRun.GetFullProductExtractedIonChromatogram(productIonMz, tolerance, precursorIonMz);
// xic2.Display();
Assert.True(xic1.Equals(xic2));
Console.WriteLine(@"Done");
}
public void TestLogLikelihoodScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
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);
}
//const string seqStr = "IAHESDDEKGHAAK";
//var composition = Composition.Parse("C(62) H(98) N(20) O(24) S(0)");
//const int charge = 4;
//const int ms2ScanNum = 12901;
var aaSet = new AminoAcidSet();
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0);
var scorer = new InformedBottomUpScorer(run, aaSet, 1, 2, new Tolerance(10));
//var refinedScore = scorer.GetScores(AminoAcid.PeptideNTerm, seqStr, AminoAcid.PeptideCTerm, composition,
// charge, ms2ScanNum);
// Console.WriteLine("RefinedScores: {0}", refinedScore.Score);
}
public void TestReadingDiaRawFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFilePath = TestRawFilePath;
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
const int SCAN = 100;
const int MAX_POINTS = 50;
var run = InMemoryLcMsRun.GetLcMsRunScanRange(rawFilePath, SCAN);
var spec = run.GetSpectrum(SCAN);
spec.Display(MAX_POINTS);
// Console.WriteLine("{0}, {1}", spec.Peaks[50].Mz, spec.Peaks[50].Intensity);
// Console.WriteLine("{0}, {1}", spec.Peaks[500].Mz, spec.Peaks[500].Intensity);
// Console.WriteLine("{0}, {1}", spec.Peaks[1000].Mz, spec.Peaks[1000].Intensity);
Assert.IsTrue(Math.Abs(spec.Peaks[50].Mz - 414.75503540039062) < 0.0001, "Invalid m/z for peak at index 50");
Assert.IsTrue(Math.Abs(spec.Peaks[50].Intensity - 1071.5673828125) < 0.01, "Invalid intensity for peak at index 50");
Assert.IsTrue(Math.Abs(spec.Peaks[500].Mz - 578.1298828125) < 0.0001, "Invalid m/z for peak at index 500");
Assert.IsTrue(Math.Abs(spec.Peaks[500].Intensity - 573.02374267578125) < 0.01, "Invalid intensity for peak at index 500");
Assert.IsTrue(Math.Abs(spec.Peaks[1000].Mz - 974.17694091796875) < 0.0001, "Invalid m/z for peak at index 1000");
Assert.IsTrue(Math.Abs(spec.Peaks[1000].Intensity - 678.13824462890625) < 0.01, "Invalid intensity for peak at index 1000");
}
public void TestReadingScanNums()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(FilePaths.TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + FilePaths.TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(FilePaths.TestRawFilePath, 20000, 20100);
var msLevel = new Dictionary <int, int>();
//for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
foreach (var scanNum in run.AllScanNumbers)
{
msLevel[scanNum] = run.GetMsLevel(scanNum);
}
//for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
foreach (var scanNum in run.AllScanNumbers)
{
var spec = run.GetSpectrum(scanNum);
Assert.True(spec.MsLevel == msLevel[scanNum]);
if (spec.MsLevel == 2)
{
var precursorScanNum = 0;
for (var prevScan = scanNum - 1; prevScan >= run.MinLcScan; prevScan--)
{
if (run.GetMsLevel(prevScan) == 1)
{
precursorScanNum = prevScan;
break;
}
}
Assert.True(run.GetPrecursorScanNum(scanNum) == precursorScanNum);
var nextScanNum = run.MaxLcScan + 1;
//for (var nextScan = scanNum + 1; nextScan <= run.MaxLcScan; nextScan++)
foreach (var nextScan in run.AllScanNumbers.Where(x => x > scanNum))
{
if (run.GetMsLevel(nextScan) == 1)
{
nextScanNum = nextScan;
break;
}
}
if (run.GetNextScanNum(scanNum) != nextScanNum)
{
Console.WriteLine("{0}\t{1}\t{2}", scanNum, run.GetNextScanNum(scanNum), nextScanNum);
}
Assert.True(run.GetNextScanNum(scanNum) == nextScanNum);
}
}
Assert.True(run.GetNextScanNum(20025) == 20032);
Console.WriteLine(run.GetNextScanNum(20025));
}
public MsAlignRescorer(string specFilePath, string msAlignFilePath, string outputFilePath, Tolerance tolerance, double ms2CorrThreshold = 0.7
, int minProductIonCharge = 1, int maxProductIonCharge = 10)
{
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
_topDownScorer = new InformedTopDownScorer(run, new AminoAcidSet(), minProductIonCharge, maxProductIonCharge, tolerance, ms2CorrThreshold);
Rescore(msAlignFilePath, outputFilePath);
}
public void TestFitScoreCalculationCid()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(FilePaths.TestTopDownRawFilePathCid))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + FilePaths.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(FilePaths.TestTopDownRawFilePathCid, 5743, 5743);
var spec = run.GetSpectrum(5743);
Assert.True(spec != null);
const string protein = "MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGIVVDYVLEFDVPDELIVDRIVGRRVHAASGRVYHVKFNPPKVEGKDDVTGEDLTTRKDDQEETVRKRLVEYHQMTAPLIGYYQKEAEAGNTKYAKVDGTQAVADVRAALEKILG";
var protComp = new AminoAcidSet().GetComposition(protein) + Composition.H2O;
Assert.True(protComp != null);
Assert.True(protComp.C == 1035);
Assert.True(protComp.H == 1683);
Assert.True(protComp.N == 289);
Assert.True(protComp.O == 318);
Assert.True(protComp.P == 0);
Assert.True(protComp.S == 7);
Assert.True(Math.Abs(protComp.Mass - 23473.245267145) < 0.0000001);
Assert.True(protComp.NominalMass == 23461);
var ion = new Ion(protComp, 20);
// ion.Composition.ComputeApproximateIsotopomerEnvelop();
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine(@"MonoMz: {0}, MonoMass: {1}", ion.GetMonoIsotopicMz(), ion.Composition.Mass);
var matchedPeaks = spec.GetAllIsotopePeaks(ion, new Tolerance(15), 0.1);
for (var i = 0; i < matchedPeaks.Length; i++)
{
var intensity = matchedPeaks[i] == null ? 0 : matchedPeaks[i].Intensity;
Console.WriteLine(@"{0,3} {1,10:F4} {2,10:F3} {3,10:F3}", i, ion.GetIsotopeMz(i), isotopomerEnvelope[i], intensity);
}
var fitScore = spec.GetFitScore(ion, new Tolerance(15), 0.1);
var cosine = spec.GetConsineScore(ion, new Tolerance(15), 0.1);
var corr = spec.GetCorrScore(ion, new Tolerance(15), 0.1);
Console.WriteLine(@"FitScore: {0}", fitScore);
Console.WriteLine(@"Cosine: {0}", cosine);
Console.WriteLine(@"Corr: {0}", corr);
Assert.True(Math.Abs(fitScore - 0.181194589537041) < 0.0001);
Assert.True(Math.Abs(cosine - 0.917609346566222) < 0.0001);
Assert.True(Math.Abs(corr - 0.808326778009839) < 0.0001);
}
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);
}
}
}
public InformedProteomicsAnalysis(
InMemoryLcMsRun run,
IEnumerable <string> peptideEnumerator,
AminoAcidSet aminoAcidSet,
int minCharge,
int maxCharge)
{
Run = run;
PeptideEnumerator = peptideEnumerator;
AminoAcidSet = aminoAcidSet;
MinCharge = minCharge;
MaxCharge = maxCharge;
}
public void Train(string outFileName, InMemoryLcMsRun run, Tolerance tolerance, string annotationFileName)
{
// charge, scan number, protein
_run = run;
_tolerance = tolerance;
var target = new Dictionary <int, Dictionary <int, Composition> >();
var decoy = new Dictionary <int, Dictionary <int, Composition> >();
_missingXicCounterTarget = new Dictionary <int, int>();
_missingXicCounterDecoy = new Dictionary <int, int>();
_xicCorrScoreCounterTarget = new Dictionary <int, Dictionary <int, int> >();
_xicCorrScoreCounterDecoy = new Dictionary <int, Dictionary <int, int> >();
}
public MsGfPostProcessor(IEnumerable <string> specFilePaths, string msGfResultPath, Tolerance tolForBaseXic, Tolerance tolFromBaseXic)
{
MsGfResultPath = msGfResultPath;
ToleranceForBaseXic = tolForBaseXic;
ToleranceFromBasicXic = tolFromBaseXic;
Run = new Dictionary <string, LcMsRun>();
foreach (var specFilePath in specFilePaths)
{
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var specFileKey = Path.GetFileNameWithoutExtension(specFilePath);
if (specFileKey != null)
{
Run[specFileKey] = run;
}
}
}
public void TestXicGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
// Test
var tolerance = new Tolerance(30);
const string peptide = "AIANGQVDGFPTQEECR";
const int targetScanNum = 37633;
const int charge = 2;
//const string peptide = "IVDTNGAGDAFAGGFMAGLTK";
//const int targetScanNum = 67513;
//const int charge = 3;
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
Console.WriteLine("Theoretical isotopomer profile:");
foreach (var p in precursorIon.GetIsotopes(0.1))
{
Console.WriteLine("{0}\t{1}", precursorIon.GetIsotopeMz(p.Index), p.Ratio);
}
var xicArr = new Dictionary <int, Xic>();
var basePeakIndex = precursorIon.Composition.GetMostAbundantIsotopeZeroBasedIndex();
for (var i = -1; i < 3; i++)
{
xicArr[i] = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetIsotopeMz(i), tolerance, targetScanNum);
}
for (var i = -1; i < 3; i++)
{
Console.WriteLine("\nIndex: {0}", i);
Console.WriteLine("m/z: {0}", precursorIon.GetIsotopeMz(i));
Console.WriteLine("#XicPeaks: {0}", xicArr[i].Count);
Console.WriteLine("Intensity: {0}", xicArr[i].GetSumIntensities() / xicArr[basePeakIndex].GetSumIntensities());
Console.WriteLine("Correlation: {0}", xicArr[i].GetCorrelation(xicArr[basePeakIndex]));
}
}
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);
}
public Ms1IsotopeMostAbundantPlusOneFilter(
InMemoryLcMsRun run,
int minCharge = 3, int maxCharge = 30,
double ppmTolerance = 10,
double minMass = 3000.0,
double maxMass = 50000.0,
int maxNumPeaksToConsider = 40)
{
_run = run;
_minCharge = minCharge;
_maxCharge = maxCharge;
MaxNumPeaksToConsider = maxNumPeaksToConsider;
_tolerance = new Tolerance(ppmTolerance);
_comparer = new MzComparerWithTolerance(ppmTolerance);
_lcMsMatchMap = new LcMsMatchMap();
PrecomputePossibleSequenceMasses();
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _tolerance, minMass, maxMass);
}
public void TestPsm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
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);
}
const char pre = 'R';
const string sequence = "LENWPPASLADDL";
const char post = 'A';
const string annotation = "R.LENWPPASLADDL._";
const int charge = 2;
const int ms2ScanNum = 25534;
var aaSet = new AminoAcidSet();
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var ms2Scorer = new ProductScorerBasedOnDeconvolutedSpectra(run, 1, 2, 10, 0, 1.1);
ms2Scorer.DeconvoluteAllProductSpectra();
var scorer = ms2Scorer.GetMs2Scorer(ms2ScanNum);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
graph.SetSink(0);
var score = graph.GetFragmentScore(scorer);
Console.WriteLine("Fast search score: " + score);
var composition = graph.GetSinkSequenceCompositionWithH2O();
var informedScorer = new InformedBottomUpScorer(run, aaSet, 1, 15, new Tolerance(10));
var refinedScore = informedScorer.GetScores(pre, sequence, post, composition, charge, ms2ScanNum);
Console.WriteLine("RefinedScores: {0}", refinedScore);
}
public void TestReadingIsolationWindows()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestLcMsRun.TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestLcMsRun.TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestRawFilePath, 10000, 10100);
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var isolationWindow = run.GetIsolationWindow(scanNum);
if (isolationWindow != null)
{
Console.WriteLine("{0}\t{1}\t{2}", scanNum, isolationWindow.MonoisotopicMz ?? 0.0, isolationWindow.Charge ?? 0.0);
}
}
}
public void TestParsingSpectrumFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
if (!File.Exists(TestTopDownRawFilePathCid))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestTopDownRawFilePathCid);
}
const int SCAN = 425;
const int MAX_POINTS = 50;
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestTopDownRawFilePathCid, SCAN, SCAN);
const int scanNum = SCAN;
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
if (spec != null)
{
spec.Display(MAX_POINTS);
var precursorInfo = spec.IsolationWindow;
Console.WriteLine("ActivationMethod: {0}", spec.ActivationMethod);
Console.WriteLine("Rt: {0}", spec.ElutionTime);
Console.WriteLine("PrecursorScan: {0}", run.GetPrecursorScanNum(spec.ScanNum));
Console.WriteLine("IsolationWindowTargetMz: {0}", precursorInfo.IsolationWindowTargetMz);
Console.WriteLine("IsolationWindowLowerOffset: {0}", precursorInfo.IsolationWindowLowerOffset);
Console.WriteLine("IsolationWindowUpperOffset: {0}", precursorInfo.IsolationWindowUpperOffset);
Console.WriteLine("MsLevel: {0}", run.GetMsLevel(scanNum));
}
Console.WriteLine(@"Done. {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestReadingPbfFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pbfFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.pbf";
if (!File.Exists(pbfFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFilePath);
}
var pbfRun = new PbfLcMsRun(pbfFilePath);
var specFilePath = Path.ChangeExtension(pbfFilePath, "raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
Console.WriteLine(@"Loading .pbf into memory");
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
Console.WriteLine(@"Comparing spectra between .pbf and in-memory spectra");
// spectrum comparison
for (var scanNum = run.MinLcScan; scanNum <= run.MaxLcScan; scanNum++)
{
var spec1 = run.GetSpectrum(scanNum);
var spec2 = pbfRun.GetSpectrum(scanNum);
Assert.IsTrue(spec1.Peaks.Length == spec2.Peaks.Length);
for (var i = 0; i < spec1.Peaks.Length; i++)
{
var p1 = spec1.Peaks[i];
var p2 = spec2.Peaks[i];
Assert.True(p1.Equals(p2));
Assert.True(Math.Abs(p1.Mz - p2.Mz) < 1e-8);
Assert.True(Math.Abs(p1.Intensity - p2.Intensity) < 0.001);
}
}
Console.WriteLine(@"Comparing XICs");
// chromatogram comparison
const double targetMz = 655.01;
var tolerance = new Tolerance(10);
var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
var xic2 = pbfRun.GetFullPrecursorIonExtractedIonChromatogram(targetMz, tolerance);
Assert.True(xic1.Count == xic2.Count);
for (var i = 0; i < xic1.Count; i++)
{
if (!xic1[i].Equals(xic2[i]))
{
Console.WriteLine(@"{0} {1} {2}", i, xic1[i], xic2[i]);
}
Assert.True(xic1[i].Equals(xic2[i]));
}
Console.WriteLine(@"Done");
}
public void TestMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(15);
var productIonTolerance = new Tolerance(15);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.MFQQEVTITAPNGLHTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISAEGEDEQKAVEHLVKLMAELE._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\protoapps\UserData\Jungkap\Joshua\testData\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 6;
const int modIndex = 0;
const int ms2ScanNum = 4448;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestCorrMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(10);
var productIonTolerance = new Tolerance(10);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.TMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASAKHEDMYTAINELINKLERQLNKVQHKGEAR._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 9;
const int modIndex = 0;
const int ms2ScanNum = 3633;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
//var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var scorer = new CorrMatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public IcBottomUpRescorer(string specFilePath, string icResultFilePath, string outputFilePath, AminoAcidSet aaSet, Tolerance tolerance)
{
_run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0.0);
Rescore(icResultFilePath, outputFilePath);
}
public void TestPrSm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownYufeng\raw\yufeng_column_test2.raw";
//const string annotation =
// "_.MKTKLSVLSAAMLAATLTMMPAVSQAAIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVG" +
// "LHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTV" +
// "TSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVG" +
// "IGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGS" +
// "AAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEA" +
// "NQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDL" +
// "KSLKELLKDQEGAVALKIVRGKSMLYLVLR._";
//var aaSet = new AminoAcidSet();
//const int charge = 60;
//const int ms2ScanNum = 46661;
const string specFilePath = @"D:\Research\Data\Jon\AH_SF_mouseliver_3-1_Intact_2_6Feb14_Bane_PL011402.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const int ms2ScanNum = 19011;
const int charge = 7;
const string annotation = "_.SKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVGSC._";
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, true);
var modVal = Modification.RegisterAndGetModification("AddVal", new Composition(5, 9, 1, 1, 0));
var searchMods = AminoAcid.StandardAminoAcidCharacters.Select(residue => new SearchModification(modVal, residue, SequenceLocation.Everywhere, false)).ToList();
searchMods.Add(acetylN);
const int numMaxModsPerProtein = 1;
var aaSet = new AminoAcidSet(searchMods, numMaxModsPerProtein);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
Console.WriteLine("NumProteoforms: " + graph.GetNumProteoformCompositions());
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
var ms2Scorer = new ProductScorerBasedOnDeconvolutedSpectra(run, 1, 15);
ms2Scorer.GetScorer(ms2ScanNum);
var scorer = ms2Scorer.GetMs2Scorer(ms2ScanNum);
Assert.NotNull(scorer, "Scorer is null!");
for (var i = 0; i < graph.GetNumProteoformCompositions(); i++)
{
graph.SetSink(i);
Console.WriteLine("ModComb: " + graph.GetModificationCombinations()[i]);
var score = graph.GetFragmentScore(scorer);
Console.WriteLine("Fast search score: " + score);
var composition = graph.GetSinkSequenceCompositionWithH2O();
var informedScorer = new InformedTopDownScorer(run, aaSet, 1, 30, new Tolerance(10));
var refinedScore = informedScorer.GetScores(AminoAcid.ProteinNTerm, SimpleStringProcessing.GetStringBetweenDots(annotation), AminoAcid.ProteinCTerm, composition, charge, ms2ScanNum);
Console.WriteLine("Modifications: {0}", refinedScore.Modifications);
Console.WriteLine("Composition: {0}", composition);
Console.WriteLine("RefinedScores: {0}", refinedScore);
}
}
public void GeneratePrmInfo(string resultFilePath, string outputFilePath)
{
Console.Write("Processing {0}", Path.GetFileName(resultFilePath));
Console.Out.Flush();
var rawFilePath =
@"D:\Research\Data\EDRN\DDA\raw\" + Path.GetFileNameWithoutExtension(resultFilePath) + ".raw";
var reader = new XCaliburReader(rawFilePath);
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath);
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
const string spikedInPeptideFile = @"D:\Research\Data\EDRN\SpikedPeptides.txt";
var spikedInPeptides = File.ReadAllLines(spikedInPeptideFile);
var spikedInPepSet = new HashSet <string>();
foreach (var p in spikedInPeptides)
{
spikedInPepSet.Add(p);
}
// const string resultFilePath = @"D:\Research\Data\EDRN\DDA\Frac7_NTT2.tsv";
//const string resultFilePath = @"D:\Research\Data\EDRN\DDA\Heavy\342865_EDRN_Serum_07_DDA_1_12Nov13_Samwise_13-07-28.tsv";
// const string resultFilePath = @"D:\Research\Data\EDRN\DDA\NTT1_NoMod\342865_EDRN_Serum_07_DDA_1_12Nov13_Samwise_13-07-28.tsv";
const double qValueThreshold = 0.01;
var pepSet = new HashSet <string>();
MsGfPlusHeaderInformation headerInfo = null;
//var prefix = new HashSet<string>();
//var suffix = new HashSet<string>();
var numPeptides = 0;
var prevScanNum = -1;
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Peptide\tCharge\tMonoMz\tMostAbundantMz\tMs2ScanNum\tRtMs2\tRtApex\tRtStart\tRtEnd\tSpecEValue\tPepQValue");
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
headerInfo = new MsGfPlusHeaderInformation(line);
continue;
}
var match = new MsGfMatch(line, headerInfo);
if (match.ScanNum == prevScanNum)
{
continue;
}
prevScanNum = match.ScanNum;
if (!match.IsValid || match.Protein.StartsWith(FastaDatabase.DecoyProteinPrefix))
{
continue;
}
if (match.PepQValue > qValueThreshold)
{
continue;
}
var peptide = match.Peptide.Replace("C+57.021", "C").Replace("K+8.014", "K").Replace("R+10.008", "R");
if (pepSet.Contains(peptide))
{
continue;
}
pepSet.Add(peptide);
if (spikedInPepSet.Contains(peptide))
{
var ion = new Ion(match.Formula, match.Charge);
var mostAbundantIonMz = ion.GetMostAbundantIsotopeMz();
var xic = run.GetPrecursorExtractedIonChromatogram(mostAbundantIonMz, tolerance, match.ScanNum);
if (xic.Count == 0)
{
continue;
}
var minScan = xic.Min().ScanNum;
var maxScan = xic.Max().ScanNum;
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}",
peptide,
match.Charge,
ion.GetMonoIsotopicMz(),
mostAbundantIonMz,
match.ScanNum,
reader.RtFromScanNum(match.ScanNum),
reader.RtFromScanNum(xic.GetApexScanNum()), // Rt apex
reader.RtFromScanNum(minScan), // Rt start
reader.RtFromScanNum(maxScan), // Rt end
match.SpecEValue,
match.PepQValue);
++numPeptides;
}
//else
//{
// foreach (var spikedInPeptide in spikedInPeptides)
// {
// if (spikedInPeptide.StartsWith(peptide)) prefix.Add(spikedInPeptide + "\t" + peptide + "\t" + match.ScanNum);
// else if (spikedInPeptide.EndsWith(peptide)) suffix.Add(spikedInPeptide + "\t" + peptide + "\t" + match.ScanNum);
// }
//}
}
}
//Console.WriteLine("*********Prefix");
//foreach(var p in prefix) Console.WriteLine(p);
//Console.WriteLine("*********Suffix");
//foreach (var p in suffix) Console.WriteLine(p);
Console.WriteLine("\t{0}", numPeptides);
}
public void TestGeneratingProductXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath);
// const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
const string rafFilePath = @"H:\Research\Jarret\10mz\raw\Q_2014_0523_50_10_fmol_uL_10mz.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping raf portion of test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
var mzArr = new double[100000];
var precursorMzArr = new double[mzArr.Length];
var rnd = new Random();
for (var i = 0; i < mzArr.Length; i++)
{
mzArr[i] = rnd.NextDouble() * 1450.0 + 50.0;
precursorMzArr[i] = rnd.NextDouble() * (810.0 - 390.0) + 390.0;
}
var sw = new System.Diagnostics.Stopwatch();
//double sec;
// method 1
sw.Start();
for (var i = 0; i < mzArr.Length; i++)
{
var mz = mzArr[i];
var tolTh = tolerance.GetToleranceAsTh(mz);
var minMz = mz - tolTh;
var maxMz = mz + tolTh;
var xic1 = run.GetFullProductExtractedIonChromatogram(minMz, maxMz, precursorMzArr[i]);
//var xic2 = rafRun.GetFullProductExtractedIonChromatogram(minMz, maxMz, precursorMzArr[i]);
//Assert.True(xic1.Equals(xic2));
}
sw.Stop();
Console.WriteLine(@"Method 1: {0:f4} sec", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
for (var i = 0; i < mzArr.Length; i++)
{
var mz = mzArr[i];
var tolTh = tolerance.GetToleranceAsTh(mz);
var minMz = mz - tolTh;
var maxMz = mz + tolTh;
rafRun.GetFullProductExtractedIonChromatogram(minMz, maxMz, precursorMzArr[i]);
}
sw.Stop();
Console.WriteLine(@"Method 2: {0:f4} sec", sw.Elapsed.TotalSeconds);
Console.WriteLine(@"Done");
}
public void TestMs1Filtering()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string resultFilePath =
// @"C:\cygwin\home\kims336\Data\TopDown\raw\CorrMatches_N30\SBEP_STM_001_02272012_Aragon.tsv";
@"C:\cygwin\home\kims336\Data\TopDown\raw\CorrMatches_N30\SBEP_STM_001_02272012_Aragon.decoy.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\DataFiles\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);
//const int minPrecursorCharge = 3;
//const int maxPrecursorCharge = 30;
//const int tolerancePpm = 15;
var tolerance = new Tolerance(15);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 0.7, 40);
////var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//ISequenceFilter ms1Filter = ms1BasedFilter;
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var qValues = tsvReader.GetData("QValue");
var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Annotation");
//var hist = new int[11];
Console.WriteLine("ScanNum\tScore\tPrecursor\tNext\tSum\tNextIsotope\tLessCharge\tMoreCharge\tMax\tNumXicPeaks");
for (var i = 0; i < compositions.Count; i++)
{
if (qValues != null)
{
var qValue = Convert.ToDouble(qValues[i]);
if (qValue > 0.01)
{
continue;
}
}
var scanNum = Convert.ToInt32(scanNums[i]);
var composition = Composition.Parse(compositions[i]);
var charge = Convert.ToInt32(charges[i]);
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
var score = Convert.ToDouble(scores[i]);
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var preIsotopeCorr = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var nextIsotopeCorr = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var xicMostAbundant = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var apexScanNum = xicMostAbundant.GetApexScanNum();
if (apexScanNum < run.MinLcScan)
{
apexScanNum = scanNum;
}
//var sumSpec = run.GetSummedMs1Spectrum(apexScanNum);
// var apexIsotopeCorr = sumSpec.GetCorrScore(precursorIon, tolerance, 0.1);
// var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
var xicNextIsotope = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz() + Constants.C13MinusC12 / charge, tolerance, scanNum);
var plusOneIsotopeCorr = xicMostAbundant.GetCorrelation(xicNextIsotope);
var precursorIonChargeMinusOne = new Ion(composition, charge - 1);
var xicChargeMinusOne = run.GetPrecursorExtractedIonChromatogram(precursorIonChargeMinusOne.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var chargeMinusOneCorr = xicMostAbundant.GetCorrelation(xicChargeMinusOne);
var precursorIonChargePlusOne = new Ion(composition, charge + 1);
var xicChargePlusOne = run.GetPrecursorExtractedIonChromatogram(precursorIonChargePlusOne.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var chargePlusOneCorr = xicMostAbundant.GetCorrelation(xicChargePlusOne);
//var max = new[] {preIsotopeCorr, nextIsotopeCorr, apexIsotopeCorr, plusOneIsotopeCorr, chargeMinusOneCorr, chargePlusOneCorr}.Max();
//Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}",
// scanNum, score, preIsotopeCorr, nextIsotopeCorr, apexIsotopeCorr, plusOneIsotopeCorr, chargeMinusOneCorr, chargePlusOneCorr, max, xicMostAbundant.Count);
}
//Console.WriteLine("Histogram");
//for (var i = 0; i < hist.Length; i++)
//{
// Console.WriteLine("{0:f1}\t{1}", i / 10.0, hist[i]);
//}
}
public void TestGettingXicVector()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run1 = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
var run2 = InMemoryLcMsRun.GetLcMsRun(TestRawFilePath, 0.0, 0.0);
Assert.True(run1 != null && run2 != null);
var comparer = new MzComparerWithBinning(27);
const double minMz = 600.0; // 600.0
const double maxMz = 2000.0; // 2000.0
var minBinNum = comparer.GetBinNumber(minMz);
var maxBinNum = comparer.GetBinNumber(maxMz);
Console.WriteLine(@"NumBins: " + (maxBinNum - minBinNum));
var warnCount = 0;
var sw = new Stopwatch();
sw.Start();
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mzStart = comparer.GetMzStart(binNum);
var mzEnd = comparer.GetMzEnd(binNum);
var vec1 = run1.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
var vec2 = run2.GetFullPrecursorIonExtractedIonChromatogramVector(mzStart, mzEnd);
Assert.True(vec1.Length == vec2.Length,
"Extracted Ion Chromatogram vector length mismatch, {0} vs. {1}", vec1.Length, vec2.Length);
var matchCount = 0;
var misMatchCount = 0;
var positiveCount = 0;
for (var i = 0; i < vec2.Length; i++)
{
if (vec1[i] > 0 || vec2[i] > 0)
{
positiveCount++;
}
if (Math.Abs(vec1[i] - vec2[i]) < float.Epsilon)
{
matchCount++;
}
else
{
misMatchCount++;
}
}
if (misMatchCount <= 0 || positiveCount == 0)
{
continue;
}
var fractionAgreement = 1 - misMatchCount / (double)positiveCount;
if (fractionAgreement < 0.80 && misMatchCount > 2)
{
Console.WriteLine(@"{0}/{1} Xic values do not match for bin {2} ({3:0.00} m/z); {4:0.0}% agreement",
misMatchCount, positiveCount, binNum, mzStart, fractionAgreement * 100);
warnCount++;
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
Assert.IsTrue(warnCount < 10, "Too many Xic mismatch warnings: {0}", warnCount);
}
public void FilteringEfficiency()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
var sequence = sequences[i];
if (sequenceCount.TryGetValue(sequence, out var 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 isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && 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 FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && 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);
}
