public void TestGettingXicVector()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 TestMsAlignPlusResults()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
const string msAlignPlusResultPath = @"C:\workspace\TopDown\E_coli_iscU_60_mock_MSAlign_ResultTable_sam.txt";
var dehydro = new SearchModification(Modification.PyroGluQ, 'C', SequenceLocation.Everywhere, false);
var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, 0);
var precursorTolerance = new Tolerance(10);
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var writer = new StreamWriter(msAlignPlusResultPath + ".txt");
var reader = new StreamReader(msAlignPlusResultPath);
string s;
while ((s = reader.ReadLine()) != null)
{
if (s.StartsWith("Data_file_name "))
{
writer.WriteLine(s + "\tScore");
continue;
}
var token = s.Split('\t');
var annotation = token[13];
// Console.WriteLine("***\t" + annotation);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
if (seqGraph == null)
{
writer.WriteLine(s + "\tN/A");
continue;
}
var protCompositions = seqGraph.GetSequenceCompositions();
var scorer = new TopDownScorer(protCompositions[0], run, precursorTolerance, null);
var score = scorer.GetScore();
writer.WriteLine(s + "\t" + score);
Console.WriteLine(score);
}
writer.Close();
reader.Close();
}
public void AnalyizeFusionDdaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
//const double relativeIntensityThreshold = 0.7;
const double precursorTolerancePpm = 20;
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
const double fdrThreshold = 0.01;
var tolerance = new Tolerance(precursorTolerancePpm);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string resultFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618_10ppm_TI2_SGD_Decoy.tsv";
Console.WriteLine("IsDecoy\tPeptide\tScanNum\tCharge\tSpecEValue\tQValue\tPrecursorMz" +
"\tTheo0\tTheo1\tTheo2\tTheo3" +
"\tObs0\tCorr0\tObs1\tCorr1\tObs2\tCorr2\tObs3\tCorr3\tObs-1\tCorr-1\tObs0.5\tCorr0.5");
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
continue;
}
var token = line.Split('\t');
if (token.Length != 16)
{
continue;
}
var qValue = Convert.ToDouble(token[14]);
if (qValue > fdrThreshold)
{
continue;
}
var peptide = token[8].Replace("C+57.021", "C");
var scanNum = Convert.ToInt32(token[2]);
var charge = Convert.ToInt32(token[7]);
var specEValue = Convert.ToDouble(token[12]);
var protein = token[9];
var isDecoy = protein.StartsWith("XXX_");
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
var baseXic = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var baseIntensity = baseXic.GetSumIntensities();
Console.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", (isDecoy ? 1 : 0), peptide, scanNum, charge, specEValue, qValue, precursorIon.GetMonoIsotopicMz());
var isotopeIndices = new double[] { 0, 1, 2, 3, -1, 0.5 };
var theoIsotopes = precursorIon.GetIsotopes(0.01);
var numIsotopes = 0;
foreach (var theoIsotope in theoIsotopes)
{
Console.Write("\t" + theoIsotope.Ratio);
if (++numIsotopes == 4)
{
break;
}
}
foreach (var isotopeIndex in isotopeIndices)
{
var isotopeMz = precursorIon.GetIsotopeMz(isotopeIndex);
var xic = run.GetPrecursorExtractedIonChromatogram(isotopeMz, tolerance, scanNum);
var relativeIntensity = xic.GetSumIntensities() / baseIntensity;
var correlation = xic.GetCorrelation(baseXic);
Console.Write("\t{0}\t{1}", relativeIntensity, correlation);
}
Console.WriteLine();
}
}
public void TestGeneratingProductXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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.GetToleranceAsMz(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.GetToleranceAsMz(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 TestFusionDdaData()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
const double relativeIntensityThreshold = 0.7;
const double precursorTolerancePpm = 20;
//const double isotopeRatioTolerance = 2;
//const double correlationThreshold = 0.3;
const double fdrThreshold = 0.01;
const string specFilePath = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var tolerance = new Tolerance(precursorTolerancePpm);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
const string resultFilePath = @"D:\Research\Data\UW\Fusion\oldResult\WT_D_DDA_130412065618_10ppm_TI2_SGD_Decoy.tsv";
var numTargets = 0;
var numValidTargets = 0;
var numDecoys = 0;
var numValidDecoys = 0;
foreach (var line in File.ReadLines(resultFilePath))
{
if (line.StartsWith("#"))
{
continue;
}
var token = line.Split('\t');
if (token.Length != 16)
{
continue;
}
var qValue = Convert.ToDouble(token[14]);
if (qValue > fdrThreshold)
{
continue;
}
var peptide = token[8].Replace("C+57.021", "C");
var scanNum = Convert.ToInt32(token[2]);
var charge = Convert.ToInt32(token[7]);
var protein = token[9];
var isDecoy = protein.StartsWith("XXX_");
if (isDecoy)
{
numDecoys++;
}
else
{
numTargets++;
}
var precursorIon = new Ion(aaSet.GetComposition(peptide) + Composition.H2O, charge);
var basePeakIndex = precursorIon.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var baseXic = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var baseIntensity = baseXic.GetSumIntensities();
var isValid = true;
foreach (var isotope in precursorIon.GetIsotopes(relativeIntensityThreshold))
{
if (isotope.Index == basePeakIndex)
{
continue;
}
var isotopeMz = precursorIon.GetIsotopeMz(isotope.Index);
var xic = run.GetPrecursorExtractedIonChromatogram(isotopeMz, tolerance, scanNum);
if (xic.Count == 0)
{
isValid = false;
break;
}
//if (xic.Count > 0)
//{
// var isotopeRatio = xic.GetSumIntensities() / baseIntensity / isotope.Item2;
// var correlation = xic.GetCorrelation(baseXic);
// if (isotopeRatio > 0.8 && isotopeRatio < 1.2
// && correlation > 0.8)
// {
// isValid = true;
// }
//}
// Check if isotope ratio is within tolerance
//if (isotopeRatio > isotopeRatioTolerance || isotopeRatio < 1 / isotopeRatioTolerance)
//{
// isValid = false;
// //Console.WriteLine("Off ratio\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", isDecoy, peptide, scanNum, charge, precursorIon.GetMonoIsotopicMz(), isotopeMz, isotopeRatio);
// break;
//}
// Check if correlation is high
//if (correlation < correlationThreshold)
//{
// isValid = false;
// //Console.WriteLine("Low correlation\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", isDecoy, peptide, scanNum, charge, precursorIon.GetMonoIsotopicMz(), isotopeMz, correlation);
// break;
//}
}
if (isValid && !isDecoy)
{
numValidTargets++;
}
else if (isValid)
{
numValidDecoys++;
}
//Console.WriteLine("{0}\t{1}\t{2}", peptide, scanNum, charge);
}
Console.WriteLine("#Targets: {0}", numTargets);
Console.WriteLine("#ValidTargets: {0}\t{1}", numValidTargets, numValidTargets / (double)numTargets);
Console.WriteLine("#Decoys: {0}", numDecoys);
Console.WriteLine("#ValidDecoys: {0}\t{1}", numValidDecoys, numValidDecoys / (double)numDecoys);
sw.Stop();
Console.WriteLine(@"TimeForPrecursorValidation {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 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 spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && 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 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 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 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 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);
}
