public static Spectrum GetDeconvolutedSpectrum(Spectrum spec, int minCharge, int maxCharge, Tolerance tolerance, double corrThreshold,
int isotopeOffsetTolerance, double filteringWindowSize = 1.1)
{
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(spec, minCharge, maxCharge, isotopeOffsetTolerance, filteringWindowSize, tolerance, corrThreshold);
var peakList = new List <Peak>();
var binHash = new HashSet <int>();
foreach (var deconvolutedPeak in deconvolutedPeaks)
{
var mass = deconvolutedPeak.Mass;
var binNum = GetBinNumber(mass);
if (!binHash.Add(binNum))
{
continue;
}
peakList.Add(new Peak(mass, deconvolutedPeak.Intensity));
}
var productSpec = spec as ProductSpectrum;
if (productSpec != null)
{
return(new ProductSpectrum(peakList, spec.ScanNum)
{
MsLevel = spec.MsLevel,
ActivationMethod = productSpec.ActivationMethod,
IsolationWindow = productSpec.IsolationWindow
});
}
return(new Spectrum(peakList, spec.ScanNum));
}
private DeconvolutedSpectrum GetDeconvolutedSpectrum(int scan, PbfLcMsRun pbfLcMsRun)
{
var spectrum = pbfLcMsRun.GetSpectrum(scan) as ProductSpectrum;
if (spectrum == null)
{
return(null);
}
return(Deconvoluter.GetCombinedDeconvolutedSpectrum(spectrum, 1, 20, 2, new Tolerance(10, ToleranceUnit.Ppm), 0.7));
}
public IScorer GetScorer(int scanNum)
{
var spec = _run.GetSpectrum(scanNum) as ProductSpectrum;
if (spec == null)
{
return(null);
}
var deconvolutedSpec = Deconvoluter.GetDeconvolutedSpectrum(spec, _minProductCharge, _maxProductCharge, IsotopeOffsetTolerance, FilteringWindowSize, _productTolerance);
return(deconvolutedSpec != null ? new CompositeScorerBasedOnDeconvolutedSpectrum(deconvolutedSpec, spec, _productTolerance, _comparer) : null);
}
public IScorer GetScorer(int scanNum)
{
try
{
if (!(_run.GetSpectrum(scanNum) is ProductSpectrum spec))
{
return(null);
}
var deconvolutedSpec = Deconvoluter.GetDeconvolutedSpectrum(spec, _minProductCharge, _maxProductCharge, IsotopeOffsetTolerance, FilteringWindowSize, _productTolerance);
return(deconvolutedSpec != null ? new CompositeScorerBasedOnDeconvolutedSpectrum(deconvolutedSpec, spec, _productTolerance, _comparer) : null);
}
catch (Exception ex)
{
throw new Exception(string.Format("Error getting the scorer for scan {0} in GetScorer: {1}", scanNum, ex.Message), ex);
}
}
public SequenceTagFinder(ProductSpectrum spec, Tolerance tolerance, int minTagLength = 5, int maxTagLength = 8, AminoAcid[] aminoAcidsArray = null)
: base(maxTagLength)
{
var baseIonTypes = spec.ActivationMethod != ActivationMethod.ETD ? BaseIonTypesCID : BaseIonTypesETD;
var ionTypeFactory = new IonTypeFactory(baseIonTypes, new List <NeutralLoss> {
NeutralLoss.NoLoss
}, MaxCharge);
// ReSharper disable once UnusedVariable
// This call is used to validate the ion types returned by ionTypeFactory
var _ionTypes = ionTypeFactory.GetAllKnownIonTypes().ToArray();
_aminoAcidsArray = aminoAcidsArray ?? AminoAcid.StandardAminoAcidArr;
_tolerance = tolerance;
if (_aminoAcidsArray.Length - 1 > Byte.MaxValue)
{
throw new Exception("Too many amino acid types");
}
_maxAminoAcidMass = 0d;
_minAminoAcidMass = 10E4;
foreach (var aa in _aminoAcidsArray)
{
if (aa.Composition.Mass > _maxAminoAcidMass)
{
_maxAminoAcidMass = aa.Composition.Mass;
}
if (aa.Composition.Mass < _minAminoAcidMass)
{
_minAminoAcidMass = aa.Composition.Mass;
}
}
_minTagLength = minTagLength;
_spectrum = spec;
_deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(_spectrum.ScanNum, _spectrum.Peaks, MinCharge, MaxCharge, IsotopeOffsetTolerance, 1.1, _tolerance, 0.7);
SetNodeCount(_deconvolutedPeaks.Count);
CollectSequenceTagGraphEdges();
_seqTagSet = new HashSet <SequenceTag>();
NumberOfProcessedPaths = 0;
MaxNumberOfProcessedPaths = 1024;
}
public void CountScansTest()
{
var file = @"C:\Users\wilk011\Documents\DataFiles\MSPF\Ecoli_Ribosome\Ecoli_intact_UVPD-3pulse0p5mJ_05-20-2017.pbf";
var pbfLcmsRun = PbfLcMsRun.GetLcMsRun(file);
var deconvoluter = new Deconvoluter(1, 20, 2, 0.1, new Tolerance(10, ToleranceUnit.Ppm));
var lcmsRunDecon = new LcmsRunDeconvoluter(pbfLcmsRun, deconvoluter, 2, 6);
var dlcms = new DPbfLcMsRun(file, lcmsRunDecon, keepDataReaderOpen: true);
int count = 0;
var scans = pbfLcmsRun.GetScanNumbers(2);
foreach (var scan in scans)
{
var spectrum = pbfLcmsRun.GetSpectrum(scan) as ProductSpectrum;
if (spectrum.Peaks.Length < 50 || spectrum.IsolationWindow.Charge == null)
{
continue;
}
count++;
}
Console.WriteLine(count);
}
public void TestCompositeScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string rawFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SpecFiles\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string rawFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
const int minCharge = 1;
const int maxCharge = 20;
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
var aminoAcidSet = new AminoAcidSet();
//var scorer = new MatchedPeakPostScorer(tolerance, minCharge, maxCharge);
var scorer = new InformedTopDownScorer(run, aminoAcidSet, minCharge, maxCharge, tolerance);
var fileExt = new string[] { "IcTarget", "IcDecoy" };
foreach (var ext in fileExt)
{
var resultFileName = string.Format(@"D:\MassSpecFiles\training\Rescoring\QC_Shew_Intact_26Sep14_Bane_C2Column3_{0}.tsv", ext);
var parser = new TsvFileParser(resultFileName);
var scans = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var charges = parser.GetData("Charge").Select(s => Convert.ToInt32(s)).ToArray();
var protSequences = parser.GetData("Sequence").ToArray();
var modStrs = parser.GetData("Modifications").ToArray();
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var protMass = parser.GetData("Mass").Select(s => Convert.ToDouble(s)).ToArray();
var outputFileName = string.Format(@"D:\MassSpecFiles\training\Rescoring\QC_Shew_Intact_26Sep14_Bane_C2Column3_{0}_Rescored.tsv", ext);
using (var writer = new StreamWriter(outputFileName))
{
writer.WriteLine(string.Join("\t", parser.GetHeaders().ToArray(), 0, 15) + "\tScore\tEValue");
var lines = new string[parser.NumData];
//for (var i = 0; i < parser.NumData; i++)
Parallel.For(0, parser.NumData, i =>
{
var scan = scans[i];
var charge = charges[i];
var protSequence = protSequences[i];
var modStr = modStrs[i];
var sequence = Sequence.CreateSequence(protSequence, modStr, aminoAcidSet);
Assert.True(sequence.Composition.Equals(compositions[i] - Composition.H2O));
var ms2Spec = run.GetSpectrum(scan) as ProductSpectrum;
Assert.True(ms2Spec != null);
var scores = scorer.GetScores(sequence, charge, scan);
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(ms2Spec, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
var deconvScorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, ms2Spec, tolerance,
comparer);
var graph = graphFactory.CreateScoringGraph(deconvScorer, protMass[i]);
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
var specEvalue = gf.GetSpectralEValue(scores.Score);
var rowStr = parser.GetRows()[i];
var items = rowStr.Split('\t').ToArray();
var newRowStr = string.Join("\t", items, 0, 15);
//writer.WriteLine("{0}\t{1}\t{2}", newRowStr, scores.Score, specEvalue);
lock (lines)
{
lines[i] = string.Format("{0}\t{1}\t{2}", newRowStr, scores.Score, specEvalue);
}
//Console.WriteLine("{0}\t{1}\t{2}", items[0], scores.Score, specEvalue);
});
foreach (var line in lines)
{
writer.WriteLine(line);
}
}
Console.WriteLine("Done");
}
}
/// <summary>
/// Get correctly filtered and/or de-convoluted spectrum
/// </summary>
/// <returns>Filtered and/or de-convoluted spectrum</returns>
private Spectrum GetSpectrum()
{
// Filtered/Deconvoluted Spectrum?
var currentSpectrum = this.Spectrum;
var tolerance = (currentSpectrum is ProductSpectrum)
? IcParameters.Instance.ProductIonTolerancePpm
: IcParameters.Instance.PrecursorTolerancePpm;
if (this.ShowFilteredSpectrum && this.ShowDeconvolutedSpectrum)
{
if (this.filteredDeconvolutedSpectrum == null)
{
this.filteredDeconvolutedSpectrum = new Spectrum(currentSpectrum.Peaks, currentSpectrum.ScanNum);
this.filteredDeconvolutedSpectrum.FilterNosieByIntensityHistogram();
this.deconvolutedSpectrum = Deconvoluter.GetCombinedDeconvolutedSpectrum(
currentSpectrum,
Constants.MinCharge,
Constants.MaxCharge,
Constants.IsotopeOffsetTolerance,
tolerance,
IcParameters.Instance.IonCorrelationThreshold);
//this.deconvolutedSpectrum = ProductScorerBasedOnDeconvolutedSpectra.GetDeconvolutedSpectrum(
// currentSpectrum,
// Constants.MinCharge,
// Constants.MaxCharge,
// tolerance,
// IcParameters.Instance.IonCorrelationThreshold,
// Constants.IsotopeOffsetTolerance);
}
currentSpectrum = this.filteredDeconvolutedSpectrum;
}
else if (this.ShowFilteredSpectrum)
{
if (this.filteredSpectrum == null)
{
this.filteredSpectrum = new Spectrum(currentSpectrum.Peaks, currentSpectrum.ScanNum);
this.filteredSpectrum.FilterNosieByIntensityHistogram();
}
currentSpectrum = this.filteredSpectrum;
}
else if (this.ShowDeconvolutedSpectrum)
{
if (this.deconvolutedSpectrum == null)
{
this.deconvolutedSpectrum = Deconvoluter.GetCombinedDeconvolutedSpectrum(
currentSpectrum,
Constants.MinCharge,
Constants.MaxCharge,
Constants.IsotopeOffsetTolerance,
tolerance,
IcParameters.Instance.IonCorrelationThreshold);
//this.deconvolutedSpectrum = ProductScorerBasedOnDeconvolutedSpectra.GetDeconvolutedSpectrum(
// currentSpectrum,
// Constants.MinCharge,
// Constants.MaxCharge,
// tolerance,
// IcParameters.Instance.IonCorrelationThreshold,
// Constants.IsotopeOffsetTolerance);
}
currentSpectrum = this.deconvolutedSpectrum;
}
if (this.ShowOnlyTop20Peaks)
{
var top20Peaks = currentSpectrum.Peaks.OrderByDescending(p => p.Intensity).Take(20).OrderBy(p => p.Mz).ToList();
currentSpectrum = new Spectrum(top20Peaks, currentSpectrum.ScanNum);
}
return(currentSpectrum);
}
} // true: target and decoy, false: target only, null: decoy only
public void QuickId()
{
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 1;
const int maxCharge = 20;
var tolerance = new Tolerance(10);
const double corrThreshold = 0.7;
var comparer = new MzComparerWithBinning(numBits);
const double minFragmentMass = 200.0;
const double maxFragmentMass = 50000.0;
var minFragMassBin = comparer.GetBinNumber(minFragmentMass);
var maxFragMassBin = comparer.GetBinNumber(maxFragmentMass);
var aminoAcidSet = new AminoAcidSet(modFilePath);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ms2ScanNumArr = run.GetScanNumbers(2).ToArray();
var sw = new Stopwatch();
sw.Start();
Console.Write("Building Spectrum Arrays...");
var massVectors = new BitArray[maxFragMassBin - minFragMassBin + 1];
for (var i = minFragMassBin; i <= maxFragMassBin; i++)
{
massVectors[i - minFragMassBin] = new BitArray(run.MaxLcScan + 1);
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
var productSpec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (productSpec == null)
{
continue;
}
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec.Peaks, minCharge, maxCharge, 2, 1.1, tolerance, corrThreshold);
if (deconvolutedPeaks == null)
{
continue;
}
foreach (var p in deconvolutedPeaks)
{
var mass = p.Mass;
var deltaMass = tolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = comparer.GetBinNumber(minMass);
var maxBinNum = comparer.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (binNum >= minFragMassBin && binNum <= maxFragMassBin)
{
massVectors[binNum - minFragMassBin][ms2ScanNum] = true;
}
}
}
}
sw.Stop();
Console.WriteLine(@"{0:f1} sec.", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var indexedDb = new IndexedDatabase(fastaDb);
var numProteins = 0;
var intactProteinAnnotationAndOffsets =
indexedDb.IntactSequenceAnnotationsAndOffsets(0, int.MaxValue);
var bestProtein = new string[run.MaxLcScan + 1];
var bestScore = new int[run.MaxLcScan + 1];
foreach (var annotationAndOffset in intactProteinAnnotationAndOffsets)
{
if (++numProteins % 10 == 0)
{
Console.WriteLine(@"Processing, {0} proteins done, {1:f1} sec elapsed",
numProteins,
sw.Elapsed.TotalSeconds);
}
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var protSequence = annotation.Substring(2, annotation.Length - 4);
// suffix
var seqGraph = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
continue;
}
for (var numNTermCleavage = 0; numNTermCleavage <= 1; numNTermCleavage++)
{
if (numNTermCleavage > 0)
{
seqGraph.CleaveNTerm();
}
var allCompositions = seqGraph.GetAllFragmentNodeCompositions();
var scoreArr = new int[run.MaxLcScan + 1];
foreach (var fragComp in allCompositions)
{
var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
var binNum = comparer.GetBinNumber(suffixMass);
if (binNum < minFragMassBin || binNum > maxFragMassBin)
{
continue;
}
var vector = massVectors[binNum - minFragMassBin];
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (vector[ms2ScanNum])
{
++scoreArr[ms2ScanNum];
}
}
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
{
bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
var proteinName = fastaDb.GetProteinName(offset);
bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
}
}
}
// prefix
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestScore[ms2ScanNum], bestProtein[ms2ScanNum] ?? "");
}
}
public void TestGetScoreDistribution(int scanNum, string protSequence)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
if (!pbfFile.Exists)
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFile);
}
const string modStr = "";
const int maxCharge = 20;
const int minCharge = 1;
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
var run = PbfLcMsRun.GetLcMsRun(pbfFile.FullName);
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
//Console.WriteLine("{0}\t{1}", comparer.NumberOfBins, comparer.GetBinNumber(proteinMass));
var stopwatch = Stopwatch.StartNew();
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
stopwatch.Stop();
Console.WriteLine(@"edge generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var stopwatch2 = Stopwatch.StartNew();
var sequence = Sequence.CreateSequence(protSequence, modStr, aaSet);
var proteinMass = sequence.Mass + Composition.H2O.Mass;
Console.WriteLine("Mass = {0}", proteinMass);
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(spectrum, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
stopwatch.Restart();
var scorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, spectrum, tolerance, comparer);
var graph = graphFactory.CreateScoringGraph(scorer, proteinMass);
stopwatch.Stop();
Console.WriteLine(@"node generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
stopwatch.Reset();
stopwatch.Start();
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
//gf.ComputeGeneratingFunction(graph);
stopwatch.Stop();
Console.WriteLine(@"computing generation function = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var scoreDist = gf.GetScoreDistribution();
Console.WriteLine("{0}-{1}", scoreDist.MinScore, scoreDist.MaxScore);
Console.WriteLine("{0} : {1}", "score", "specEValue");
for (var score = 15; score <= gf.MaximumScore; score++)
{
var specEvalue = gf.GetSpectralEValue(score);
Console.WriteLine("{0} : {1}", score, specEvalue);
}
stopwatch2.Stop();
Console.WriteLine(@"TOTAL computing generation function = {0:0.000} sec", stopwatch2.ElapsedMilliseconds / 1000.0d);
}
public void TestCompositeScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
var run = PbfLcMsRun.GetLcMsRun(pbfFile.FullName);
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
const int minCharge = 1;
const int maxCharge = 20;
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
var aminoAcidSet = new AminoAcidSet();
//var scorer = new MatchedPeakPostScorer(tolerance, minCharge, maxCharge);
var scorer = new InformedTopDownScorer(run, aminoAcidSet, minCharge, maxCharge, tolerance);
if (pbfFile.DirectoryName == null)
{
Assert.Ignore("Ignoring test since cannot determine the parent directory of " + pbfFile.FullName);
}
var fileExt = new string[] { "IcTarget", "IcDecoy" };
foreach (var ext in fileExt)
{
var resultFileName = Path.Combine(pbfFile.DirectoryName, Path.GetFileNameWithoutExtension(pbfFile.Name)) + string.Format("_{0}.tsv", ext);
var parser = new TsvFileParser(resultFileName);
var scans = parser.GetData("Scan").Select(s => Convert.ToInt32((string)s)).ToArray();
var charges = parser.GetData("Charge").Select(s => Convert.ToInt32(s)).ToArray();
var protSequences = parser.GetData("Sequence").ToArray();
var modStrs = parser.GetData("Modifications").ToArray();
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var protMass = parser.GetData("Mass").Select(s => Convert.ToDouble(s)).ToArray();
var outputFileName = Path.Combine(pbfFile.DirectoryName, Path.GetFileNameWithoutExtension(pbfFile.Name)) + string.Format("_{0}_Rescored.tsv", ext);
using (var writer = new StreamWriter(outputFileName))
{
writer.WriteLine(string.Join("\t", parser.GetHeaders().ToArray(), 0, 15) + "\tScore\tEValue");
var lines = new string[parser.NumData];
//for (var i = 0; i < parser.NumData; i++)
Parallel.For(0, 30, i =>
{
var scan = scans[i];
var charge = charges[i];
var protSequence = protSequences[i];
var modStr = modStrs[i];
var sequence = Sequence.CreateSequence(protSequence, modStr, aminoAcidSet);
// Assert.True(sequence.Composition.Equals(compositions[i] - Composition.H2O));
var ms2Spec = run.GetSpectrum(scan) as ProductSpectrum;
if (ms2Spec == null)
{
Console.WriteLine("Could not get the spectrum datafor scan {0}", scan);
}
else
{
Assert.True(ms2Spec != null);
var scores = scorer.GetScores(sequence, charge, scan);
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(ms2Spec, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
var deconvScorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, ms2Spec, tolerance,
comparer);
var graph = graphFactory.CreateScoringGraph(deconvScorer, protMass[i]);
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
var specEvalue = gf.GetSpectralEValue(scores.Score);
var rowStr = parser.GetRows()[i];
var items = rowStr.Split('\t').ToArray();
var newRowStr = string.Join("\t", items, 0, 15);
//writer.WriteLine("{0}\t{1}\t{2}", newRowStr, scores.Score, specEvalue);
lines[i] = string.Format("{0}\t{1}\t{2}", newRowStr, scores.Score, specEvalue);
//Console.WriteLine("{0}\t{1}\t{2}", items[0], scores.Score, specEvalue);
}
});
foreach (var line in (from item in lines where !string.IsNullOrWhiteSpace(item) select item).Take(20))
{
Console.WriteLine(line);
}
}
Console.WriteLine("Done");
}
}
public void TestGetScoreDistribution()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string idFileFolder = @"D:\MassSpecFiles\training\IdScoring\MSPF_trainset";
const int scanNum = 5927;
const string protSequence = "MNKSELIEKIASGADISKAAAGRALDSFIAAVTEGLKEGDKISLVGFGTFEVRERAERTGRNPQTGEEIKIAAAKIPAFKAGKALKDAVN";
const string modStr = "";
var idFile = string.Format(@"{0}\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv", idFileFolder);
if (!File.Exists(idFile))
{
return;
}
//Console.WriteLine(dataset);
if (!File.Exists(rawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFile);
}
const int maxCharge = 20;
const int minCharge = 1;
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
//Console.WriteLine("{0}\t{1}", comparer.NumberOfBins, comparer.GetBinNumber(proteinMass));
var stopwatch = Stopwatch.StartNew();
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
stopwatch.Stop();
Console.WriteLine(@"edge generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var n = 0;
var stopwatch2 = Stopwatch.StartNew();
var sequence = Sequence.CreateSequence(protSequence, modStr, aaSet);
var proteinMass = sequence.Mass + Composition.H2O.Mass;
Console.WriteLine("Mass = {0}", proteinMass);
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(spectrum, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
stopwatch.Restart();
var scorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, spectrum, tolerance, comparer);
var graph = graphFactory.CreateScoringGraph(scorer, proteinMass);
stopwatch.Stop();
Console.WriteLine(@"node generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
stopwatch.Reset();
stopwatch.Start();
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
//gf.ComputeGeneratingFunction(graph);
stopwatch.Stop();
Console.WriteLine(@"computing generation function = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var scoreDist = gf.GetScoreDistribution();
Console.WriteLine("{0}-{1}", scoreDist.MinScore, scoreDist.MaxScore);
for (var score = 45; score <= gf.MaximumScore; score++)
{
var specEvalue = gf.GetSpectralEValue(score);
Console.WriteLine("{0} : {1}", score, specEvalue);
}
stopwatch2.Stop();
Console.WriteLine(@"TOTAL computing generation function = {0:0.000} sec", (stopwatch2.ElapsedMilliseconds) / 1000.0d);
}
