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");
}
}
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);
}
private DatabaseSequenceSpectrumMatch[] RunGeneratingFunction(SortedSet <DatabaseSequenceSpectrumMatch>[] sortedMatches, CancellationToken?cancellationToken = null, IProgress <ProgressData> progress = null)
{
var progData = new ProgressData(progress)
{
Status = "Calculating spectral E-values for matches"
};
if (_cachedScoreDistributions == null)
{
_cachedScoreDistributions = new LinkedList <Tuple <double, ScoreDistribution> > [_run.MaxLcScan + 1];
foreach (var scanNum in _ms2ScanNums)
{
_cachedScoreDistributions[scanNum] = new LinkedList <Tuple <double, ScoreDistribution> >();
}
}
var sw = new Stopwatch();
var topDownScorer = new InformedTopDownScorer(_run, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
// Rescore and Estimate #proteins for GF calculation
var matches = new LinkedList <DatabaseSequenceSpectrumMatch> [sortedMatches.Length];
long estimatedProteins = 0;
foreach (var scanNum in _ms2ScanNums)
{
var prsms = sortedMatches[scanNum];
if (prsms == null)
{
continue;
}
var spec = _run.GetSpectrum(scanNum) as ProductSpectrum;
if (spec == null)
{
return(null);
}
foreach (var match in prsms)
{
var sequence = match.Sequence;
var ion = match.Ion;
// Re-scoring
var scores = topDownScorer.GetScores(spec, sequence, ion.Composition, ion.Charge, scanNum);
if (scores == null)
{
continue;
}
match.Score = scores.Score;
match.ModificationText = scores.Modifications;
match.NumMatchedFragments = scores.NumMatchedFrags;
if (match.Score > CompositeScorer.ScoreParam.Cutoff)
{
if (matches[scanNum] == null)
{
matches[scanNum] = new LinkedList <DatabaseSequenceSpectrumMatch>();
}
matches[scanNum].AddLast(match);
}
}
if (matches[scanNum] != null)
{
estimatedProteins += matches[scanNum].Count;
}
}
Console.WriteLine(@"Estimated matched proteins: " + estimatedProteins);
var numProteins = 0;
var lastUpdate = DateTime.MinValue; // Force original update of 0%
sw.Reset();
sw.Start();
var scanNums = _ms2ScanNums.Where(scanNum => matches[scanNum] != null).ToArray();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
Parallel.ForEach(scanNums, pfeOptions, scanNum =>
{
var currentTask = "?";
try
{
var scoreDistributions = _cachedScoreDistributions[scanNum];
foreach (var match in matches[scanNum])
{
var currentIteration = "for scan " + scanNum + " and mass " + match.Ion.Composition.Mass;
currentTask = "Calling GetMs2ScoringGraph " + currentIteration;
var graph = _ms2ScorerFactory2.GetMs2ScoringGraph(scanNum, match.Ion.Composition.Mass);
if (graph == null)
{
continue;
}
currentTask = "Calling ComputeGeneratingFunction " + currentIteration;
var scoreDist = (from distribution in scoreDistributions
where Math.Abs(distribution.Item1 - match.Ion.Composition.Mass) < PrecursorIonTolerance.GetToleranceAsTh(match.Ion.Composition.Mass)
select distribution.Item2).FirstOrDefault();
if (scoreDist == null)
{
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
scoreDist = gf.GetScoreDistribution();
scoreDistributions.AddLast(new Tuple <double, ScoreDistribution>(match.Ion.Composition.Mass, scoreDist));
}
currentTask = "Calling GetSpectralEValue " + currentIteration + " and score " + (int)match.Score;
match.SpecEvalue = scoreDist.GetSpectralEValue(match.Score);
currentTask = "Reporting progress " + currentIteration;
SearchProgressReport(ref numProteins, ref lastUpdate, estimatedProteins, sw, progData);
}
}
catch (Exception ex)
{
var errMsg = string.Format("Exception while {0}: {1}", currentTask, ex.Message);
Console.WriteLine(errMsg);
throw new Exception(errMsg, ex);
}
});
var finalMatches = new DatabaseSequenceSpectrumMatch[matches.Length];
foreach (var scanNum in scanNums)
{
finalMatches[scanNum] = matches[scanNum].OrderBy(m => m.SpecEvalue).First();
}
progData.StatusInternal = string.Empty;
progData.Report(100.0);
return(finalMatches);
}
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);
}
