public IcRescorer(string specFilePath, string icResultFilePath, string outputFilePath, AminoAcidSet aaSet, 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, aaSet, minProductIonCharge, maxProductIonCharge, tolerance, ms2CorrThreshold);
Rescore(icResultFilePath, outputFilePath);
}
public void TestRescoring()
{
//const string specFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string specFilePath = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
//const string sequence = "SGWYELSKSSNDQFKFVLKAGNGEVILTSELYTGKSGAMNGIESVQTNSPIEARYAKEVAKNDKPYFNLKAANHQIIGTSQMYSSTA";
//const int scanNum = 4084;
const string sequence = "SKTKHPLPEQWQKNQEAAKATQVAFDLDEKFQYSIRKAALDAGVSPSDQIRTILGLSVSRRPTRPRLTVSLNADDYVQLAEKYDLNADAQLEIKRRVLEDLVRFVAED";
const int scanNum = 5448;
const int charge = 11;
// Configure amino acid set
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List<SearchModification>
{
dehydroC,
glutathioneC,
oxM,
acetylN,
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var informedScorer = new InformedTopDownScorer(run, aaSet, 1, 15, new Tolerance(10));
var scores = informedScorer.GetScores(AminoAcid.ProteinNTerm, sequence, AminoAcid.ProteinCTerm, composition, charge, scanNum);
Console.WriteLine("Total Score = " + scores.Score);
Console.WriteLine("#Fragments = " + scores.NumMatchedFrags);
}
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;
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 TestSumMs2Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\NewQC_LongSep_29Sep14_141001104925.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + specFilePath);
}
const int minScanNum = 1289;
//const int maxScanNum = 1389;
const int minCharge = 6;
//const int maxCharge = 6;
const string sequence = "EIRGYRPPEPYKGKGVRYDDEEVRRKEAKKK";
var aaSet = new AminoAcidSet();
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
var scorer = new InformedTopDownScorer(run, aaSet, 1, minCharge - 1, new Tolerance(10));
scorer.GetScores(AminoAcid.ProteinNTerm, sequence, AminoAcid.ProteinCTerm,
Composition.Parse("C(166) H(270) N(52) O(49) S(0)"), minCharge, minScanNum);
}
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);
}
}
