public IcTopDownLauncher(
string specFilePath,
string dbFilePath,
string outputDir,
AminoAcidSet aaSet,
string featureFilePath = null)
{
ErrorMessage = string.Empty;
SpecFilePath = specFilePath;
DatabaseFilePath = dbFilePath;
AminoAcidSet = aaSet;
OutputDir = outputDir;
FeatureFilePath = featureFilePath;
MinSequenceLength = 21;
MaxSequenceLength = 300;
MaxNumNTermCleavages = 1;
MaxNumCTermCleavages = 0;
MinPrecursorIonCharge = 2;
MaxPrecursorIonCharge = 60;
MinProductIonCharge = 1;
MaxProductIonCharge = 20;
MinSequenceMass = 2000.0;
MaxSequenceMass = 50000.0;
PrecursorIonTolerance = new Tolerance(10);
ProductIonTolerance = new Tolerance(10);
RunTargetDecoyAnalysis = DatabaseSearchMode.Both;
SearchMode = InternalCleavageType.SingleInternalCleavage;
MaxNumThreads = 4;
ScanNumbers = null;
NumMatchesPerSpectrum = 3;
TagBasedSearch = true;
}
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 InformedProteomicsAnalysis(
InMemoryLcMsRun run,
IEnumerable<string> peptideEnumerator,
AminoAcidSet aminoAcidSet): this(run, peptideEnumerator, aminoAcidSet, 1, 3)
{
}
private static void TestCountingPeptides()
{
var aaSet = new AminoAcidSet();
var sw = new Stopwatch();
sw.Start();
//const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002166_F86E3B2F.fasta";
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_003456_9B916A8B.fasta";
// const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_004208_295531A4.fasta";
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
indexedDb.Read();
//var numPeptides = indexedDb.AnnotationsAndOffsetsNoEnzyme(7, 150).LongCount();
var peptides =
indexedDb.AnnotationsAndOffsets(7, 40, 2, 2, Enzyme.Trypsin);
Parallel.ForEach(peptides, annotationAndOffset =>
//foreach(var annotationAndOffset in peptides)
{
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
}
)
;
// Console.WriteLine("NumPeptides: {0}", numPeptides);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"{0:f4} sec", sec);
}
public ShiftedSequenceGraph(AminoAcidSet aminoAcidSet, double shiftedMass, bool isForward, int maxSequenceLength, double maxSequenceMass = 50000.0)
{
_aminoAcidSet = aminoAcidSet;
_modificationParams = aminoAcidSet.GetModificationParams();
_isForward = isForward;
_index = 0;
_maxSeqIndex = maxSequenceLength + 2; // shift + Term + length
_maxSequenceMass = maxSequenceMass;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
var shiftAa = new AminoAcid('\0', "Shift", new CompositionWithDeltaMass(shiftedMass));
_aminoAcidSequence[0] = shiftAa;
ShiftMass = shiftedMass;
_fragmentComposition = new Composition.Composition[_maxSeqIndex];
_fragmentComposition[0] = shiftAa.Composition;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
IsValid = true;
}
public FeatureBasedTagSearchEngine(
LcMsRun run,
Ms1FtParser featureParser,
ProductScorerBasedOnDeconvolutedSpectra ms2Scorer,
SequenceTagParser tagParser,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
{
_run = run;
_ms2Scorer = ms2Scorer;
_featureParser = featureParser;
_ms1FtFilter = new Ms1FtFilter(run, tolerance, featureParser.Ms1FtFileName);
_tagParser = tagParser;
_fastaDb = fastaDb;
_searchableDb = new SearchableDatabase(fastaDb);
_tolerance = tolerance;
_aaSet = aaSet;
_maxSequenceMass = maxSequenceMass;
_minProductIonCharge = minProductIonCharge;
_maxProductIonCharge = maxProductIonCharge;
}
public void TestBuildingReverseGraph()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string annotation = "_.MARTKQTARK._";
// Configure amino acid set
var methylK = new SearchModification(Modification.Methylation, 'K', SequenceLocation.Everywhere, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List<SearchModification>
{
methylK,
//pyroGluQ,
oxM
};
const int numMaxModsPerProtein = 2;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
foreach (var composition in seqGraph.GetSequenceCompositions())
{
Console.WriteLine("{0}\t{1}", composition, composition.Mass);
}
}
public ProteinScoringGraphFactory(IMassBinning comparer, AminoAcidSet aminoAcidSet)
{
_comparer = comparer;
_adjList = new LinkedList<ScoringGraphEdge>[_comparer.NumberOfBins];
for (var i = 0; i < _comparer.NumberOfBins; i++) _adjList[i] = new LinkedList<ScoringGraphEdge>();
var terminalModifications = FilteredProteinMassBinning.GetTerminalModifications(aminoAcidSet);
var aminoAcidArray = FilteredProteinMassBinning.GetExtendedAminoAcidArray(aminoAcidSet);
for (var i = 0; i < _comparer.NumberOfBins; i++)
{
var mi = _comparer.GetMass(i);
var fineNodeMass = mi;
for (var a = 0; a < aminoAcidArray.Length; a++)
{
var aa = aminoAcidArray[a];
var j = _comparer.GetBinNumber(fineNodeMass + aa.Mass);
if (j < 0 || j >= _comparer.NumberOfBins) continue;
_adjList[j].AddLast(new ScoringGraphEdge(i));
if (i == 0 && !(aa is ModifiedAminoAcid))
{
foreach (var terminalMod in terminalModifications)
{
var modifiedAa = new ModifiedAminoAcid(aa, terminalMod);
j = _comparer.GetBinNumber(fineNodeMass + modifiedAa.Mass);
if (j < 0 || j >= _comparer.NumberOfBins) continue;
_adjList[j].AddLast(new ScoringGraphEdge(i));
}
}
}
}
}
public void TestPsm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.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 ScanBasedTagSearchEngine(
LcMsRun run,
ISequenceTagFinder seqTagFinder,
LcMsPeakMatrix featureFinder,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
CompositeScorerFactory ms2ScorerFactory = null,
int minMatchedTagLength = DefaultMinMatchedTagLength,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
{
_run = run;
_featureFinder = featureFinder;
_searchableDb = new SearchableDatabase(fastaDb);
_tolerance = tolerance;
_aaSet = aaSet;
_minMatchedTagLength = minMatchedTagLength;
_maxSequenceMass = maxSequenceMass;
_minProductIonCharge = minProductIonCharge;
_maxProductIonCharge = maxProductIonCharge;
MinScan = int.MinValue;
MaxScan = int.MaxValue;
_ms2ScorerFactory = ms2ScorerFactory;
_seqTagFinder = seqTagFinder;
}
public void TestFitScoreCalculationEtd()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestLcMsRun.TestTopDownRawFilePathEtd))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestLcMsRun.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestLcMsRun.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 IList<SpectrumMatch> Read()
{
var specMatches = new List<SpectrumMatch>();
var tsvFile = new TsvFileParser(_fileName);
var precursorCharges = tsvFile.GetData(PrecursorChargeHeader);
var scans = tsvFile.GetData(ScanHeader);
var peptides = tsvFile.GetData(TopDownPeptideHeader);
if (peptides != null)
{
var peptideSet = new HashSet<string>();
const double filterThreshold = QValueThreshold;
var filterValues = tsvFile.GetData(QValueHeader);
var aset = new AminoAcidSet();
for (int i = 0; i < peptides.Count; i++)
{
if (Convert.ToDouble(filterValues[i]) > filterThreshold || peptideSet.Contains(peptides[i])) continue;
peptideSet.Add(peptides[i]);
var scanNum = Convert.ToInt32(scans[i]);
int precursorCharge = Convert.ToInt32(precursorCharges[i]);
specMatches.Add(new SpectrumMatch(new Sequence(peptides[i], aset), _lcms, scanNum, precursorCharge, _decoy));
}
}
return specMatches;
}
public MatchedTagSet(string sequence,
AminoAcidSet aminoAcidSet, Tolerance tolerance, Tolerance relaxedTolerance)
{
_sequence = sequence;
_aminoAcidSet = aminoAcidSet;
_tolerance = tolerance;
_relaxedTolerance = relaxedTolerance;
_tags = new List<MatchedTag>();
}
public InformedTopDownScorer(LcMsRun run, AminoAcidSet aaSet, int minProductCharge, int maxProductCharge, Tolerance tolerance, double ms2CorrThreshold = 0.7)
{
Run = run;
AminoAcidSet = aaSet;
MinProductCharge = minProductCharge;
MaxProductCharge = maxProductCharge;
Tolerance = tolerance;
Ms2CorrThreshold = ms2CorrThreshold;
}
public InformedBottomUpScorer(LcMsRun run, AminoAcidSet aaSet, int minProductCharge, int maxProductCharge, Tolerance tolerance)
{
Run = run;
AminoAcidSet = aaSet;
MinProductCharge = minProductCharge;
MaxProductCharge = maxProductCharge;
Tolerance = tolerance;
_rankScorer = new RankScore(ActivationMethod.HCD, Ms2DetectorType.Orbitrap, Enzyme.Trypsin, Protocol.Standard);
_scoredSpectra = new Dictionary<int, ScoredSpectrum>();
}
public InformedProteomicsAnalysis(
InMemoryLcMsRun run,
IEnumerable<string> peptideEnumerator,
AminoAcidSet aminoAcidSet,
int minCharge,
int maxCharge)
{
Run = run;
PeptideEnumerator = peptideEnumerator;
AminoAcidSet = aminoAcidSet;
MinCharge = minCharge;
MaxCharge = maxCharge;
}
public CompositeScorerFactory(
ILcMsRun run,
IMassBinning comparer,
AminoAcidSet aaSet,
int minProductCharge = 1, int maxProductCharge = 20,
double productTolerancePpm = 10,
int isotopeOffsetTolerance = 2,
double filteringWindowSize = 1.1
)
: this(run, comparer, aaSet, minProductCharge, maxProductCharge, new Tolerance(productTolerancePpm), isotopeOffsetTolerance, filteringWindowSize)
{
}
public void TestParsingManyMods()
{
const string modFilePath = @"\\protoapps\UserData\Jungkap\Lewy\db\Mods.txt";
var aaSet = new AminoAcidSet(modFilePath);
//aaSet.Display();
//SequenceLocation.ProteinNTerm
var residue = AminoAcid.ProteinNTerm.Residue;
var location = SequenceLocation.ProteinNTerm;
var aa = aaSet.GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
{
var modification = aaSet.GetModificationParams().GetModification(modIndex);
Console.WriteLine(modification.Mass);
//Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
Console.WriteLine();
residue = AminoAcid.ProteinCTerm.Residue;
location = SequenceLocation.ProteinCTerm;
aa = aaSet.GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
{
var modification = aaSet.GetModificationParams().GetModification(modIndex);
Console.WriteLine(modification.Mass);
//Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
//foreach (var aa in AminoAcid.StandardAminoAcidArr)
/*
var keys = _locationSpecificResidueMap[location].Keys.ToArray();
Array.Sort(keys);
foreach (var residue in keys)
{
var aa = GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in GetModificationIndices(residue, location))
{
Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
Console.WriteLine();
}
} */
}
public void TestFitScoreCalculationCid()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(TestLcMsRun.TestTopDownRawFilePathCid))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestLcMsRun.TestTopDownRawFilePathCid);
}
var run = InMemoryLcMsRun.GetLcMsRunScanRange(TestLcMsRun.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 isotopomerEnvelop = 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++)
{
Console.WriteLine(@"{0} {1} {2} {3}", i, ion.GetIsotopeMz(i), isotopomerEnvelop[i], matchedPeaks[i] == null ? 0 : matchedPeaks[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);
}
/// <summary>
/// Create a graph representing the annotation. Annotation is reversed.
/// </summary>
/// <param name="aaSet">amino acid set</param>
/// <param name="annotation">annotation (e.g. G.PEPTIDER.K or _.PEPTIDER._)</param>
/// <returns></returns>
public static SequenceGraph CreateGraph(AminoAcidSet aaSet, string annotation)
{
const char delimiter = (char)FastaDatabase.Delimiter;
if (annotation == null || !Regex.IsMatch(annotation, @"^[A-Z" + delimiter + @"]\.[A-Z]+\.[A-Z" + delimiter + @"]$")) return null;
var nTerm = annotation[0] == FastaDatabase.Delimiter
? AminoAcid.ProteinNTerm
: AminoAcid.PeptideNTerm;
var cTerm = annotation[annotation.Length - 1] == FastaDatabase.Delimiter
? AminoAcid.ProteinCTerm
: AminoAcid.PeptideCTerm;
var sequence = annotation.Substring(2, annotation.Length - 4);
return CreateGraph(aaSet, nTerm, sequence, cTerm);
}
public void TestBuildingSequenceGraphLongProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Configure amino acid set
const int numMaxModsPerProtein = 6;
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.ProteinNTerm, false);
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 oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List<SearchModification>
{
pyroGluQ,
//dehydro,
//cysteinylC,
//glutathioneC,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
//const string protAnnotation = "A.HAHLTHQYPAANAQVTAAPQAITLNFSEGVETGFSGAKITGPKNENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK.-";
//const string protAnnotation =
// "_.QQ._";
const string protAnnotation =
"_.MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAALRKLMMNHQ._";
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
var seqCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < seqCompositions.Length; modIndex++)
{
var seqComposition = seqCompositions[modIndex];
Console.WriteLine("SequenceComposition: {0}", seqComposition);
foreach (var composition in seqGraph.GetFragmentCompositions(modIndex, 0))
{
//if (composition.GetMass() > seqComposition.GetMass())
{
Console.WriteLine("***Seq: {0}, Frag: {1}", seqComposition, composition);
}
}
}
}
public TagMatchFinder(
ProductSpectrum spec,
IScorer ms2Scorer,
LcMsPeakMatrix featureFinder,
string proteinSequence,
Tolerance tolerance,
AminoAcidSet aaSet,
double maxSequenceMass)
{
_spec = spec;
_ms2Scorer = ms2Scorer;
_featureFinder = featureFinder;
_proteinSequence = proteinSequence;
_tolerance = tolerance;
_aaSet = aaSet;
_maxSequenceMass = maxSequenceMass;
}
public IcBottomUpLauncher(
string specFilePath,
string dbFilePath,
string outputDir,
AminoAcidSet aaSet,
Enzyme enzyme)
{
ErrorMessage = string.Empty;
SpecFilePath = specFilePath;
DatabaseFilePath = dbFilePath;
AminoAcidSet = aaSet;
Enzyme = enzyme;
if (outputDir == null)
{
OutputDir = Path.GetDirectoryName(SpecFilePath);
}
else
{
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
throw new Exception(outputDir + " is not a directory!");
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
}
OutputDir = outputDir;
MinSequenceLength = 6;
MaxSequenceLength = 30;
MinPrecursorIonCharge = 1;
MaxPrecursorIonCharge = 4;
MinProductIonCharge = 1;
MaxProductIonCharge = 3;
PrecursorIonTolerance = new Tolerance(10);
ProductIonTolerance = new Tolerance(10);
RunTargetDecoyAnalysis = DatabaseSearchMode.Both;
NumTolerableTermini = 1;
NumMatchesPerSpectrum = 10;
}
public void TestSearchWithTagGeneration()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
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);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const string fastaFilePath = @"D:\MSPathFinder\Fasta\ID_002216_235ACCEA.fasta";
//const string fastaFilePath = @"D:\MassSpecFiles\60k\ID_004973_9BA6912F.fasta";
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var tolerance = new Tolerance(10);
var modsFilePath = @"D:\MSPathFinder\Fasta\Mods.txt";
if (!File.Exists(modsFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modsFilePath);
}
var aaSet = new AminoAcidSet(modsFilePath);
//TestTagBasedSearch(run, fastaDb, tolerance, aaSet);
var tagSearchEngine = new ScanBasedTagSearchEngine(run, new SequenceTagGenerator(run, new Tolerance(8)), new LcMsPeakMatrix(run), fastaDb, tolerance,aaSet);
var matchedTags = tagSearchEngine.RunSearch(4672);
foreach (var match in matchedTags)
{
Console.Write(match.Sequence);
Console.WriteLine("\t{0}\t{1}\t{2}", match.TagMatch.StartIndex, match.TagMatch.EndIndex, match.TagMatch.Mass);
}
}
public CompositeScorerFactory(
ILcMsRun run,
IMassBinning comparer,
AminoAcidSet aaSet,
int minProductCharge, int maxProductCharge,
Tolerance productTolerance,
int isotopeOffsetTolerance = 2,
double filteringWindowSize = 1.1)
{
_run = run;
_minProductCharge = minProductCharge;
_maxProductCharge = maxProductCharge;
_productTolerance = productTolerance;
FilteringWindowSize = filteringWindowSize;
IsotopeOffsetTolerance = isotopeOffsetTolerance;
_ms2Scorer = new Dictionary<int, IScorer>();
_comparer = comparer;
_scoringGraphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
}
public void TestScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var rawFile = @"\\protoapps\UserData\Jungkap\Joshua\testData\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf" ;
var resultFile = @"\\protoapps\UserData\Jungkap\Joshua\IdResult\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(rawFile))
{
Console.WriteLine(@"Warning: Skipping test {0} since file not found: {1}", methodName, rawFile);
return;
}
if (!File.Exists(resultFile))
{
Console.WriteLine(@"Warning: Skipping test {0} since file not found: {1}", methodName, resultFile);
return;
}
var tsvParser = new TsvFileParser(resultFile);
var tsvData = tsvParser.GetAllData();
var ms2ScanNumbers = tsvData["Scan"];
var run = PbfLcMsRun.GetLcMsRun(rawFile, 0, 0);
for (int i = 0; i < 1; i++)
{
var scanNum = Int32.Parse(ms2ScanNumbers[i]);
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
int tsvIndex = ms2ScanNumbers.FindIndex(x => Int32.Parse(x) == scanNum);
var seqStr = tsvData["Sequence"].ElementAt(tsvIndex).Trim();
var seqMod = tsvData["Modifications"].ElementAt(tsvIndex).Trim();
var aaSet = new AminoAcidSet();
var sequence = Sequence.CreateSequence(seqStr, seqMod, aaSet);
Console.WriteLine(sequence.Count);
var score = GetScoreTest(sequence, spectrum);
Console.WriteLine(scanNum + ":" + score);
}
}
static MgfSequenceReader()
{
StandardAminoAcidSet = new AminoAcidSet(Modification.Carbamidomethylation);
Modifications = new Dictionary<string, Tuple<AminoAcid, List<Modification>>>();
Modifications.Add("99.032",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('G'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("113.048",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('A'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("129.043",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('S'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("141.079",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('V'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("143.059",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('T'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("147.035",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('M'),
new List<Modification> { Modification.Oxidation }));
Modifications.Add("157.038",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('D'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("160.03",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('C'),
new List<Modification> { Modification.Carbamidomethylation }));
Modifications.Add("171.054",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('E'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("173.051",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('M'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("189.046",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('F'),
new List<Modification> { Modification.Acetylation }));
Modifications.Add("202.041",
new Tuple<AminoAcid, List<Modification>>(StandardAminoAcidSet.GetAminoAcid('C'),
new List<Modification> { Modification.Carbamidomethylation,
Modification.Acetylation }));
}
public FeatureBasedTagSearchEngine(
LcMsRun run,
Ms1FtParser featureParser,
SequenceTagParser tagParser,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
: this(
run,
featureParser,
null,
tagParser,
fastaDb,
tolerance,
aaSet,
maxSequenceMass,
minProductIonCharge,
maxProductIonCharge)
{
}
public void ValidateIcResultsWithModifications()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownJia\raw\Synocho_D1_1_Rescored.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var parser = new TsvFileParser(resultFilePath);
var sequences = parser.GetData("Sequence");
var modifications = parser.GetData("Modifications");
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var scanNums = parser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray();
var aaSet = new AminoAcidSet();
for (var i = 0; i < parser.NumData; i++)
{
var sequenceComp = aaSet.GetComposition(sequences[i]) + Composition.H2O;
var modComposition = Composition.Zero;
var modsStr = modifications[i].Substring(1, modifications[i].Length - 2);
var mods = modsStr.Split(',');
foreach(var modStr in mods)
{
if (modStr.Length == 0) continue;
var modName = modStr.Split()[0];
var mod = Modification.Get(modName);
modComposition += mod.Composition;
}
var compFromSeqAndMods = sequenceComp + modComposition;
Assert.True(compFromSeqAndMods.Equals(compositions[i]));
}
}
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);
}
public static AminoAcidSet GetStandardAminoAcidSet()
{
return(_standardAminoAcidSet ?? (_standardAminoAcidSet = new AminoAcidSet()));
}
/// <summary>
/// Add an amino acid residue to this generator.
/// </summary>
/// <param name="index">index to add the amino acid. 0 is C-term. 1 is the C-term amino acid.</param>
/// <param name="residue">amino acid residue to add.</param>
/// <param name="loc">location of the residue</param>
/// <returns>true if residue is a valid amino acid; false otherwise.</returns>
private bool PutAminoAcid(int index, char residue, SequenceLocation loc)
{
_index = index + 1;
var aminoAcid = AminoAcidSet.GetAminoAcid(residue, loc);
if (aminoAcid == null) // residue is not valid
{
return(false);
}
var fragmentComposition = _fragmentComposition[_index - 1] + aminoAcid.Composition;
if (fragmentComposition.Mass > _maxSequenceMass)
{
return(false);
}
_aminoAcidSequence[_index] = aminoAcid;
_fragmentComposition[_index] = fragmentComposition;
var modIndices = AminoAcidSet.GetModificationIndices(residue, loc);
if (!modIndices.Any()) // No modification
{
_graph[_index] = new Node[_graph[_index - 1].Length];
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
_graph[_index][i] = new Node(_graph[_index - 1][i].ModificationCombinationIndex, i);
}
}
else
{
var modCombIndexToNodeMap = new Dictionary <int, Node>();
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
var prevNodeIndex = i;
var prevNode = _graph[_index - 1][i];
var prevModCombIndex = prevNode.ModificationCombinationIndex;
// unmodified edge
if (modCombIndexToNodeMap.TryGetValue(prevModCombIndex, out var unmodifiedEdgeNode))
{
unmodifiedEdgeNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(prevModCombIndex, new Node(prevModCombIndex, prevNodeIndex));
}
// modified edge
foreach (var modIndex in modIndices)
{
var modCombIndex = ModificationParams.GetModificationCombinationIndex(
prevNode.ModificationCombinationIndex, modIndex);
if (modCombIndex < 0) // too many modifications
{
continue;
}
if (modCombIndexToNodeMap.TryGetValue(modCombIndex, out var modifiedEdgeNode))
{
modifiedEdgeNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(modCombIndex, new Node(modCombIndex, prevNodeIndex));
}
}
_graph[_index] = modCombIndexToNodeMap.Values.ToArray();
}
}
return(true);
}
/// <summary>
/// Create a graph representing the sequence. Sequence is reversed.
/// </summary>
/// <param name="aaSet">amino acid set</param>
/// <param name="nTerm">N-term amino acid</param>
/// <param name="sequence">sequence</param>
/// <param name="cTerm">C-term amino acid</param>
/// <returns>sequence graph</returns>
public static SequenceGraph CreateGraph(AminoAcidSet aaSet, AminoAcid nTerm, string sequence, AminoAcid cTerm)
{
var seqGraph = new SequenceGraph(aaSet, nTerm, sequence, cTerm);
return(seqGraph.IsValid ? seqGraph : null);
}
/// <summary>
/// Add an amino acid residue to this generator.
/// </summary>
/// <param name="index">index to add the amino acid. 0 is C-term. 1 is the C-term amino acid.</param>
/// <param name="residue">amino acid residue to add.</param>
/// <returns>true if residue is a valid amino acid; false otherwise.</returns>
private bool PutAminoAcid(int index, char residue)
{
_index = index + 1;
SequenceLocation?location = null;
if (_index == 1) // C-term residue
{
if (residue == AminoAcid.PeptideCTerm.Residue)
{
location = SequenceLocation.PeptideCTerm;
}
else if (residue == AminoAcid.ProteinCTerm.Residue)
{
location = SequenceLocation.ProteinCTerm;
}
}
else if (_index == _aminoAcidSequence.Length - 1 - NumNTermCleavages) // N-term residue
{
if (residue == AminoAcid.PeptideNTerm.Residue)
{
location = SequenceLocation.PeptideNTerm;
}
else if (residue == AminoAcid.ProteinNTerm.Residue)
{
location = SequenceLocation.ProteinNTerm;
}
}
else if (_index == 2) // Amino acid at the C-term
{
if (_aminoAcidSequence[1] == AminoAcid.PeptideCTerm)
{
location = SequenceLocation.PeptideCTerm;
}
else if (_aminoAcidSequence[1] == AminoAcid.ProteinCTerm)
{
location = SequenceLocation.ProteinCTerm;
}
}
else if (_index == _aminoAcidSequence.Length - 2 - NumNTermCleavages) // Amino acid at the N-term
{
if (_aminoAcidSequence[_aminoAcidSequence.Length - 1] == AminoAcid.PeptideNTerm)
{
location = SequenceLocation.PeptideNTerm;
}
else if (_aminoAcidSequence[_aminoAcidSequence.Length - 1] == AminoAcid.ProteinNTerm)
{
location = SequenceLocation.ProteinNTerm;
}
}
else
{
location = SequenceLocation.Everywhere;
}
if (location == null)
{
return(false);
}
var loc = (SequenceLocation)location;
var aminoAcid = AminoAcidSet.GetAminoAcid(residue, loc);
if (aminoAcid == null) // residue is not valid
{
return(false);
}
_aminoAcidSequence[_index] = aminoAcid;
_suffixComposition[_index] = _suffixComposition[_index - 1] + aminoAcid.Composition;
var modIndices = AminoAcidSet.GetModificationIndices(residue, loc);
if (!modIndices.Any()) // No modification
{
_graph[_index] = new Node[_graph[_index - 1].Length];
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
_graph[_index][i] = new Node(_graph[_index - 1][i].ModificationCombinationIndex, i);
}
}
else
{
var modCombIndexToNodeMap = new Dictionary <int, Node>();
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
var prevNodeIndex = i;
var prevNode = _graph[_index - 1][i];
var prevModCombIndex = prevNode.ModificationCombinationIndex;
Node newNode;
// unmodified edge
if (modCombIndexToNodeMap.TryGetValue(prevModCombIndex, out newNode))
{
newNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(prevModCombIndex, new Node(prevModCombIndex, prevNodeIndex));
}
// modified edge
foreach (var modIndex in modIndices)
{
var modCombIndex = ModificationParams.GetModificationCombinationIndex(
prevNode.ModificationCombinationIndex, modIndex);
if (modCombIndex < 0) // too many modifications
{
continue;
}
if (modCombIndexToNodeMap.TryGetValue(modCombIndex, out newNode))
{
newNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(modCombIndex, new Node(modCombIndex, prevNodeIndex));
}
}
_graph[_index] = modCombIndexToNodeMap.Values.ToArray();
}
}
return(true);
}
/// <summary>
/// Build a sequence from the supplied character sequence, using the provided amino acid set
/// </summary>
/// <param name="sequence"></param>
/// <param name="aminoAcidSet"></param>
public Sequence(string sequence, AminoAcidSet aminoAcidSet) : this(sequence.Select(aminoAcidSet.GetAminoAcid))
{
}
public static AminoAcidSet GetStandardAminoAcidSetWithCarboamidomethylCys()
{
return(_standardAminoAcidSetWithCarboamidomethylCys ??
(_standardAminoAcidSetWithCarboamidomethylCys = new AminoAcidSet(Modification.Carbamidomethylation)));
}
