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 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);
}
/// <summary>
/// Create the correct scoring graph for the given scorer and parent mass.
/// </summary>
/// <param name="scorer">The scorer to create the scoring graph for.</param>
/// <param name="parentMass">The maximum mass of the scoring graph.</param>
/// <returns>The initialized scoring graph.</returns>
public IScoringGraph GetScoringGraph(IScorer scorer, double parentMass)
{
IScoringGraph scoringGraph;
if (scorer is CompositeScorerBasedOnDeconvolutedSpectrum)
{
var compositeScorer = (CompositeScorerBasedOnDeconvolutedSpectrum)scorer;
var scoringGraphFactory = new ProteinScoringGraphFactory(this.massBins, this.aminoAcidSet);
scoringGraph = scoringGraphFactory.CreateScoringGraph(compositeScorer, parentMass);
}
else if (scorer is FlipScorer <DeconvolutedSpectrum> )
{
var flipScorer = (FlipScorer <DeconvolutedSpectrum>)scorer;
var scoringGraphFactory = new FlipScoringGraphFactory(this.massBins, this.aminoAcidSet, this.aminoAcidProbabilities);
scoringGraph = scoringGraphFactory.GetScoringGraph(flipScorer, parentMass);
}
else
{
throw new ArgumentException("No scoring graph exists for that scorer.");
}
return(scoringGraph);
}
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()
{
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);
}