private void SubTrain(Dictionary<int, Dictionary<int, Composition>> dictionary, bool isTarget)
{
Dictionary<int, int> missingXicCounter;
Dictionary<int, Dictionary<int, int>> corrScoreCounter;
if (isTarget)
{
missingXicCounter = _missingXicCounterTarget;
corrScoreCounter = _xicCorrScoreCounterTarget;
}
else
{
missingXicCounter = _missingXicCounterDecoy;
corrScoreCounter = _xicCorrScoreCounterDecoy;
}
foreach (var charge in dictionary.Keys)
{
var subDictionary = dictionary[charge];
foreach (var scanNumber in subDictionary.Keys)
{
var composition = subDictionary[scanNumber];
var scorer = new TopDownScorer(composition, _run, _tolerance, null);
var areXicMissing = scorer.AreXicMissing(charge, scanNumber);
var corrScores = scorer.GetIsotopeCorrelationIntensityRawScores(charge, scanNumber);
for (var c = TopDownScorer.MinCharge; c <= TopDownScorer.MaxCharge;c++ )
{
if (areXicMissing[c - TopDownScorer.MinCharge])
{
var t = missingXicCounter[charge];
missingXicCounter[charge] = t + 1;
}
else
{
var t = corrScoreCounter[c] ?? new Dictionary<int, int>();
var score = corrScores[c - TopDownScorer.MinCharge];
t[score] = t[score] + 1;
}
}
}
}
}
private void SubTrain(Dictionary <int, Dictionary <int, Composition> > dictionary, bool isTarget)
{
Dictionary <int, int> missingXicCounter;
Dictionary <int, Dictionary <int, int> > corrScoreCounter;
if (isTarget)
{
missingXicCounter = _missingXicCounterTarget;
corrScoreCounter = _xicCorrScoreCounterTarget;
}
else
{
missingXicCounter = _missingXicCounterDecoy;
corrScoreCounter = _xicCorrScoreCounterDecoy;
}
foreach (var charge in dictionary.Keys)
{
var subDictionary = dictionary[charge];
foreach (var scanNumber in subDictionary.Keys)
{
var composition = subDictionary[scanNumber];
var scorer = new TopDownScorer(composition, _run, _tolerance, null);
var areXicMissing = scorer.AreXicMissing(charge, scanNumber);
var corrScores = scorer.GetIsotopeCorrelationIntensityRawScores(charge, scanNumber);
for (var c = TopDownScorer.MinCharge; c <= TopDownScorer.MaxCharge; c++)
{
if (areXicMissing[c - TopDownScorer.MinCharge])
{
var t = missingXicCounter[charge];
missingXicCounter[charge] = t + 1;
}
else
{
var t = corrScoreCounter[c] ?? new Dictionary <int, int>();
var score = corrScores[c - TopDownScorer.MinCharge];
t[score] = t[score] + 1;
}
}
}
}
}
public void TestTopDownScoringForAllXics()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Search parameters
const int numNTermCleavages = 1; // 30
const int minLength = 7;
const int maxLength = 1000;
//const int minCharge = 5; // 3
//const int maxCharge = 15; // 67
const int numMaxModsPerProtein = 0; // 6
var precursorTolerance = new Tolerance(10);
const string dbFilePath = @"..\..\..\TestFiles\sprot.Ecoli.2012_07.fasta";
//const string dbFilePath = @"..\..\..\TestFiles\sprot.Ecoli.2012_07.icdecoy.KR.fasta";
//const string dbFilePath = @"..\..\..\TestFiles\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
// const string dbFilePath =
// @"C:\cygwin\home\kims336\Data\TopDown\ID_003558_56D73071.fasta";
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
Console.Write("Reading raw file...");
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
// Configure amino acid set
// 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);
var targetDb = new FastaDatabase(dbFilePath);
// targetDb.CreateDecoyDatabase(Enzyme.Trypsin);
// System.Environment.Exit(1);
var indexedDb = new IndexedDatabase(targetDb);
var numProteins = 0;
long totalProtCompositions = 0;
//long numXics = 0;
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
sw.Reset();
sw.Start();
Console.WriteLine("Generating XICs...");
foreach (var protAnnotationAndOffset in indexedDb.IntactSequenceAnnotationsAndOffsets(minLength, maxLength))
{
++numProteins;
//if (numProteins > 2000) break;
if (numProteins % 1000 == 0)
{
Console.WriteLine("Processed {0} proteins", numProteins);
}
//Console.WriteLine(protAnnotation);
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotationAndOffset.Annotation);
//Console.WriteLine(seqGraph.GetSequenceCompositions()[0]);
if (seqGraph == null) continue;
for (var nTermCleavages = 0; nTermCleavages <= numNTermCleavages; nTermCleavages++)
{
if(nTermCleavages > 0) seqGraph.CleaveNTerm();
var protCompositions = seqGraph.GetSequenceCompositions();
foreach (var protComposition in protCompositions)
{
totalProtCompositions++;
// Console.WriteLine(protComposition);
var scorer = new TopDownScorer(protComposition, run, precursorTolerance, null);
var score = scorer.GetScore();
Console.WriteLine(score);
}
}
}
sw.Stop();
Console.WriteLine("NumProteins: {0}", numProteins);
Console.WriteLine("NumProteinCompositions: {0}", totalProtCompositions);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestTopDownScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
const string protAnnotation = "A.AHAHLTHQYPAANAQVTAAPQAITLNFSEGVETGFSGAKITGPKNENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK.";
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 searchModifications = new List<SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
//var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var aaSet = new AminoAcidSet(searchModifications, 0);
var precursorTolerance = new Tolerance(10);
//Console.WriteLine(aaSet.GetAminoAcid('C').GetComposition());
// Create a sequence graph
//var protSeq = protAnnotation.Substring(2, protAnnotation.Length - 4);
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
// TopDownScorer.MaxCharge = 60;
// TopDownScorer.MinCharge = 3;
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
foreach (var protComposition in seqGraph.GetSequenceCompositions())
{
var mostAbundantIsotopeIndex = protComposition.GetMostAbundantIsotopeZeroBasedIndex();
Console.WriteLine("Composition\t{0}", protComposition);
Console.WriteLine("MostAbundantIsotopeIndex\t{0}", mostAbundantIsotopeIndex);
Console.WriteLine(new Ion(protComposition + Composition.H2O, 11).GetIsotopeMz(mostAbundantIsotopeIndex));
Console.WriteLine();
//for (var charge = TopDownScorer.MinCharge; charge <= TopDownScorer.MaxCharge; charge++)
//{
var scorer = new TopDownScorer(protComposition, run, precursorTolerance, null);
var score = scorer.GetScore();
Console.WriteLine(score);
//var precursorIon = new Ion(protComposition + Composition.H2O, charge);
//var xic = run.GetExtractedIonChromatogram(precursorIon.GetIsotopeMz(mostAbundantIsotopeIndex), precursorTolerance);
//Console.WriteLine(xic[0].ScanNum + " " + xic[1].ScanNum);
//Console.WriteLine("ScanNum\t{0}", string.Join("\t", xic.Select(p => p.ScanNum.ToString())));
//Console.WriteLine("precursorCharge " + charge + "\t" + string.Join("\t", xic.Select(p => p.Intensity.ToString())));
// }
Console.WriteLine("\nCharge\tm/z");
for (var charge = 9; charge <= 18; charge++)
{
var precursorIon = new Ion(protComposition + Composition.H2O, charge);
Console.WriteLine("{0}\t{1}", charge, precursorIon.GetIsotopeMz(mostAbundantIsotopeIndex));
}
}
// sw.Stop();
// Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestMsAlignPlusResults()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
TopDownScorer.MaxCharge = 25;
TopDownScorer.MinCharge = 8;
const string specFilePath = @"C:\workspace\TopDown\E_coli_iscU_60_mock.raw";
const string msAlignPlusResultPath = @"C:\workspace\TopDown\E_coli_iscU_60_mock_MSAlign_ResultTable_sam.txt";
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 searchModifications = new List<SearchModification>
{
//pyroGluQ,
dehydro,
cysteinylC,
glutathioneC,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, 0);
var precursorTolerance = new Tolerance(10);
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath);
var writer = new StreamWriter(msAlignPlusResultPath+ ".txt");
var reader = new StreamReader(msAlignPlusResultPath);
string s;
while ((s=reader.ReadLine())!=null)
{
if (s.StartsWith("Data_file_name "))
{
writer.WriteLine(s+"\tScore");
continue;
}
var token = s.Split('\t');
var annotation = token[13];
// Console.WriteLine("***\t" + annotation);
var seqGraph = SequenceGraph.CreateGraph(aaSet, annotation);
if (seqGraph == null)
{
writer.WriteLine(s+"\tN/A");
continue;
}
var protCompositions = seqGraph.GetSequenceCompositions();
var scorer = new TopDownScorer(protCompositions[0], run, precursorTolerance, null);
var score = scorer.GetScore();
writer.WriteLine(s+"\t"+score);
Console.WriteLine(score);
}
writer.Close();
reader.Close();
}
