public void TestReadingTmtResultFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string filePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSGFPlusResultTMT10.tsv";
if (!File.Exists(filePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, filePath);
}
var parser = new TsvFileParser(filePath);
var pepStrs = parser.GetData("Peptide");
var formulaStrs = parser.GetData("Formula");
Assert.True(pepStrs.Count == formulaStrs.Count);
var peptides = pepStrs.Select(Sequence.GetSequenceFromMsGfPlusPeptideStr).ToList();
var formulae = formulaStrs.Select(Composition.Parse).ToList();
Assert.True(peptides.Count == formulae.Count);
for (var i = 0; i < peptides.Count; i++)
{
Assert.True((peptides[i].Composition + Composition.H2O).Equals(formulae[i]));
}
}
private void Rescore(string icResultFilePath, string outputFilePath)
{
var parser = new TsvFileParser(icResultFilePath);
var sequences = parser.GetData("Sequence");
var scanNums = parser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray();
var charges = parser.GetData("Charge").Select(c => Convert.ToInt32(c)).ToArray();
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var modIndex = parser.GetHeaders().IndexOf("Modifications");
var rows = parser.GetRows();
var headers = parser.GetHeaders();
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("{0}\t{1}", string.Join("\t", headers), IcScores.GetScoreNames());
for (var i = 0; i < parser.NumData; i++)
{
var row = rows[i];
var seqStr = sequences[i];
var charge = charges[i];
var scanNum = scanNums[i];
var composition = compositions[i];
var scores = _topDownScorer.GetScores(AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm, composition, charge, scanNum);
var token = row.Split('\t');
for (var j = 0; j < token.Length; j++)
{
if(j != modIndex) writer.Write(token[j]+"\t");
else writer.Write("["+scores.Modifications+"]"+"\t");
}
writer.WriteLine(scores);
}
}
}
private void Read(string isosFileName)
{
var icrToolsparser = new TsvFileParser(isosFileName, ',');
var monoMassArr = icrToolsparser.GetData("monoisotopic_mw").Select(Convert.ToDouble).ToArray();
var scanArray = icrToolsparser.GetData("scan_num").Select(s => Convert.ToInt32(s)).ToArray();
var chargeArray = icrToolsparser.GetData("charge").Select(s => Convert.ToInt32(s)).ToArray();
var fitStringArr = icrToolsparser.GetData("fit");
var fitArray = fitStringArr == null ? null : icrToolsparser.GetData("fit").Select(Convert.ToDouble).ToArray();
var featureCountFiltered = 0;
var minMass = double.MaxValue;
var maxMass = 0.0;
for (var i = 0; i < monoMassArr.Length; i++)
{
if (fitArray != null && fitArray[i] > _fitScoreThreshold || chargeArray[i] <= 1)
continue;
featureCountFiltered++;
var scan = scanArray[i];
var monoMass = monoMassArr[i];
if (minMass > monoMass) minMass = monoMass;
if (maxMass < monoMass) maxMass = monoMass;
var minScan = _run.GetPrevScanNum(scan, 1);
var maxScan = _run.GetNextScanNum(scan, 1);
_lcMsMatchMap.SetMatches(monoMass, minScan, maxScan);
}
Console.Write(@"{0}/{1} features loaded...", featureCountFiltered, monoMassArr.Length);
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _massTolerance, minMass, maxMass);
}
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(BottomUpPeptideHeader);
if (scans == null)
throw new FormatException();
var pepQValues = tsvFile.GetData(PepQValueHeader);
var formulas = tsvFile.GetData(FormulaHeader);
var peptideSet = new HashSet<string>();
for (int i = 0; i < peptides.Count; i++)
{
if (Convert.ToDouble(pepQValues[i]) > PepQValueThreshold || peptideSet.Contains(peptides[i])) continue;
peptideSet.Add(peptides[i]);
var scanNum = Convert.ToInt32(scans[i]);
// var spectrum = lcms.GetSpectrum(scanNum);
// var spec = spectrum as ProductSpectrum;
// if (spec == null || spec.ActivationMethod != Act) continue;
int precursorCharge = Convert.ToInt32(precursorCharges[i]);
specMatches.Add((formulas != null && formulas[i] != null)
? new SpectrumMatch(peptides[i], DataFileFormat.IcBottomUp, _lcms, scanNum, precursorCharge, _decoy, formulas[i])
: new SpectrumMatch(peptides[i], DataFileFormat.IcBottomUp, _lcms, scanNum, precursorCharge, _decoy));
}
return specMatches;
}
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 void AddMostAbundantIsotopePeakIntensity()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\QC_ShewIntact_40K_LongSeparation_1_141016155143.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const string resultFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\QC_ShewIntact_40K_LongSeparation_1_141016155143_IcTda.tsv";
var parser = new TsvFileParser(resultFilePath);
var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var scanNums = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var charges = parser.GetData("Charge").Select(s => Convert.ToInt32(s)).ToArray();
var precursorIntensities = new double[parser.NumData];
var tolerance = new Tolerance(10);
for (var i = 0; i < parser.NumData; i++)
{
var scanNum = scanNums[i];
var composition = compositions[i];
var charge = charges[i];
var precursorIon = new Ion(composition, charge);
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var isotopePeaks = precursorSpec.GetAllIsotopePeaks(precursorIon, tolerance, 0.1);
if (isotopePeaks != null)
{
var maxIntensity = 0.0;
for (var j = 0; j < isotopePeaks.Length; j++)
{
if (isotopePeaks[j] != null && isotopePeaks[j].Intensity > maxIntensity)
maxIntensity = isotopePeaks[j].Intensity;
}
precursorIntensities[i] = maxIntensity;
}
}
// Writing
const string newResultFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TestYufengData\QC_ShewIntact_40K_LongSeparation_1_141016155143_IcTdaWithIntensities.tsv";
using (var writer = new StreamWriter(newResultFilePath))
{
writer.WriteLine(string.Join("\t", parser.GetHeaders())+"\t"+"PrecursorIntensity");
for (var i = 0; i < parser.NumData; i++)
{
writer.WriteLine(parser.GetRows()[i]+"\t"+precursorIntensities[i]);
}
}
Console.WriteLine("Done");
}
public void SummarizeAnilResults()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFolder = @"H:\Research\Anil\Oct28";
if (!Directory.Exists(resultFolder))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, resultFolder);
}
var actMethods = new[] { ActivationMethod.CID, ActivationMethod.ETD, ActivationMethod.HCD };
Console.WriteLine("Data\tCID\t\tETD\t\tHCD\t");
Console.WriteLine("\tNumId\tMaxMass\tNumId\tMaxMass\tNumId\tMaxMass");
foreach (var rawFile in Directory.GetFiles(resultFolder, "*.raw"))
{
var datasetName = Path.GetFileNameWithoutExtension(rawFile);
var resultFile = Path.Combine(Path.GetDirectoryName(rawFile), datasetName + "_IcTda.tsv");
var numId = new Dictionary<ActivationMethod, int>();
var maxMass = new Dictionary<ActivationMethod, double>();
foreach (var actMethod in actMethods)
{
numId[actMethod] = 0;
maxMass[actMethod] = 0.0;
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var tsvParser = new TsvFileParser(resultFile);
var qValues = tsvParser.GetData("QValue").Select(Convert.ToDouble).ToArray();
var scanNums = tsvParser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var masses = tsvParser.GetData("Mass").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < qValues.Length; i++)
{
if (qValues[i] > 0.01) break;
var scanNum = scanNums[i];
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
Assert.True(spec != null);
++numId[spec.ActivationMethod];
var mass = masses[i];
if (mass > maxMass[spec.ActivationMethod]) maxMass[spec.ActivationMethod] = mass;
}
Console.Write(datasetName);
foreach (var actMethod in actMethods)
{
Console.Write("\t" + numId[actMethod]);
Console.Write("\t" + maxMass[actMethod]);
}
Console.WriteLine();
}
}
private void Read(string ms1FtFileName)
{
var ftFileParser = new TsvFileParser(ms1FtFileName);
var monoMassArr = ftFileParser.GetData("MonoMass").Select(Convert.ToDouble).ToArray();
var minScanArray = ftFileParser.GetData("MinScan").Select(s => Convert.ToInt32(s)).ToArray();
var maxScanArray = ftFileParser.GetData("MaxScan").Select(s => Convert.ToInt32(s)).ToArray();
var repScanArray = ftFileParser.GetData("RepScan").Select(s => Convert.ToInt32(s)).ToArray();
var minChargeArray = ftFileParser.GetData("MinCharge").Select(s => Convert.ToInt32(s)).ToArray();
var maxChargeArray = ftFileParser.GetData("MaxCharge").Select(s => Convert.ToInt32(s)).ToArray();
var scoreArray = ftFileParser.GetData("LikelihoodRatio").Select(Convert.ToDouble).ToArray();
var featureCountFiltered = 0;
for (var i = 0; i < monoMassArr.Length; i++)
{
//if (flagArray[i] == 0 && probArray[i] < _minProbability) continue;
if (scoreArray[i] < _minLikelihoodRatio) continue;
featureCountFiltered++;
var monoMass = monoMassArr[i];
_lcMsChargeMap.SetMatches(monoMass, minScanArray[i], maxScanArray[i], repScanArray[i], minChargeArray[i], maxChargeArray[i]);
}
// NOTE: The DMS Analysis Manager looks for this statistic; do not change it
Console.Write(@"{0}/{1} features loaded...", featureCountFiltered, monoMassArr.Length);
_lcMsChargeMap.CreateMassToScanNumMap();
}
public void TestClusterCentricSearch()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string pfResultFilePath = @"H:\Research\QCShew_TopDown\Production\M1_V4_JP_Len500\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(pfResultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pfResultFilePath);
}
var tsvReader = new TsvFileParser(pfResultFilePath);
var ms2Scans = tsvReader.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var compositions = tsvReader.GetData("Composition").ToArray();
var qValues = tsvReader.GetData("QValue").Select(Convert.ToDouble).ToArray();
var compScanTable = new Dictionary<string, IList<int>>();
for(var i=0; i<qValues.Length; i++)
{
var qValue = qValues[i];
if (qValue > 0.01) break;
IList<int> scanNums;
if(compScanTable.TryGetValue(compositions[i], out scanNums))
{
scanNums.Add(ms2Scans[i]);
}
else
{
compScanTable.Add(compositions[i], new List<int> {ms2Scans[i]});
}
}
Console.Write("NumCompositions: {0}", compScanTable.Keys.Count);
//const string featureFilePath = @"H:\Research\QCShew_TopDown\Production\M1_V4_JP_Len500\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
}
private void Parse(string tagFilePath)
{
var tagParser = new TsvFileParser(tagFilePath);
var scan = tagParser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray();
var sequence = tagParser.GetData("SequenceTag").ToArray();
var isPrefix = tagParser.GetData("IsPrefix").Select(s => s.Equals("1")).ToArray();
var flankingMass = tagParser.GetData("FlankingMass").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < tagParser.NumData; i++)
{
if (sequence[i].Length < _minTagLength) continue;
var tag = new SequenceTag(scan[i], sequence[i], isPrefix[i], flankingMass[i]);
IList<SequenceTag> tagList;
if (_scanToTags.TryGetValue(scan[i], out tagList))
{
if (tagList.Count < _numTagsPerScan) tagList.Add(tag);
}
else
{
_scanToTags.Add(scan[i], new List<SequenceTag> { tag });
}
}
}
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]));
}
}
private void Rescore(string msAlignFilePath, string outputFilePath)
{
var parser = new TsvFileParser(msAlignFilePath);
var sequences = parser.GetData("Peptide");
var scanNums = parser.GetData("Scan(s)").Select(s => Convert.ToInt32(s)).ToArray();
var charges = parser.GetData("Charge").Select(c => Convert.ToInt32(c)).ToArray();
var rows = parser.GetRows();
var headers = parser.GetHeaders();
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("{0}\t{1}", string.Join("\t", headers), IcScores.GetScoreNames());
for (var i = 0; i < parser.NumData; i++)
{
var row = rows[i];
var seqStr = SimpleStringProcessing.GetStringBetweenDots(sequences[i]);
if (seqStr == null || seqStr.Contains("(")) continue; //TODO: currently ignore ids with modifications
var composition = AASet.GetComposition(seqStr);
//var sequence = new Sequence(seqStr, AASet);
//if (sequence == null)
//{
// Console.WriteLine("Ignore illegal sequence: {0}", seqStr);
// continue;
//}
var charge = charges[i];
var scanNum = scanNums[i];
var scores = _topDownScorer.GetScores(AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm, composition, charge, scanNum);
if (scores == null) continue;
writer.WriteLine("{0}\t{1}", row, scores);
}
}
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.7, 0.7, 0.7, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
//const string prot =
// "ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKKTEVSAVSIVVAAAKKLLA";
//var protMass = (new AminoAcidSet().GetComposition(prot) + Composition.H2O).Mass;
//Console.WriteLine("************ScanNums: " + string.Join("\t", ms1Filter.GetMatchingMs2ScanNums(protMass)));
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\MSAlign\NoMod.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var scanNums = tsvReader.GetData("Scan(s)");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("E-value");
var sequences = tsvReader.GetData("Peptide");
//const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_N30_C30.tsv";
//var tsvReader = new TsvFileParser(resultFilePath);
//var scanNums = tsvReader.GetData("ScanNum");
//var charges = tsvReader.GetData("Charge");
//var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Sequence");
var aaSet = new AminoAcidSet();
var seqSet = new HashSet<string>();
var allSeqSet = new HashSet<string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < scores.Count; i++)
{
var score = Convert.ToDouble(scores[i]);
if (score > 1E-4) continue;
//if (score < 10) continue;
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var sequence = SimpleStringProcessing.GetStringBetweenDots(sequences[i]);
if (sequence == null || sequence.Contains("(")) continue;
//var sequence = sequences[i];
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestMs1Filtering()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFilePath =
// @"C:\cygwin\home\kims336\Data\TopDown\raw\CorrMatches_N30\SBEP_STM_001_02272012_Aragon.tsv";
@"C:\cygwin\home\kims336\Data\TopDown\raw\CorrMatches_N30\SBEP_STM_001_02272012_Aragon.decoy.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\DataFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
//const int minPrecursorCharge = 3;
//const int maxPrecursorCharge = 30;
//const int tolerancePpm = 15;
var tolerance = new Tolerance(15);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 0.7, 40);
////var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//ISequenceFilter ms1Filter = ms1BasedFilter;
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var qValues = tsvReader.GetData("QValue");
var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Annotation");
//var hist = new int[11];
Console.WriteLine("ScanNum\tScore\tPrecursor\tNext\tSum\tNextIsotope\tLessCharge\tMoreCharge\tMax\tNumXicPeaks");
for (var i = 0; i < compositions.Count; i++)
{
if (qValues != null)
{
var qValue = Convert.ToDouble(qValues[i]);
if (qValue > 0.01) continue;
}
var scanNum = Convert.ToInt32(scanNums[i]);
var composition = Composition.Parse(compositions[i]);
var charge = Convert.ToInt32(charges[i]);
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
var score = Convert.ToDouble(scores[i]);
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var preIsotopeCorr = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var nextIsotopeCorr = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var xicMostAbundant = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var apexScanNum = xicMostAbundant.GetApexScanNum();
if (apexScanNum < run.MinLcScan) apexScanNum = scanNum;
//var sumSpec = run.GetSummedMs1Spectrum(apexScanNum);
// var apexIsotopeCorr = sumSpec.GetCorrScore(precursorIon, tolerance, 0.1);
// var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
var xicNextIsotope = run.GetPrecursorExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz() + Constants.C13MinusC12/charge, tolerance, scanNum);
var plusOneIsotopeCorr = xicMostAbundant.GetCorrelation(xicNextIsotope);
var precursorIonChargeMinusOne = new Ion(composition, charge - 1);
var xicChargeMinusOne = run.GetPrecursorExtractedIonChromatogram(precursorIonChargeMinusOne.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var chargeMinusOneCorr = xicMostAbundant.GetCorrelation(xicChargeMinusOne);
var precursorIonChargePlusOne = new Ion(composition, charge + 1);
var xicChargePlusOne = run.GetPrecursorExtractedIonChromatogram(precursorIonChargePlusOne.GetMostAbundantIsotopeMz(), tolerance, scanNum);
var chargePlusOneCorr = xicMostAbundant.GetCorrelation(xicChargePlusOne);
//var max = new[] {preIsotopeCorr, nextIsotopeCorr, apexIsotopeCorr, plusOneIsotopeCorr, chargeMinusOneCorr, chargePlusOneCorr}.Max();
//Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}",
// scanNum, score, preIsotopeCorr, nextIsotopeCorr, apexIsotopeCorr, plusOneIsotopeCorr, chargeMinusOneCorr, chargePlusOneCorr, max, xicMostAbundant.Count);
}
//Console.WriteLine("Histogram");
//for (var i = 0; i < hist.Length; i++)
//{
// Console.WriteLine("{0:f1}\t{1}", i / 10.0, hist[i]);
//}
}
public void FilteringEfficiency()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
//var ms1BasedFilter = new Ms1BasedFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm);
//
//var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//var ms1BasedFilter = new ProductScorerBasedOnDeconvolutedSpectra(run,
// minPrecursorCharge, maxPrecursorCharge,
// 0, 0,
// 600.0, 1800.0, new Tolerance(tolerancePpm), null);
//ms1BasedFilter.CachePrecursorMatchesBinCentric();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.5, 0.5, 0.5, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon_4PTMs.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("Score");
var qvalues = tsvReader.GetData("QValue");
var sequences = tsvReader.GetData("Sequence");
var sequenceCount = new Dictionary<string, int>();
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01) continue;
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13) continue;
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
var sequence = sequences[i];
int count;
if (sequenceCount.TryGetValue(sequence, out count)) sequenceCount[sequence] = count + 1;
else sequenceCount[sequence] = 1;
}
//var sequences = tsvReader.GetData("Annotation");
var seqSet = new HashSet<string>();
var allSeqSet = new HashSet<string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01) continue;
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13) continue;
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var isValid = spec != null && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid) continue;
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
//var xic = run.GetFullPrecursorIonExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance);
////xic.Display();
//var apexScanNum = xic.GetNearestApexScanNum(run.GetPrecursorScanNum(scanNum), false);
//var apexSpec = run.GetSpectrum(apexScanNum);
//var corr3 = apexSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax, sequenceCount[sequences[i]]);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons/(double)(maxBinNum-minBinNum+1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs/(double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count/(double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public List<ProteinSpectrumMatch> ReadMsPathFinderResult(string msPathFinderResultPath, int maxPrsm, double minScore = 3, double maxScore = int.MaxValue)
{
var parser = new TsvFileParser(msPathFinderResultPath);
var prsmList = new List<ProteinSpectrumMatch>();
var scoreColumn = parser.GetData("#MatchedFragments") ?? parser.GetData("Score");
var qValColumn = parser.GetData("QValue");
var evalueColumn = parser.GetData("SpecEValue");
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Sequence")[i];
var scanNum = int.Parse(parser.GetData("Scan")[i]);
var mass = double.Parse(parser.GetData("Mass")[i]);
var protName = parser.GetData("ProteinName")[i];
var protDesc = parser.GetData("ProteinDesc")[i];
var charge = int.Parse(parser.GetData("Charge")[i]);
var firstResId = int.Parse(parser.GetData("Start")[i]);
var lastResId = int.Parse(parser.GetData("End")[i]);
var score = double.Parse(scoreColumn[i]);
var mod = parser.GetData("Modifications")[i];
var evalue = (evalueColumn != null) ? double.Parse(parser.GetData("SpecEValue")[i]) : 0;
var pre = parser.GetData("Pre")[i];
var post = parser.GetData("Post")[i];
var proteinLen = int.Parse(parser.GetData("ProteinLength")[i]);
if (score < minScore || score > maxScore) continue;
if (qValColumn != null)
{
var fdr = double.Parse(qValColumn[i]);
if (fdr > FdrCutoff) continue;
}
var sequenceText = GetSequenceText(sequence, mod);
var prsm = new ProteinSpectrumMatch(sequence, scanNum, mass, charge, protName, protDesc, firstResId, lastResId, score, ProteinSpectrumMatch.SearchTool.MsPathFinder)
{
SequenceText = sequenceText,
Modifications = mod,
Pre = pre,
Post = post,
ProteinLength = proteinLen,
SpectralEvalue = evalue,
};
prsmList.Add(prsm);
if (prsmList.Count >= maxPrsm) break;
}
return prsmList;
}
private double[][] LoadTable(string fname)
{
if (!File.Exists(fname)) throw new FileNotFoundException("Missing score datafile: " + fname);
var parser = new TsvFileParser(fname);
var table = new double[_massBins.Length][];
for (var i = 0; i < _massBins.Length; i++)
{
table[i] = new double[NumberOfBins];
for (var k = 0; k < NumberOfBins; k++)
{
var colData = parser.GetData(string.Format("{0}", k));
table[i][k] = double.Parse(colData[i]);
}
}
return table;
}
public void DiaRankScore()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataFile =
@"\\protoapps\UserData\Wilkins\BottomUp\HCD_QCShew\raw\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raw";
const string tsvFile =
@"\\protoapps\UserData\Wilkins\BottomUp\HCD_QCShew\tsv\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.tsv";
if (!File.Exists(dataFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dataFile);
}
if (!File.Exists(tsvFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tsvFile);
}
var parser = new TsvFileParser(tsvFile);
var sequences = parser.GetData("Peptide");
var charges = parser.GetData("Charge");
var scans = parser.GetData("ScanNum");
var lcms = InMemoryLcMsRun.GetLcMsRun(dataFile, 0, 0);
var rankScorer =
new DiaRankScore(
@"C:\Users\wilk011\Documents\DataFiles\TestFolder\HCD_QExactive_Tryp.txt");
using (
var outFile = new StreamWriter(@"C:\Users\wilk011\Documents\DataFiles\TestFolder\HCD_QCShew_Score_2.txt"))
{
outFile.WriteLine("Target\tDecoy");
for (int i = 0; i < sequences.Count; i++)
{
string sequenceStr = sequences[i];
int charge = Convert.ToInt32(charges[i]);
int scan = Convert.ToInt32(scans[i]);
var sequence = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequenceStr);
var decoySeq = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequenceStr);
decoySeq.Reverse();
var decoyStr = decoySeq.Aggregate("", (current, aa) => current + aa);
decoyStr = SimpleStringProcessing.Mutate(decoyStr, sequence.Count/2);
decoySeq = Sequence.GetSequenceFromMsGfPlusPeptideStr(decoyStr);
var sequenceScore = rankScorer.GetScore(sequence, charge, scan, lcms);
var decoyScore = rankScorer.GetScore(decoySeq, charge, scan, lcms);
outFile.WriteLine("{0}\t{1}", sequenceScore, decoyScore);
}
}
}
public void TestFeatureIdMatching()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFilePath = @"H:\Research\QCShew_TopDown\Production\M1_V092\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var resultParser = new MsPathFinderParser(resultFilePath);
const double qValueThreshold = 0.01;
const double tolerancePpm = 13;
const string dataSet = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3";
var rawFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".raw");
if (!File.Exists(rawFileName))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFileName);
}
var run = PbfLcMsRun.GetLcMsRun(rawFileName);
var idList =
resultParser.GetIdList().TakeWhile(id => id.QValue <= qValueThreshold).OrderBy(id => id.Mass).ToList();
var idMassList = idList.Select(id => id.Mass).ToList();
var idFlag = new bool[idList.Count];
// Parse sequence tags
var tagFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".seqtag");
const int minTagLength = 6;
const int numProtMatches = 4;
// const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.icsfldecoy.fasta";
if (!File.Exists(tagFileName))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFileName);
}
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
var tagParser = new SequenceTagParser(tagFileName, minTagLength);
var featureFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".ms1ft");
var featureParser = new TsvFileParser(featureFileName);
var minScan = featureParser.GetData("MinScan").Select(s => Convert.ToInt32(s)).ToArray();
var maxScan = featureParser.GetData("MaxScan").Select(s => Convert.ToInt32(s)).ToArray();
var minCharge = featureParser.GetData("MinCharge").Select(s => Convert.ToInt32(s)).ToArray();
var maxCharge = featureParser.GetData("MaxCharge").Select(s => Convert.ToInt32(s)).ToArray();
var monoMass = featureParser.GetData("MonoMass").Select(Convert.ToDouble).ToArray();
var numFeaturesWithId = 0;
var numFeaturesWithMs2 = 0;
var numFeaturesWithTags = 0;
var numFeaturesWithMatchingTags = 0;
var numFeaturesWithTwoOrMoreMatchingTags = 0;
var numFeaturesWithNoIdAndMatchingTags = 0;
for (var i = 0; i < featureParser.NumData; i++)
{
var mass = monoMass[i];
// Find Id
var tolDa = new Tolerance(tolerancePpm).GetToleranceAsDa(mass, 1);
var minMass = mass - tolDa;
var maxMass = mass + tolDa;
var index = idMassList.BinarySearch(mass);
if (index < 0) index = ~index;
var matchedId = new List<MsPathFinderId>();
// go down
var curIndex = index - 1;
while (curIndex >= 0)
{
var curId = idList[curIndex];
if (curId.Mass < minMass) break;
if (curId.Scan > minScan[i] && curId.Scan < maxScan[i]
&& curId.Charge >= minCharge[i] && curId.Charge <= maxCharge[i])
{
matchedId.Add(curId);
idFlag[curIndex] = true;
}
--curIndex;
}
// go up
curIndex = index;
while (curIndex < idList.Count)
{
var curId = idList[curIndex];
if (curId.Mass > maxMass) break;
if (curId.Scan >= minScan[i] && curId.Scan <= maxScan[i]
&& curId.Charge >= minCharge[i] && curId.Charge <= maxCharge[i])
{
matchedId.Add(curId);
idFlag[curIndex] = true;
}
++curIndex;
}
var hasId = false;
if (matchedId.Any())
{
++numFeaturesWithId;
hasId = true;
}
// Find MS2 scans
// var numMs2Scans = 0;
var tags = new List<SequenceTag>();
var hasMs2 = false;
for (var scanNum = minScan[i]; scanNum <= maxScan[i]; scanNum++)
{
var isolationWindow = run.GetIsolationWindow(scanNum);
if (isolationWindow == null) continue;
var isolationWindowTargetMz = isolationWindow.IsolationWindowTargetMz;
var charge = (int)Math.Round(mass / isolationWindowTargetMz);
if (charge < minCharge[i] || charge > maxCharge[i]) continue;
var mz = Ion.GetIsotopeMz(mass, charge,
Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex);
if (isolationWindow.Contains(mz))
{
// ++numMs2Scans;
tags.AddRange(tagParser.GetSequenceTags(scanNum));
hasMs2 = true;
}
}
if (hasMs2) ++numFeaturesWithMs2;
if (tags.Any()) ++numFeaturesWithTags;
var protHist = new Dictionary<string, int>();
var hasMatchedTag = false;
foreach (var tag in tags)
{
var matchedProteins = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).Select(idx => fastaDb.GetProteinName(idx)).ToArray();
if (matchedProteins.Any())
{
hasMatchedTag = true;
foreach (var protein in matchedProteins)
{
int num;
if (protHist.TryGetValue(protein, out num)) protHist[protein] = num + 1;
else protHist[protein] = 1;
}
}
}
if (hasMatchedTag)
{
++numFeaturesWithMatchingTags;
if (!hasId) ++numFeaturesWithNoIdAndMatchingTags;
}
if (protHist.Any())
{
var maxOcc = protHist.Values.Max();
if (maxOcc >= numProtMatches) ++numFeaturesWithTwoOrMoreMatchingTags;
}
}
Console.WriteLine("NumFeatures: {0}", featureParser.NumData);
Console.WriteLine("NumId: {0}", idList.Count);
Console.WriteLine("NumFeaturesWithId: {0} ({1})", numFeaturesWithId, numFeaturesWithId / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithMs2: {0} ({1})", numFeaturesWithMs2, numFeaturesWithMs2 / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithTag: {0} ({1})", numFeaturesWithTags, numFeaturesWithTags / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithMatchedTag: {0} ({1})", numFeaturesWithMatchingTags, numFeaturesWithMatchingTags / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithMoreThanOneMatchedTag: {0} ({1})", numFeaturesWithTwoOrMoreMatchingTags, numFeaturesWithTwoOrMoreMatchingTags / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithNoIdAndMatchedTag: {0} ({1})", numFeaturesWithNoIdAndMatchingTags, numFeaturesWithNoIdAndMatchingTags / (float)featureParser.NumData);
for (var i = 0; i < idFlag.Length; i++)
{
if (!idFlag[i])
{
Console.WriteLine(idList[i].Scan);
}
}
// Console.WriteLine(string.Join(",", filter.GetMatchingMs2ScanNums(8115.973001)));
//
// Console.WriteLine(featureFileName);
}
public void TestInitialScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string icResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT2_03_NoMod_NoRescoring\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTarget.tsv";
if (!File.Exists(icResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, icResultPath);
}
var icParser = new TsvFileParser(icResultPath);
var icScans = icParser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var icPeptides = icParser.GetData("Sequence");
var icScore = icParser.GetData("Score").Select(s => Convert.ToInt32(s)).ToArray();
var map = new Dictionary<string, int>();
for (var i = 0; i < icParser.NumData; i++)
{
map.Add(icScans[i]+":"+icPeptides[i], icScore[i]);
}
const string msgfPlusResultPath = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod.tsv";
if (!File.Exists(msgfPlusResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, msgfPlusResultPath);
}
var msgfPlusResults = new MsGfResults(msgfPlusResultPath);
var matches = msgfPlusResults.GetMatchesAtPsmFdr(0.01);
//Console.WriteLine("NumMatches: {0}", matches.Count);
Console.WriteLine("ScanNum\tPeptide\tSpecEValue\tIcScore");
foreach (var match in matches)
{
var scanNum = match.ScanNum;
var peptide = match.Peptide;
var specEValue = match.SpecEValue;
int score;
if (!map.TryGetValue(scanNum + ":" + peptide, out score)) score = -1;
Console.WriteLine("{0}\t{1}\t{2}\t{3}", scanNum, peptide, specEValue, score);
}
}
public List<ProteinSpectrumMatch> ReadMsGfPlusResult(string msgfResultPath, int maxPrsm)
{
var parser = new TsvFileParser(msgfResultPath);
var prsmList = new List<ProteinSpectrumMatch>();
var prevScanNum = -1;
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Peptide")[i];
var scanNum = int.Parse(parser.GetData("Scan")[i]);
if (prevScanNum == scanNum) continue;
prevScanNum = scanNum;
var mz = double.Parse(parser.GetData("PrecursorMZ")[i]);
var protName = parser.GetData("Protein")[i];
var protDesc = "";
var score = double.Parse(parser.GetData("MSGFScore")[i]);
var charge = int.Parse(parser.GetData("Charge")[i]);
var seq = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequence);
var sequenceText = GetSequenceText(seq);
var mass = (mz - Constants.Proton)*charge;
var firstResId = 0;
var lastResId = 0;
var fdr = Double.Parse(parser.GetData("QValue")[i]);
if (fdr > FdrCutoff) continue;
var prsm = new ProteinSpectrumMatch(sequence, scanNum, mass, charge, protName, protDesc, firstResId, lastResId, score, ProteinSpectrumMatch.SearchTool.MsGfPlus)
{
SequenceText = sequenceText,
};
prsmList.Add(prsm);
if (prsmList.Count >= maxPrsm) break;
}
return prsmList;
}
public void CompareRt()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Q-Exactive
//const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
//const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
// Fusion
const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
const string specFileDda = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.raw";
var ddaReader = new XCaliburReader(specFileDda);
var specFileToReader = new Dictionary<string, XCaliburReader>();
var specFilesDia = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
foreach (var specFile in specFilesDia)
{
var specFileNoExt = Path.GetFileNameWithoutExtension(specFile);
if (specFileNoExt == null) continue;
var reader = new XCaliburReader(specFile);
specFileToReader.Add(specFileNoExt, reader);
}
const string resultPath1 = qeDdaResult;
const string resultPath2 = qeDiaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
var result1Peptides = result1.GetData("Peptide");
var result1ScanNums = result1.GetData("ScanNum");
var result2Peptides = result2.GetData("Peptide");
var result2ScanNums = result2.GetData("ScanNum");
var result2SpecFile = result2.GetData("#SpecFile");
Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2");
foreach (var peptide in intersectionPeptides)
{
var index1 = result1Peptides.IndexOf(peptide);
var index2 = result2Peptides.IndexOf(peptide);
var scanNum1 = Convert.ToInt32(result1ScanNums[index1]);
var scanNum2 = Convert.ToInt32(result2ScanNums[index2]);
var diaFile = Path.GetFileNameWithoutExtension(result2SpecFile[index2]);
var reader1 = ddaReader;
var reader2 = specFileToReader[diaFile];
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2));
}
}
public void GenerateVennDiagramsPeMmr()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// No PE-MMR
//const string noPeMmr = @"D:\Research\Data\PEMMR\iTRAQ_N33T34_10ug_100cm_300min_C2_061213.tsv";
// PE-MMR Scan based FDR
//const string scanBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_ScanFDR.tsv";
// UMC based FDR
const string umcBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_UMCFDR.tsv";
// IPA
const string ipa = @"D:\Research\Data\PEMMR\Ox\IPA_Summary_TargetOnly.tsv";
const string resultPath1 = umcBasedPeMmr;
const string resultPath2 = ipa;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count);
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count);
foreach (var peptide in vennDiagram.Set2Only)
{
Console.WriteLine(peptide);
var peptides = result2.GetData("Peptide");
}
}
private bool Parse(string fileName)
{
var parser = new TsvFileParser(fileName);
var scan = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var pre = parser.GetData("Pre").Where(s => s.Length == 1).Select(p => p[0]).ToArray();
if (pre.Length != parser.NumData) return false;
var sequence = parser.GetData("Sequence").ToArray();
var post = parser.GetData("Post").Where(s => s.Length == 1).Select(p => p[0]).ToArray();
if (post.Length != parser.NumData) return false;
var mod = parser.GetData("Modifications").ToArray();
var composition = parser.GetData("Composition").Select(Composition.Parse).ToArray();
var proteinName = parser.GetData("ProteinName").ToArray();
var proteinDesc = parser.GetData("ProteinDesc").ToArray();
var proteinLength = parser.GetData("ProteinLength").Select(s => Convert.ToInt32(s)).ToArray();
var start = parser.GetData("Start").Select(s => Convert.ToInt32(s)).ToArray();
var end = parser.GetData("End").Select(s => Convert.ToInt32(s)).ToArray();
var charge = parser.GetData("Charge").Select(s => Convert.ToInt32(s)).ToArray();
var mostAbundantIsotopeMz = parser.GetData("MostAbundantIsotopeMz").Select(Convert.ToDouble).ToArray();
var mass = parser.GetData("Mass").Select(Convert.ToDouble).ToArray();
var numMatchedFragment = parser.GetData("#MatchedFragments").Select(s => Convert.ToInt32(s)).ToArray();
var qValue = parser.GetData("QValue").Select(Convert.ToDouble).ToArray();
var pepQValue = parser.GetData("PepQValue").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < parser.NumData; i++)
{
var id = new MsPathFinderId(scan[i], pre[i], sequence[i], post[i], mod[i],
composition[i], proteinName[i], proteinDesc[i], proteinLength[i],
start[i], end[i], charge[i], mostAbundantIsotopeMz[i], mass[i],
numMatchedFragment[i], qValue[i], pepQValue[i])
;
_idList.Add(id);
if(!_scanNumToPrSm.ContainsKey(scan[i])) _scanNumToPrSm.Add(scan[i], id);
}
return true;
}
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 CompareIpaIc()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultDir = @"D:\Research\Data\UW\QExactive\Ic_NTT2_03";
if (!Directory.Exists(resultDir))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, resultDir);
}
var targetPeptides = new HashSet<string>();
foreach (var icResultFilePath in Directory.GetFiles(resultDir, "*DIA*IcTarget.tsv"))
{
var icParser = new TsvFileParser(icResultFilePath);
foreach (var peptide in icParser.GetData("Sequence")) targetPeptides.Add(peptide);
}
const string ipaResultPath = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
if (!File.Exists(ipaResultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, methodName);
}
var parser = new TsvFileParser(ipaResultPath);
var ipaPeptides = parser.GetPeptides(0.005).Select(p => p.Replace("C+57.021", "C"));
var ipaOnly = 0;
var both = 0;
foreach (var ipaPeptide in ipaPeptides)
{
if (targetPeptides.Contains(ipaPeptide)) ++both;
else
{
++ipaOnly;
Console.WriteLine(ipaPeptide);
}
}
Console.WriteLine("Both: {0}, IpaOnly: {1}, Sum: {2}", both, ipaOnly, both+ipaOnly);
}
public void CountMatchedProteins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int minTagLength = 3;
var scanToProtein = new Dictionary<int, string>();
var idTag = new Dictionary<int, bool>();
const string resultFilePath = @"H:\Research\ProMex\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var parser = new TsvFileParser(resultFilePath);
var scans = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var proteinNames = parser.GetData("ProteinName").ToArray();
var qValues = parser.GetData("QValue").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < qValues.Length; i++)
{
if (qValues[i] > 0.01) break;
scanToProtein.Add(scans[i], proteinNames[i]);
idTag.Add(scans[i], false);
}
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
// const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.icsfldecoy.fasta";
// const string fastaFilePath =
// @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
Console.WriteLine("Sequence length: {0}", fastaDb.GetSequence().Length);
const string tagFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.seqtag";
if (!File.Exists(tagFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFilePath);
}
var hist = new Dictionary<int, int>();
var scanSet = new HashSet<int>();
HashSet<string> proteinSetForThisScan = null;
var prevScan = -1;
var totalNumMatches = 0L;
var isHeader = true;
foreach (var line in File.ReadAllLines(tagFilePath))
{
if (isHeader)
{
isHeader = false;
continue;
}
var token = line.Split('\t');
if (token.Length < 3) continue;
var scan = Convert.ToInt32(token[0]);
var proteinId = scanToProtein.ContainsKey(scan) ? scanToProtein[scan] : null;
if (scan != prevScan)
{
if (proteinSetForThisScan != null)
{
var numMatches = proteinSetForThisScan.Count;
int numOcc;
if (hist.TryGetValue(numMatches, out numOcc)) hist[numMatches] = numOcc + 1;
else hist.Add(numMatches, 1);
}
prevScan = scan;
proteinSetForThisScan = new HashSet<string>();
}
scanSet.Add(scan);
var tag = token[1];
if (tag.Length < minTagLength) continue;
if (proteinSetForThisScan == null) continue;
var numMatchesForThisTag = 0;
foreach (var matchedProtein in searchableDb.FindAllMatchedSequenceIndices(tag)
.Select(index => fastaDb.GetProteinName(index)))
{
proteinSetForThisScan.Add(matchedProtein);
++numMatchesForThisTag;
if (proteinId != null && matchedProtein.Equals(proteinId))
{
idTag[scan] = true;
}
}
totalNumMatches += numMatchesForThisTag;
// if (numMatchesForThisTag > 10)
// {
// Console.WriteLine("{0}\t{1}", tag, numMatchesForThisTag);
// }
}
if (proteinSetForThisScan != null)
{
var numMatches = proteinSetForThisScan.Count;
int numOcc;
if (hist.TryGetValue(numMatches, out numOcc)) hist[numMatches] = numOcc + 1;
else hist.Add(numMatches, 1);
}
Console.WriteLine("AvgNumMatches: {0}", totalNumMatches/(float)scanSet.Count);
Console.WriteLine("Histogram:");
foreach (var entry in hist.OrderBy(e => e.Key))
{
Console.WriteLine("{0}\t{1}", entry.Key, entry.Value);
}
Console.WriteLine("NumId: {0}", idTag.Count);
Console.WriteLine("NumIdByTag: {0}", idTag.Select(e => e.Value).Count(v => v));
}
public List<ProteinSpectrumMatch> ReadMsAlignResult(string msAlignResultTablePath, int maxPrsm)
{
var parser = new TsvFileParser(msAlignResultTablePath);
var prsmList = new List<ProteinSpectrumMatch>();
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Peptide")[i];
var scanNum = int.Parse(parser.GetData("Scan(s)")[i]);
var mass = double.Parse(parser.GetData("Precursor_mass")[i]);
var protNameDesc = parser.GetData("Protein_name")[i];
var k = protNameDesc.IndexOf(' ');
var protName = (k < 0) ? protNameDesc : protNameDesc.Substring(0, k);
var protDesc = (k < 0) ? protNameDesc : protNameDesc.Substring(k+1);
var firstResId = int.Parse(parser.GetData("First_residue")[i]);
var lastResId = int.Parse(parser.GetData("Last_residue")[i]);
var score = double.Parse(parser.GetData("#matched_fragment_ions")[i]);
var sequenceText = parser.GetData("Peptide")[i];
var charge = int.Parse(parser.GetData("Charge")[i]);
var evalue = double.Parse(parser.GetData("E-value")[i]);
var fdr = Double.Parse(parser.GetData("FDR")[i]);
if (fdr > FdrCutoff) continue;
var prsm = new ProteinSpectrumMatch(sequence, scanNum, mass, charge, protName, protDesc, firstResId, lastResId, score, ProteinSpectrumMatch.SearchTool.MsAlign)
{
SequenceText = sequenceText,
SpectralEvalue = evalue,
};
prsmList.Add(prsm);
if (prsmList.Count >= maxPrsm) break;
}
return prsmList;
}
private void OutputMergedResult(StreamWriter writer, TsvFileParser parser, FastaDatabase fastaDb)
{
var scoreColumn = parser.GetData("#MatchedFragments") ?? parser.GetData("Score");
var qValColumn = parser.GetData("QValue");
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Sequence")[i];
var scanNum = int.Parse(parser.GetData("Scan")[i]);
var mass = double.Parse(parser.GetData("Mass")[i]);
var protName = parser.GetData("ProteinName")[i];
var protDesc = fastaDb.GetProteinDescription(protName);
var firstResId = int.Parse(parser.GetData("Start")[i]);
var lastResId = int.Parse(parser.GetData("End")[i]);
var score = double.Parse(scoreColumn[i]);
var mod = parser.GetData("Modifications")[i];
var qvalue = (qValColumn != null) ? qValColumn[i] : "0";
writer.Write(scanNum);
writer.Write("\t");
writer.Write(sequence);
writer.Write("\t");
writer.Write(mod);
writer.Write("\t");
writer.Write(mass);
writer.Write("\t");
writer.Write(protName);
writer.Write("\t");
writer.Write(protDesc);
writer.Write("\t");
writer.Write(firstResId);
writer.Write("\t");
writer.Write(lastResId);
writer.Write("\t");
writer.Write(score);
writer.Write("\t");
writer.Write(qvalue);
writer.Write("\n");
}
}
public void CompareRtFusion()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Fusion
const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
const string specFileDda = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var ddaReader = new XCaliburReader(specFileDda);
const string specFileDia = @"D:\Research\Data\UW\Fusion\WT_D_DIA_130412091220.raw";
var diaReader = new XCaliburReader(specFileDia);
const string resultPath1 = qeDdaResult;
const string resultPath2 = qeDiaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
var result1Peptides = result1.GetData("Peptide");
var result1ScanNums = result1.GetData("ScanNum");
var result2Peptides = result2.GetData("Peptide");
var result2ScanNums = result2.GetData("ScanNum");
Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2");
foreach (var peptide in intersectionPeptides)
{
var index1 = result1Peptides.IndexOf(peptide);
var index2 = result2Peptides.IndexOf(peptide);
var scanNum1 = Convert.ToInt32(result1ScanNums[index1]);
var scanNum2 = Convert.ToInt32(result2ScanNums[index2]);
var reader1 = ddaReader;
var reader2 = diaReader;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2));
}
}