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 TestVennDiagram()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string result1Path = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod_NTT1.tsv";
const string result2Path = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT1_Test\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTda.tsv";
if (!File.Exists(result1Path))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result1Path);
}
if (!File.Exists(result2Path))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result2Path);
}
const double pepQValueThreshold = 0.01;
var result1 = new TsvFileParser(result1Path);
var result2 = new TsvFileParser(result2Path);
var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Set2);
Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Intersection + " " + vennDiagram.Set2Only);
}
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 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]));
}
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// DIA
const string dir = @"H:\Research\EDRN\Ic\DIA_Replicate";
const string rep1 = dir + @"\EDRN_Serum_07_DIA_1_01_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep2 = dir + @"\EDRN_Serum_07_DIA_1_02_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep3 = dir + @"\EDRN_Serum_07_DIA_1_03_13Nov13_Samwise_13-07-28_IcTda.tsv";
const string rep4 = dir + @"\EDRN_Serum_07_DIA_1_04_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep5 = dir + @"\EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28_IcTda.tsv";
const string resultPath1 = rep1;
const string resultPath2 = rep4;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptidesAboveQValueThreshold(pepQValueThreshold),
result2.GetPeptidesAboveQValueThreshold(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count, // + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count //+ vennDiagram.Intersection.Count
);
}
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.SequenceTag(scan[i], sequence[i], isPrefix[i], flankingMass[i]);
IList <SequenceTag.SequenceTag> tagList;
if (_scanToTags.TryGetValue(scan[i], out tagList))
{
if (tagList.Count < _numTagsPerScan)
{
tagList.Add(tag);
}
}
else
{
_scanToTags.Add(scan[i], new List <SequenceTag.SequenceTag> {
tag
});
}
}
}
public void TestReadingTmtResultFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var filePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, "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]));
}
}
/*
* public static List<LcMsFeature> LoadProMexResult(string featureFilePath)
* {
* return LoadProMexResult(0, featureFilePath);
* }
*/
public static List <LcMsFeature> LoadProMexResult(int dataId, string featureFilePath, LcMsRun run, double minMass = 2000, double maxMass = 50000)
{
var featureList = new List <LcMsFeature>();
var tsvReader = new TsvFileParser(featureFilePath);
//var run = (rawFilePath == null || !File.Exists(rawFilePath)) ? null : PbfLcMsRun.GetLcMsRun(rawFilePath);
var featureIds = tsvReader.GetData("FeatureID");
var minScans = tsvReader.GetData("MinScan");
var maxScans = tsvReader.GetData("MaxScan");
var abu = tsvReader.GetData("Abundance");
var minCharges = tsvReader.GetData("MinCharge");
var maxCharges = tsvReader.GetData("MaxCharge");
var monoMass = tsvReader.GetData("MonoMass");
var minElutionTime = tsvReader.GetData("MinElutionTime");
var maxElutionTime = tsvReader.GetData("MaxElutionTime");
var repCharges = tsvReader.GetData("RepCharge");
var repScans = tsvReader.GetData("RepScan");
var repMzs = tsvReader.GetData("RepMz");
var scores = tsvReader.GetData("LikelihoodRatio");
for (var i = 0; i < tsvReader.NumData; i++)
{
var abundance = double.Parse(abu[i]);
var repMass = double.Parse(monoMass[i]);
if (repMass < minMass || repMass > maxMass)
{
continue;
}
var minCharge = int.Parse(minCharges[i]);
var maxCharge = int.Parse(maxCharges[i]);
var minScan = int.Parse(minScans[i]);
var maxScan = int.Parse(maxScans[i]);
var fid = int.Parse(featureIds[i]);
var repCharge = (repCharges != null) ? int.Parse(repCharges[i]) : (int)Math.Round(0.5 * (minCharge + maxCharge));
var repMz = (repMzs != null) ? double.Parse(repMzs[i]) : (repMass / repCharge) + Constants.Proton;
var repScanNum = (repScans != null) ? int.Parse(repScans[i]) : minScan;
var score = (scores != null) ? double.Parse(scores[i]) : 0;
var minEt = double.Parse(minElutionTime[i]);
var maxEt = double.Parse(maxElutionTime[i]);
var minNet = minEt / run.GetElutionTime(run.MaxLcScan);
var maxNet = maxEt / run.GetElutionTime(run.MaxLcScan);
var feature = new LcMsFeature(repMass, repCharge, repMz, repScanNum, abundance, minCharge, maxCharge, minScan, maxScan, minEt, maxEt, minNet, maxNet)
{
FeatureId = fid,
DataSetId = dataId,
Score = score,
};
featureList.Add(feature);
}
return(featureList);
}
public void TestPredictPTMfromMs1ft()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFilePath = @"\\protoapps\UserData\Jungkap\FeatureFinding\ProMex_v1.1\test\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
// const string ms1ftFilePath = @"\\protoapps\UserData\Jungkap\FeatureFinding\ProMex_v1.1\test\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft";
var parser = new TsvFileParser(resultFilePath);
var sequences = parser.GetData("Sequence");
var modifications = parser.GetData("Modifications");
var scanNums = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var qValues = parser.GetData("QValue").Select(s => Convert.ToDouble(s)).ToArray();
var nMacthed = parser.GetData("#MatchedFragments");
var aaSet = new AminoAcidSet();
var ptmList = new List <Tuple <int, double, double> >();
for (var i = 0; i < parser.NumData; i++)
{
if (qValues[i] > 0.01)
{
continue;
}
//var sequenceComp = aaSet.GetComposition(sequences[i]) + Composition.H2O;
var seq = new Sequence(sequences[i], aaSet);
var sequenceComp = seq.Composition + Composition.H2O;
var modComposition = Composition.Zero;
var modsStr = modifications[i];
if (modsStr.Length == 0)
{
continue;
}
var mods = modsStr.Split(',');
foreach (var modStr in mods.Where(str => str.Length > 0))
{
var modName = modStr.Split()[0];
var mod = Modification.Get(modName);
modComposition += mod.Composition;
}
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}", scanNums[i], sequenceComp.Mass, modComposition.Mass, nMacthed[i], sequences[i], modsStr);
//var compFromSeqAndMods = sequenceComp + modComposition;
//Assert.True(compFromSeqAndMods.Equals(compositions[i]));
ptmList.Add(new Tuple <int, double, double>(scanNums[i], sequenceComp.Mass, modComposition.Mass));
}
//var featureParser = new TsvFileParser(ms1ftFilePath);
//var minScan = featureParser.GetData("MinScan").Select(s => Convert.ToInt32(s)).ToArray();
//var maxScan = featureParser.GetData("MaxScan").Select(s => Convert.ToInt32(s)).ToArray();
//var monoMass = featureParser.GetData("MonoMass").Select(s => Convert.ToDouble(s)).ToArray();
}
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 TestTempCompRefLcMsFeatureAlign()
{
const string dataFolder = @"D:\MassSpecFiles\CompRef";
const string fastaFilePath = @"D:\MassSpecFiles\CompRef\db\ID_003278_4B4B3CB1.fasta";
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var fileEntries = Directory.GetFiles(dataFolder);
var dataset = (from fileName in fileEntries where fileName.EndsWith("pbf") select Path.GetFileNameWithoutExtension(fileName)).ToList();
dataset.Sort();
for (var i = 0; i < dataset.Count; i++)
{
var writer =
new StreamWriter(string.Format(@"D:\MassSpecFiles\CompRef\MsPathFinderMerged\{0}_IcTda.tsv",
dataset[i]));
writer.Write("Scan");
writer.Write("\t");
writer.Write("Sequence");
writer.Write("\t");
writer.Write("Modifications");
writer.Write("\t");
writer.Write("Mass");
writer.Write("\t");
writer.Write("ProteinName");
writer.Write("\t");
writer.Write("ProteinDesc");
writer.Write("\t");
writer.Write("Start");
writer.Write("\t");
writer.Write("End");
writer.Write("\t");
writer.Write("#MatchedFragments");
writer.Write("\t");
writer.Write("QValue");
writer.Write("\n");
var path1 = string.Format(@"D:\MassSpecFiles\CompRef\MsPathFinder\{0}_IcTda.tsv", dataset[i]);
var parser1 = new TsvFileParser(path1);
OutputMergedResult(writer, parser1, fastaDb);
var path2 = string.Format(@"D:\MassSpecFiles\CompRef\seqtag\{0}_tagmatch.tsv", dataset[i]);
var parser2 = new TsvFileParser(path2);
OutputMergedResult(writer, parser2, fastaDb);
writer.Close();
}
}
public void CompareIpaIc()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 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));
}
}
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 string ProcessFile(string rawFile, string resultFile, string methodName)
{
if (!File.Exists(rawFile))
{
Console.WriteLine(@"Warning: Skipping test {0} since file not found: {1}", methodName, rawFile);
return("\n");
}
if (!File.Exists(resultFile))
{
Console.WriteLine(@"Warning: Skipping test {0} since file not found: {1}", methodName, resultFile);
return("\n");
}
var tsvParser = new TsvFileParser(resultFile);
var headerList = tsvParser.GetHeaders();
var tsvData = tsvParser.GetAllData();
var ms2ScanNumbers = tsvData["Scan"];
var run = PbfLcMsRun.GetLcMsRun(rawFile, 0, 0);
var resultLine = "";
for (int i = 0; i < ms2ScanNumbers.Count; i++)
{
var scanNum = Int32.Parse(ms2ScanNumbers[i]);
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
int tsvIndex = ms2ScanNumbers.FindIndex(x => Int32.Parse(x) == scanNum);
var qValue = Double.Parse(tsvData["QValue"].ElementAt(tsvIndex));
if (qValue > 0.01)
{
continue;
}
var seqStr = tsvData["Sequence"].ElementAt(tsvIndex).Trim();
var seqMod = tsvData["Modifications"].ElementAt(tsvIndex).Trim();
var matchedFrags = tsvData["#MatchedFragments"].ElementAt(tsvIndex).Trim();
var aaSet = new AminoAcidSet();
var sequence = Sequence.CreateSequence(seqStr, seqMod, aaSet);
var tol = new Tolerance(10);
var sequenceFinder = new SequenceTagIndexFinder(tol, 1, 10);
var results = sequenceFinder.GetLongestSequence(spectrum, sequence);
resultLine += String.Format("{0},{1},{2},{3},{4},{5},{6},{7},{8},\n", scanNum, matchedFrags, seqStr, results.Item1, results.Item2, results.Item3, results.Item4, results.Item5, results.Item6);
}
return(resultLine);
}
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 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);
}
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 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 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");
}
}
public void ValidateIcResultsWithModifications()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 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);
}
}
private void OutputMergedResult(TextWriter 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 TestClusterCentricSearch(double qValueThreshold, int expectedNumCompositions)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var resultFilePath = Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "QC_Shew_Intact_26Sep14_Bane_C2Column3_Excerpt_IcTda.tsv");
var resultFile = Utils.GetTestFile(methodName, resultFilePath);
var tsvReader = new TsvFileParser(resultFile.FullName);
var ms2Scans = tsvReader.GetData("Scan").Select(s => Convert.ToInt32((string)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 > qValueThreshold)
{
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);
Assert.AreEqual(expectedNumCompositions, compScanTable.Keys.Count);
}
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);
}
}
}
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);
}
}
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// DIA
const string dir = @"H:\Research\DDAPlus\NTT2";
//const string dda1 = dir + @"\20140701_yeast_DDA_01_IcTda.tsv";
//const string dda2 = dir + @"\20140701_yeast_DDA_02_2_IcTda.tsv";
const string ddaPlus1 = dir + @"\20140701_yeast_DDAp_binCharge_01_IcTda.tsv";
const string ddaPlus2 = dir + @"\20140701_yeast_DDAp_binCharge_02_IcTda.tsv";
const string resultPath1 = ddaPlus1;
const string resultPath2 = ddaPlus2;
if (!File.Exists(resultPath1))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath1);
}
if (!File.Exists(resultPath2))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath2);
}
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptidesAboveQValueThreshold(pepQValueThreshold),
result2.GetPeptidesAboveQValueThreshold(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count, // + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count //+ vennDiagram.Intersection.Count
);
}
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 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);
}
