public void TestFeatureAlignment()
{
const string outFilePath = @"\\protoapps\UserData\Jungkap\Lewy\aligned\promex_crosstab_temp.tsv";
//CPTAC_Intact_CR32A_24Aug15_Bane_15-02-06-RZ
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(10);
var alignment = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));
for (var i = 0; i < NdataSet; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", PbfPath, GetDataSetNames(i));
var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder, GetDataSetNames(i));
var mspFile2 = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder2, GetDataSetNames(i));
var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", Ms1FtFolder, GetDataSetNames(i));
Console.WriteLine(rawFile);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var prsmList1 = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
var prsmList2 = prsmReader.LoadIdentificationResult(mspFile2, ProteinSpectrumMatch.SearchTool.MsPathFinder);
prsmList1.AddRange(prsmList2);
var prsmList = MergePrsm(prsmList1);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
for (var i = 0; i < NdataSet; i++)
{
alignment.FillMissingFeatures(i);
Console.WriteLine("{0} has been processed", GetDataSetNames(i));
}
OutputCrossTabWithId(outFilePath, alignment);
}
public void TestMaxEntDeconvoluter()
{
const string rawFileFolder = @"\\proto-11\MSXML_Cache\PBF_Gen_1_214\2015_4";
const string fname = "WHIM2_LoHi_T2DD_HCD_GF07_02";
var rawFile = string.Format(@"{0}\{1}.pbf", rawFileFolder, fname);
var ms1ft = string.Format(@"\\protoapps\UserData\Jungkap\CompRef\lowRes\{0}.ms1ft", fname);
var run = PbfLcMsRun.GetLcMsRun(rawFile, 1.4826, 0);
var ms1ScanNums = run.GetMs1ScanVector();
var featureFinder = new LcMsPeakMatrixLowResolution(run);
foreach (var scan in ms1ScanNums)
{
var fts = featureFinder.DetectMs1Features(scan);
//Console.WriteLine("{0}\t{1}",scan, fts.Count);
}
var features = featureFinder.GetLcMsFeatures();
var writer = new StreamWriter(ms1ft);
var id = 1;
writer.WriteLine("FeatureID\tMinScan\tMaxScan\tMinCharge\tMaxCharge\tMonoMass\tAbundance\tRepScan\tMaxElutionTime\tElutionLength\tLikelihoodRatio");
foreach (var feature in features.OrderBy(f => f.Mass))
{
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}", id, feature.MinScanNum, feature.MaxScanNum, feature.MinCharge,
feature.MaxCharge, feature.Mass, feature.Abundance, feature.RepresentativeScanNum, feature.MinElutionTime, feature.MaxElutionTime, 0);
id++;
}
writer.Close();
}
public void TestSumMs2Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var specFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TestYufengData\NewQC_LongSep_29Sep14_141001104925.raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + specFilePath);
}
const int minScanNum = 1289;
//const int maxScanNum = 1389;
const int minCharge = 6;
//const int maxCharge = 6;
const string sequence = "EIRGYRPPEPYKGKGVRYDDEEVRRKEAKKK";
var aaSet = new AminoAcidSet();
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
var scorer = new InformedTopDownScorer(run, aaSet, 1, minCharge - 1, new Tolerance(10));
scorer.GetScores(AminoAcid.ProteinNTerm, sequence, AminoAcid.ProteinCTerm,
Composition.Parse("C(166) H(270) N(52) O(49) S(0)"), minCharge, minScanNum);
}
public void TestIsosFilter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string isosFilePath = @"H:\Research\QCShew_TopDown\Production\ICRTools\QC_Shew_Intact_26Sep14_Bane_C2Column3_Isos.csv";
if (!File.Exists(isosFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, isosFilePath);
}
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);
var filter = new IsosFilter(run, new Tolerance(10), isosFilePath);
Console.WriteLine(string.Join("\t", filter.GetMatchingMs2ScanNums(30261.68374)));
}
public void TestAbpSumMs1Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var specFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TestYufengData\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + specFilePath);
}
const int minScanNum = 5657;
const int maxScanNum = 5699;
const int MAX_POINTS = 50;
var run = PbfLcMsRun.GetLcMsRun(specFilePath);
if (run == null)
{
return;
}
var summedSpec = run.GetSummedMs1Spectrum(minScanNum, maxScanNum);
var peakList = summedSpec.GetPeakListWithin(1180.0, 1192.0);
var filteredPeakList = new List <Peak>();
PeakListUtils.FilterNoise(peakList, ref filteredPeakList);
new Spectrum(filteredPeakList, 0).Display(MAX_POINTS);
}
public void TestSumMs1Spectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
const int minScanNum = 46454;
const int maxScanNum = 46661;
const int MAX_POINTS = 50;
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
if (run == null)
{
return;
}
var summedSpec = run.GetSummedMs1Spectrum(minScanNum, maxScanNum);
summedSpec.Display(MAX_POINTS);
}
public void TestRunningTimeSummingSpectra()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath, 1.4826, 1.4826) as PbfLcMsRun;
var sw = new Stopwatch();
sw.Start();
const int windowSize = 5;
foreach (var scanNum in run.GetScanNumbers(1))
{
//var spec = run.GetSpectrum(scanNum);
var spec = run.GetSummedMs1Spectrum(Math.Max(scanNum - windowSize, run.MinLcScan),
Math.Min(scanNum + windowSize, run.MaxLcScan));
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestProMexFilter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0);
const string ms1FtPath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\TopDown\ProductionQCShew\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft";
if (!File.Exists(ms1FtPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, ms1FtPath);
}
var filter = new Ms1FtFilter(run, new Tolerance(10), ms1FtPath);
// Console.WriteLine("ScanNums: {0}", string.Join("\t",filter.GetMatchingMs2ScanNums(8480.327609)));
Assert.IsTrue(filter.GetMatchingMs2ScanNums(8480.327609).Contains(5255));
}
public void ScorePSM(int scan, string sequenceStr)
{
// Set input file paths.
const string specFilePath =
@"\\protoapps\userdata\Wilkins\UIMF Files\9 pep mix 365 mTorr with ims 45V CID\9 pep mix 365 mTorr with ims 45V CID.pbf";
var lcmsRun = PbfLcMsRun.GetLcMsRun(specFilePath);
var productSpectrum = lcmsRun.GetSpectrum(scan) as ProductSpectrum;
Assert.NotNull(productSpectrum);
var modification = Modification.RegisterAndGetModification("oh->nh2", new Composition(0, 1, 1, -1, 0));
Assert.NotNull(modification);
var searchModifications = new List <SearchModification>
{
new SearchModification(Modification.Get("oh->nh2"), 'M', SequenceLocation.ProteinCTerm, true),
new SearchModification(Modification.Get("oh->nh2"), 'Q', SequenceLocation.ProteinCTerm, true),
new SearchModification(Modification.PyroGluE, 'R', SequenceLocation.ProteinNTerm, true)
};
var aminoAcidSet = new AminoAcidSet(searchModifications, 1);
var sequence = this.LoadSequence(sequenceStr, aminoAcidSet);
//var scorerFactory = new ScorerFactory(new Tolerance(30, ToleranceUnit.Ppm), 1, 5);
//var scorer = scorerFactory.GetScorer(productSpectrum);
//var score = IonUtils.ScoreSequence(scorer, sequence);
//Console.WriteLine(score);
}
public void TestDisplaySpectra(string rawFile, string idFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init XicPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumViewModel = new SpectrumViewModel(dialogService, lcms);
// init test ions
var baseIonTypes = new List <BaseIonType> {
BaseIonType.B, BaseIonType.Y
};
var neutralLosses = new List <NeutralLoss> {
NeutralLoss.NoLoss
};
const int charge = 1;
const int minCharge = 1, maxCharge = 2;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = IonUtils.GetIonTypes(ionTypeFactory, baseIonTypes, neutralLosses, minCharge, maxCharge);
var ions = IonUtils.GetFragmentIonLabels(prsm.Sequence, charge, ionTypes);
var ionVms = ions.Select(label => new LabeledIonViewModel(label.Composition, label.IonType, label.IsFragmentIon, lcms, label.PrecursorIon, label.IsChargeState, label.Index)).ToList();
}
public void TestDisplaySpectrum(string rawFile, string tsvFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(tsvFile);
var ids = idFileReader.Read();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
// init SpectrumPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumPlotViewModel = new SpectrumPlotViewModel(dialogService, new FragmentationSequenceViewModel(), 1.05, false);
// init test data
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init test ions
var ions = new ReactiveList <LabeledIonViewModel>();
spectrumPlotViewModel.Spectrum = prsm.Ms2Spectrum;
////spectrumPlotViewModel.Ions = ions;
// plot should not be null
Assert.NotNull(spectrumPlotViewModel.PlotModel);
// plot should contain 1 stem series (the spectrum stem series)
Assert.True(spectrumPlotViewModel.PlotModel.Series.Count == 1);
}
/// <summary>
/// Returns InformedProteomics LcMsRun object from mass spec data types including .raw and .mzml
/// </summary>
/// <param name="rawFilePath"></param>
/// <returns></returns>
public LcMsRun GetLcMsData(string rawFilePath)
{
var progress = new Progress <ProgressData>();
progress.ProgressChanged += Progress_ProgressChanged;
var run = PbfLcMsRun.GetLcMsRun(rawFilePath, progress);
/*
* string ext = Path.GetExtension(rawFilePath);
* switch (ext.ToLower())
* {
* case ".raw":
* run = PbfLcMsRun.GetLcMsRun(rawFilePath, MassSpecDataType.XCaliburRun);
* break;
* case ".mzml":
* run = PbfLcMsRun.GetLcMsRun(rawFilePath, MassSpecDataType.MzMLFile);
* break;
* case ".gz":
* if (rawFilePath.ToLower().EndsWith(".mzml.gz"))
* {
* run = PbfLcMsRun.GetLcMsRun(rawFilePath, MassSpecDataType.MzMLFile);
* }
* break;
* }*/
return(run);
}
public void TestFeatureAlignment()
{
const string outFilePath = @"\\protoapps\UserData\Jungkap\CompRef\aligned\promex_crosstab_temp.tsv";
var runLabels = new[] { "32A", "32B", "32C", "32D", "32E", "32F", "32G", "33A", "33B", "33C", "33D", "33E", "33F", "33G" };
var nDataset = runLabels.Length;
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(10);
var alignment = new LcMsFeatureAlignment(new CompRefFeatureComparer(tolerance));
for (var i = 0; i < nDataset; i++)
{
var rawFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ.pbf", RawFolder, runLabels[i]);
var mspFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ_IcTda.tsv", MsPfFolder, runLabels[i]);
var ms1FtFile = string.Format(@"{0}\CPTAC_Intact_CR{1}_24Aug15_Bane_15-02-06-RZ.ms1ft", Ms1FtFolder, runLabels[i]);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
if (File.Exists(mspFile))
{
var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsMz(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
for (var i = 0; i < nDataset; i++)
{
alignment.FillMissingFeatures(i);
Console.WriteLine("{0} has been processed", runLabels[i]);
}
OutputCrossTabWithId(outFilePath, alignment, runLabels);
}
public void DoAnalysis()
{
InitilizeMatrix(_spectrumMatchesMatrix);
InitilizeMatrix(_tagsGeneratedMatrix);
InitilizeMatrix(_dataBaseHitMatrix);
GetFilteredFeatures(_filteredFile);
for (var i = 0; i < _rawFiles.Length; i++)
{
Console.WriteLine("Processing File {0}...............", i);
var run = PbfLcMsRun.GetLcMsRun(_rawFiles[i]);
var ms2List = run.GetScanNumbers(2);
Console.WriteLine("# of scans {0}", ms2List.Count);
for (var j = 0; j < _filteredFeatures.Count; j++)
{
var matchedSpecList = GetMatchedSpectrums(run, ms2List, _filteredFeatures[j], i);
_spectrumMatchesMatrix[j][i] = matchedSpecList.Count;
var tags = GetTags(matchedSpecList);
_tagsGeneratedMatrix[j][i] = tags.Count;
var hitCount = TagsInDatabase(tags);
_dataBaseHitMatrix[j][i] = hitCount;
}
}
}
private void AlignFeatures(List <string> datasets, string mspfFolder, string ms1ftFolder, string outFilePath)
{
var nDataset = datasets.Count;
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(12);
var alignment = new LcMsFeatureAlignment(new AnalysisCompRef.CompRefFeatureComparer(tolerance));
for (var i = 0; i < nDataset; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", PbfPath, datasets[i]);
var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", mspfFolder, datasets[i]);
var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", ms1ftFolder, datasets[i]);
var ms1FtFile2 = string.Format(@"{0}\{1}.seqtag.ms1ft", ms1ftFolder, datasets[i]);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
var features2 = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile2, run);
features.AddRange(features2);
if (File.Exists(mspFile))
{
var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
//var prsmFeatureMatch = new bool[prsmList.Count];
foreach (var match in prsmList)
{
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
foreach (var feature in features)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsMz(feature.Mass);
foreach (var match in prsmList)
{
if (feature.MinScanNum < match.ScanNum && match.ScanNum < feature.MaxScanNum && Math.Abs(feature.Mass - match.Mass) < massTol)
{
feature.ProteinSpectrumMatches.Add(match);
//prsmFeatureMatch[k] = true;
}
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
for (var i = 0; i < nDataset; i++)
{
alignment.FillMissingFeatures(i);
Console.WriteLine("{0} has been processed", datasets[i]);
}
AnalysisCompRef.OutputCrossTabWithId(outFilePath, alignment, datasets);
}
public void TestMatchedPeakPostScorer()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Parameters
var productIonTolerance = new Tolerance(10);
var scorer = new MatchedPeakPostScorer(productIonTolerance, 1, 10);
var sw = new System.Diagnostics.Stopwatch();
const int ms2ScanNum = 4658;
var sequence = new Sequence("GYSIKDIIYQGEKSGVHNWQTLSGQNFYWHPDWLHIAEDLTGHKATASIQAEGTKATQNEAEQTIVKHLNKS", new AminoAcidSet());
var specFilePath = Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "QC_Shew_Intact_26Sep14_Bane_C2Column3.raw");
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(specFilePath, 0, 0);
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
sw.Start();
var score = scorer.ComputeScore(spec, sequence);
Console.WriteLine("{0}\t{1}\t{2}", sequence, ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestDeconvolution()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
const int minScanNum = 46454; // 635.43
const int maxScanNum = 46661; // 638.90
const int MAX_POINTS = 50;
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
if (run == null)
{
return;
}
var summedSpec = run.GetSummedMs1Spectrum(minScanNum, maxScanNum);
summedSpec.FilterNoise(50.0);
// summedSpec.Display(MAX_POINTS);
var deconvoluted = ProductScorerBasedOnDeconvolutedSpectra.GetDeconvolutedSpectrum(summedSpec, 2, 45, new Tolerance(10), 0.9, 2);
deconvoluted.Display(MAX_POINTS);
}
public void TestFeatureAlignment()
{
const string outFilePath = @"\\protoapps\UserData\Jungkap\Quant\aligned\promex_crosstab.tsv";
//const string outFolder = @"\\protoapps\UserData\Jungkap\CompRef\aligned";
var runLabels = new string[] { "1x1", "1x2", "1x3", "1x4", "1x5", "5x1", "5x2", "5x3", "5x4", "5x5", "10x1", "10x2", "10x3", "10x4", "10x5", };
var nDataset = runLabels.Length;
var prsmReader = new ProteinSpectrumMatchReader();
var tolerance = new Tolerance(10);
var alignment = new LcMsFeatureAlignment(new SpikeInFeatureComparer(tolerance));
for (var i = 0; i < nDataset; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", RawFolder, datasets[i]);
var mspFile = string.Format(@"{0}\{1}_IcTda.tsv", MsPfFolder, datasets[i]);
var ms1FtFile = string.Format(@"{0}\{1}.ms1ft", Ms1FtFolder, datasets[i]);
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var prsmList = prsmReader.LoadIdentificationResult(mspFile, ProteinSpectrumMatch.SearchTool.MsPathFinder);
var features = LcMsFeatureAlignment.LoadProMexResult(i, ms1FtFile, run);
for (var j = 0; j < prsmList.Count; j++)
{
var match = prsmList[j];
match.ProteinId = match.ProteinName;
}
// tag features by PrSMs
for (var j = 0; j < features.Count; j++)
{
//features[j].ProteinSpectrumMatches = new ProteinSpectrumMatchSet(i);
var massTol = tolerance.GetToleranceAsTh(features[j].Mass);
foreach (var match in prsmList)
{
if (features[j].MinScanNum < match.ScanNum && match.ScanNum < features[j].MaxScanNum && Math.Abs(features[j].Mass - match.Mass) < massTol)
{
features[j].ProteinSpectrumMatches.Add(match);
}
}
}
alignment.AddDataSet(i, features, run);
}
alignment.AlignFeatures();
Console.WriteLine("{0} alignments ", alignment.CountAlignedFeatures);
/*
* for (var i = 0; i < nDataset; i++)
* {
* alignment.FillMissingFeatures(i);
* Console.WriteLine("{0} has been processed", runLabels[i]);
* }
*/
OutputCrossTabWithId(outFilePath, alignment, runLabels);
}
private void FeatureMapGeneration()
{
var resultsFilePath = Path.Combine(Path.GetTempPath(), Path.GetFileNameWithoutExtension(mFeatureMapPbfFile) + "_FeatureMap.png");
var map = new LcMsFeatureMap(PbfLcMsRun.GetLcMsRun(mFeatureMapPbfFile), mFeatureMapResultsFile, 2000, 50000);
map.SaveImage(resultsFilePath);
Console.WriteLine("Image saved to " + resultsFilePath);
}
public void TestFitMinusOneScore(int precursor, string adduct, string commonName, string id, string rawFilePath)
{
var lipid = new Lipid()
{
AdductFull = adduct, CommonName = commonName
};
var lipidTarget = lipid.CreateLipidTarget();
var composition = lipidTarget.Composition;
var compMinus1 = new Composition(composition.C, composition.H - 1, composition.N, composition.O, composition.S, composition.P); //Subtract one hydrogen to make this a minus1 fit score
var lcmsRun = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spectrum = lcmsRun.GetSpectrum(precursor);
var relativeIntensityThreshold = 0.1;
var tolerance = new Tolerance(30, ToleranceUnit.Ppm);
//Get the values to use to calculate pearson correlation
var observedPeaks = LipidUtil.GetAllIsotopePeaks(spectrum, compMinus1, tolerance,
relativeIntensityThreshold);
if (observedPeaks == null)
{
Console.WriteLine("Observed peaks is null for scan " + id);
}
var isotopomerEnvelope = IsoProfilePredictor.GetIsotopomerEnvelop(
compMinus1.C,
compMinus1.H,
compMinus1.N,
compMinus1.O,
compMinus1.S);
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
Console.WriteLine("The theoretical y values are: ");
foreach (var value in isotopomerEnvelope.Envolope)
{
Console.WriteLine(value + ", ");
}
Console.WriteLine("The observed peak intensity x values are: ");
foreach (var value in observedIntensities)
{
Console.WriteLine(value + ", ");
}
}
public void TestSumIsoProfilesAcrossDifferentCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
//var spec = run.GetSpectrum(46452); // 635.37
var spec = run.GetSummedMs1Spectrum(46437, 46466);
var tolerance = new Tolerance(10);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O();
var theoProfile = neutral.GetIsotopomerEnvelopeRelativeIntensities();
var expProfile = new double[theoProfile.Length];
for (var charge = 22; charge <= 45; charge++)
{
var ion = new Ion(neutral, charge);
var isotopePeaks = spec.GetAllIsotopePeaks(ion, tolerance, 0.1);
if (isotopePeaks == null)
{
continue;
}
Assert.True(isotopePeaks.Length == theoProfile.Length);
for (var i = 0; i < isotopePeaks.Length; i++)
{
if (isotopePeaks[i] != null)
{
expProfile[i] += isotopePeaks[i].Intensity;
}
}
}
for (var i = 0; i < theoProfile.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", neutral.GetIsotopeMass(i), theoProfile[i], expProfile[i] / expProfile.Max());
}
Console.WriteLine("Corr: " + FitScoreCalculator.GetPearsonCorrelation(theoProfile, expProfile));
}
public void CountTagMatches()
{
for (var i = 1; i < 52; i++)
{
var dataName = "Lewy_intact_" + i.ToString("D2");
var filePath = string.Format(@"{0}\{1}.pbf", PbfPath, dataName);
var run = PbfLcMsRun.GetLcMsRun(filePath);
var scans = run.GetScanNumbers(2);
Console.WriteLine(scans.Count);
}
}
/// <summary>
/// Implementation for <see cref="RunCommand"/>.
/// Gets a command that validates search settings and closes the window.
/// </summary>
/// <returns>The <see cref="Task"/>.</returns>
private async Task RunImplementation()
{
this.SearchRunning = true;
this.runSearchCancellationToken = new CancellationTokenSource();
// Read spectrum file
var lcms = await Task.Run(() => PbfLcMsRun.GetLcMsRun(this.SpectrumFilePath, 0, 0), this.runSearchCancellationToken.Token);
// Get MS/MS scan numbers
IEnumerable <int> ms2Scans = null;
if (this.MaxScanNumber > 0 && (this.MaxScanNumber - this.MinScanNumber) >= 0)
{
var allMs2Scans = lcms.GetScanNumbers(2);
ms2Scans = allMs2Scans.Where(scan => scan >= this.MinScanNumber && scan <= this.MaxScanNumber);
}
// Create truncated FASTA
this.truncatedFastaDbFilePath = this.CreateTruncatedFastaFile();
// Progress updater
this.SearchProgressPercent = 0.0;
this.SearchProgressStatus = "Searching...";
var progress = new Progress <ProgressData>(progressData =>
{
this.SearchProgressPercent = progressData.Percent;
this.SearchProgressStatus = progressData.Status;
});
// Run Search
var topDownLauncher = this.GetTopDownLauncher(ms2Scans);
this.runSearchTask = Task.Run(
() => topDownLauncher.RunSearch(
IcParameters.Instance.IonCorrelationThreshold,
this.runSearchCancellationToken.Token,
progress),
this.runSearchCancellationToken.Token);
await this.runSearchTask;
////topDownLauncher.RunSearch(IcParameters.Instance.IonCorrelationThreshold);
this.SearchRunning = false;
this.runSearchCancellationToken = null;
// Results delivered on close
this.Status = true;
if (this.ReadyToClose != null)
{
this.ReadyToClose(this, EventArgs.Empty);
}
}
public void TestTagBasedSearchCompRef()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataSetPath = @"D:\MassSpecFiles\CompRef";
const string fastaFilePath = @"D:\MassSpecFiles\CompRef\ID_003278_4B4B3CB1.fasta";
const string modsFilePath = @"D:\MassSpecFiles\CompRef\Mods.txt";
if (!Directory.Exists(dataSetPath))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, dataSetPath);
}
if (!File.Exists(modsFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modsFilePath);
}
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fileEntries = Directory.GetFiles(dataSetPath);
var dataset = (from fileName in fileEntries where fileName.EndsWith("pbf") select Path.GetFileNameWithoutExtension(fileName)).ToList();
dataset.Sort();
var fastaDb = new FastaDatabase(fastaFilePath);
var tolerance = new Tolerance(10);
var aaSet = new AminoAcidSet(modsFilePath);
for (var i = 0; i < dataset.Count; i++)
{
var rawFile = string.Format(@"{0}\{1}.pbf", dataSetPath, dataset[i]);
var ms1File = string.Format(@"{0}\{1}.ms1ft", dataSetPath, dataset[i]);
var tagFilePath = MassSpecDataReaderFactory.ChangeExtension(rawFile, ".seqtag");
var run = PbfLcMsRun.GetLcMsRun(rawFile);
const int minTagLength = 5;
//var tagParser = new SequenceTagParser(tagFilePath, minTagLength, 100);
Console.WriteLine("-----------------{0}--------------------", rawFile);
TestTagBasedSearch(run, fastaDb, tolerance, aaSet);
Console.WriteLine("-----------------------------------------------------------------------");
}
}
public void TestTagBasedSearch()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// const string rawFilePath = @"H:\Research\Lewy\raw\Lewy_intact_01.raw";
// const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
// const string rawFilePath = @"H:\Research\Yufeng\TopDownYufeng\raw\yufeng_column_test2.raw";
// const string rawFilePath = @"H:\Research\Weijun_TopDown\raw\UC4_Intact_plasmaTest_90_6May15_Bane_14-09-01RZ.raw";
// const string rawFilePath = @"H:\Research\Charles\TopDown\raw\SBEP_STM_001_02272012_Aragon.raw";
const string rawFilePath = @"D:\MassSpecFiles\60k\Yufeng_SampleTest1_150614113438.pbf";
//const string rawFilePath = @"D:\MassSpecFiles\60k\NCR_50K_Test_24Jun15_Bane_15-02-02RZ.pbf";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
//const int minTagLength = 5;
var tagFilePath = MassSpecDataReaderFactory.ChangeExtension(rawFilePath, ".seqtag");
//var tagParser = new SequenceTagParser(tagFilePath, minTagLength, 100);
const string fastaFilePath = @"D:\MassSpecFiles\60k\ID_003836_DA9CC1E4.fasta";
//const string fastaFilePath = @"D:\MassSpecFiles\60k\ID_004973_9BA6912F.fasta";
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var tolerance = new Tolerance(10);
// var modsFilePath = @"H:\Research\QCShew_TopDown\Production\Mods_Methyl.txt";
var modsFilePath = @"D:\MassSpecFiles\60k\Mods.txt";
// var modsFilePath = "";
if (!File.Exists(modsFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modsFilePath);
}
var aaSet = new AminoAcidSet(modsFilePath);
TestTagBasedSearch(run, fastaDb, tolerance, aaSet);
}
public void TestIanCidData()
{
const string specFilePath =
@"\\protoapps\userdata\Wilkins\UIMF Files\9 pep mix 365 mTorr with ims 45V CID\9 pep mix 365 mTorr with ims 45V CID.UIMF";
const string fastaFilePath = @"\\protoapps\userdata\Wilkins\UIMF Files\melittin.fasta";
const string outputDirectory =
@"\\protoapps\userdata\Wilkins\UIMF Files\9 pep mix 365 mTorr with ims 45V CID";
const double correlationThreshold = 0.7;
// Add missing modifications
// Initialize search modifications
var searchModifications = new List <SearchModification> {
};
var aminoAcidSet = new AminoAcidSet(searchModifications, 1);
// Initialize spectrum file
var lcmsRun = PbfLcMsRun.GetLcMsRun(specFilePath);
var scanNumbers = lcmsRun.GetScanNumbers(2);
// Initialize MSPathFinder
//var launcher = new IcTopDownLauncher(
// specFilePath,
// fastaFilePath,
// outputDirectory,
// aminoAcidSet)
//{
// MinSequenceLength = 1,
// MaxSequenceLength = 100,
// MaxNumNTermCleavages = 1,
// MaxNumCTermCleavages = 0,
// MinPrecursorIonCharge = 1,
// MaxPrecursorIonCharge = 20,
// MinProductIonCharge = 1,
// MaxProductIonCharge = 20,
// MinSequenceMass = 1,
// MaxSequenceMass = 30000,
// PrecursorIonTolerancePpm = 100,
// ProductIonTolerancePpm = 100,
// RunTargetDecoyAnalysis = DatabaseSearchMode.Both,
// SearchMode = InternalCleavageType.NoInternalCleavage,
// MaxNumThreads = 4,
// ScanNumbers = scanNumbers,
// NumMatchesPerSpectrum = 1,
// TagBasedSearch = false,
//};
//launcher.RunSearch(correlationThreshold);
}
public void TestFeatureMapGeneration()
{
Console.WriteLine("Testing Working");
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFile = @"\\protoapps\UserData\Jungkap\Joshua\testData\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string testFile = @"\\protoapps\UserData\Jungkap\Joshua\FeatureMap\QC_Shew_Intact_26Sep14_Bane_C2Column3.ms1ft";
const string outputFile = @"D:\MassSpecFiles\training\raw\";
var map = new LcMsFeatureMap(PbfLcMsRun.GetLcMsRun(rawFile), testFile, 2000, 50000);
map.SaveImage(outputFile + "test.png");
}
public void TestReadingProMexFile(double massToFind, string expectedScanNumbers)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
var promexFilePath = Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "QC_Shew_Intact_26Sep14_Bane_C2Column3_Excerpt.ms1ft");
var promexFile = Utils.GetTestFile(methodName, promexFilePath);
var run = PbfLcMsRun.GetLcMsRun(pbfFile.FullName);
Console.Write("Reading ProMex results...");
var ms1Filter = new Ms1FtFilter(run, new Tolerance(10), promexFile.FullName);
Console.WriteLine();
var matchingScanNums = new SortedSet <int>();
foreach (var item in ms1Filter.GetMatchingMs2ScanNums(massToFind))
{
matchingScanNums.Add(item);
}
var scanNumList = string.Join(",", matchingScanNums);
Console.WriteLine("Scans with mass {0}:", massToFind);
Console.WriteLine(scanNumList);
var expectedScanNumList = expectedScanNumbers.Split(',');
var matchCount = 0;
foreach (var scanNumText in expectedScanNumList)
{
var scanNum = int.Parse(scanNumText);
if (!matchingScanNums.Contains(scanNum))
{
Assert.Fail("Did not find scan {0} for mass {1}", scanNum, massToFind);
}
matchCount++;
}
Assert.AreEqual(matchCount, matchingScanNums.Count, "Found extra matching scan nums vs. what was expected");
}
public void TestCptacSpikeIn()
{
const string featureFolder = @"D:\MassSpecFiles\CPTAC_spike_in\promex";
const string rawFolder = @"D:\MassSpecFiles\CPTAC_spike_in\raw";
var outFilePath = string.Format(@"{0}\aligned_features.tsv", featureFolder);
var align = new LcMsFeatureAlignment(new LcMsFeatureAlignComparer(new Tolerance(10)));
for (var i = 0; i < spikeDatasets.Length; i++)
{
var featureFilePath = string.Format(@"{0}\{1}.ms1ft", featureFolder, spikeDatasets[i]);
var rawFile = string.Format(@"{0}\{1}.pbf", rawFolder, spikeDatasets[i]);
if (!File.Exists(rawFile))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", rawFile);
continue;
}
if (!File.Exists(featureFilePath))
{
Console.WriteLine(@"Warning: Skipping file not found: {0}", featureFilePath);
continue;
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var s = 0d;
foreach (var scanNum in run.GetMs1ScanVector())
{
var spec = run.GetSpectrum(scanNum);
var summedIntensity = spec.Peaks.Sum(p => p.Intensity);
s += summedIntensity;
}
foreach (var scanNum in run.GetScanNumbers(2))
{
var spec = run.GetSpectrum(scanNum);
var summedIntensity = spec.Peaks.Sum(p => p.Intensity);
s += summedIntensity;
}
Console.WriteLine("{0}\t{1}", i, s);
//var features = LcMsFeatureAlignment.LoadProMexResult(i, featureFilePath, run);
//align.AddDataSet(i, features, run);
}
//align.AlignFeatures();
//Console.WriteLine("# of aligned features = {0}", align.CountAlignedFeatures);
//align.RefineAbundance();
//OutputAlignmentResult(align, outFilePath, spikeDatasets);
}
public void TestFeatureExampleForFigure()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string rawFile = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_1\CPTAC_Intact_rep6_15Jan15_Bane_C2-14-08-02RZ.pbf";
//const string rawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
if (!File.Exists(rawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFile);
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var scorer = new LcMsFeatureLikelihood();
var featureFinder = new LcMsPeakMatrix(run, scorer);
var feature = featureFinder.GetLcMsPeakCluster(28061.6177, 20, 34, 7624, 7736);
var resultsFilePath = Path.Combine(Path.GetTempPath(), Path.GetFileNameWithoutExtension(rawFile) + "_peaks.txt");
var writer = new StreamWriter(resultsFilePath);
writer.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n", "Scan", "Elution_Time", "Charge", "ID", "MZ", "Intensity", "Pearson_Correlation");
var envelope = feature.TheoreticalEnvelope;
foreach (var e in envelope.Isotopes)
{
Console.WriteLine(e.Ratio);
}
foreach (var env in feature.EnumerateEnvelopes())
{
var corr = env.PearsonCorrelation;
for (var i = 0; i < envelope.Size; i++)
{
var peak = env.Peaks[i];
if (peak == null)
{
continue;
}
writer.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n", env.ScanNum, run.GetElutionTime(env.ScanNum), env.Charge, i, peak.Mz, peak.Intensity, corr);
}
}
writer.Close();
Console.WriteLine("Results are in file " + resultsFilePath);
}