/// <summary>
/// Initializes static members of the <see cref="MsgfPlusSequenceReader"/> class.
/// </summary>
static MsgfPlusSequenceReader()
{
AminoAcidSet = new AminoAcidSet();
}
public void TestPrSm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string specFilePath = @"C:\cygwin\home\kims336\Data\TopDownYufeng\raw\yufeng_column_test2.raw";
//const string annotation =
// "_.MKTKLSVLSAAMLAATLTMMPAVSQAAIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVG" +
// "LHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTV" +
// "TSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVG" +
// "IGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGS" +
// "AAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEA" +
// "NQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDL" +
// "KSLKELLKDQEGAVALKIVRGKSMLYLVLR._";
//var aaSet = new AminoAcidSet();
//const int charge = 60;
//const int ms2ScanNum = 46661;
const string specFilePath = @"D:\Research\Data\Jon\AH_SF_mouseliver_3-1_Intact_2_6Feb14_Bane_PL011402.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const int ms2ScanNum = 19011;
const int charge = 7;
const string annotation = "_.SKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVGSC._";
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, true);
var modVal = Modification.RegisterAndGetModification("AddVal", new Composition(5, 9, 1, 1, 0));
var searchMods = AminoAcid.StandardAminoAcidCharacters.Select(residue => new SearchModification(modVal, residue, SequenceLocation.Everywhere, false)).ToList();
searchMods.Add(acetylN);
const int numMaxModsPerProtein = 1;
var aaSet = new AminoAcidSet(searchMods, numMaxModsPerProtein);
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
Console.WriteLine("NumProteoforms: " + graph.GetNumProteoformCompositions());
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
var ms2Scorer = new ProductScorerBasedOnDeconvolutedSpectra(run, 1, 15);
ms2Scorer.GetScorer(ms2ScanNum);
var scorer = ms2Scorer.GetMs2Scorer(ms2ScanNum);
Assert.NotNull(scorer, "Scorer is null!");
for (var i = 0; i < graph.GetNumProteoformCompositions(); i++)
{
graph.SetSink(i);
Console.WriteLine("ModComb: " + graph.GetModificationCombinations()[i]);
var score = graph.GetFragmentScore(scorer);
Console.WriteLine("Fast search score: " + score);
var composition = graph.GetSinkSequenceCompositionWithH2O();
var informedScorer = new InformedTopDownScorer(run, aaSet, 1, 30, new Tolerance(10));
var refinedScore = informedScorer.GetScores(AminoAcid.ProteinNTerm, SimpleStringProcessing.GetStringBetweenDots(annotation), AminoAcid.ProteinCTerm, composition, charge, ms2ScanNum);
Console.WriteLine("Modifications: {0}", refinedScore.Modifications);
Console.WriteLine("Composition: {0}", composition);
Console.WriteLine("RefinedScores: {0}", refinedScore);
}
}
/// <summary>
/// Parse a protein/peptide sequence in the LCMSSpectator style.
/// </summary>
/// <param name="sequence">The sequence as a string.</param>
/// <returns>The parsed sequence.</returns>
public Sequence Read(string sequence)
{
if (this.trimAnnotations)
{
var firstIndex = sequence.IndexOf('.');
if (firstIndex >= 0)
{
var index = Math.Min(firstIndex + 1, sequence.Length - 1);
sequence = sequence.Substring(index, sequence.Length - index - 1);
}
var lastIndex = sequence.LastIndexOf('.');
if (lastIndex >= 0)
{
var index = Math.Min(lastIndex, sequence.Length - 1);
sequence = sequence.Substring(0, index);
}
}
const string AminoAcidRegex = @"[" + AminoAcid.StandardAminoAcidCharacters + "]";
////const string modRegex = @"\[([A-Z]|[a-z])+\]";
const string ModRegex = @"\[([A-Z]|[a-z]|[0-9]|-|>)+\]";
if (string.IsNullOrEmpty(sequence))
{
return(new Sequence(new List <AminoAcid>()));
}
if (!Regex.IsMatch(sequence, "(" + AminoAcidRegex + "|" + ModRegex + ")+"))
{
return(null);
}
var stdAaSet = new AminoAcidSet();
var aminoAcidList = new List <AminoAcid>();
var matches = Regex.Matches(sequence, "(" + AminoAcidRegex + "|" + ModRegex + ")");
AminoAcid aa = null;
var mods = new List <Modification>();
foreach (Match match in matches)
{
var element = match.Value;
if (element.Length == 0)
{
continue;
}
if (element.Length == 1 && char.IsLetter(element[0]))
{ // amino acid
if (aa != null)
{
aa = mods.Aggregate(aa, (current, mod) => new ModifiedAminoAcid(current, mod));
aminoAcidList.Add(aa);
mods = new List <Modification>();
}
aa = stdAaSet.GetAminoAcid(element[0]);
if (aa == null)
{
throw new FormatException("Unrecognized amino acid character: " + element[0]);
}
//// Console.WriteLine("{0} {1} {2}", aa.Residue, aa.Composition, aa.GetMass());
}
else
{
var modName = element.Substring(1, element.Length - 2);
var mod = Modification.Get(modName);
if (mod == null)
{
throw new FormatException("Unrecognized modification: " + modName);
}
mods.Add(mod);
//// Console.WriteLine("{0} {1} {2}", mod.Name, mod.Composition, mod.Composition.AveragineMass);
}
}
if (aa != null)
{
aa = mods.Aggregate(aa, (current, mod) => new ModifiedAminoAcid(current, mod));
aminoAcidList.Add(aa);
}
return(new Sequence(aminoAcidList));
}
private void TestTopDownSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet,
int minSequenceLength, int maxSequenceLength,
int minPrecursorIonCharge, int maxPrecursorIonCharge,
int minProductIonCharge, int maxProductIonCharge,
double minSequenceMass, double maxSequenceMass,
DatabaseSearchMode tda, InternalCleavageType searchMode)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Search parameters
const int maxNumNTermCleavages = 1; // 30
const int maxNumCTermCleavages = 0;
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var topDownOptions = new MsPfParameters(
specFilePath,
dbFilePath,
outputDir,
aaSet, "")
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MaxNumNTermCleavages = maxNumNTermCleavages,
MaxNumCTermCleavages = maxNumCTermCleavages,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
MinSequenceMass = minSequenceMass,
MaxSequenceMass = maxSequenceMass,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
TargetDecoySearchMode = tda,
InternalCleavageMode = searchMode,
};
var topDownLauncher = new IcTopDownLauncher(topDownOptions);
//topDownLauncher.ForceParallel = true;
//topDownLauncher.MaxNumThreads = -1;
topDownLauncher.RunSearch(0.7);
//topDownLauncher.RunIntactProteinSearch();
}
public void TestTopDownSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet,
bool?tda, int searchMode)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int minSequenceLength = 21; // 7
const int maxSequenceLength = 500; // 1000
const int minPrecursorIonCharge = 2; // 3
const int maxPrecursorIonCharge = 60; // 67
const int minProductIonCharge = 1; // 1
const int maxProductIonCharge = 20; // 15
const double minSequenceMass = 3000.0;
const double maxSequenceMass = 50000.0;
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet,
minSequenceLength, maxSequenceLength,
minPrecursorIonCharge, maxPrecursorIonCharge,
minProductIonCharge, maxProductIonCharge,
minSequenceMass, maxSequenceMass,
tda, searchMode
);
}
public void TestFeatureId()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataSet = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3";
if (!File.Exists(dataSet))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dataSet);
}
// Feature: 5236-5286 6-12 8480.3681 5
const int minScanNum = 5236;
const int maxScanNum = 5286;
const double featureMass = 8480.3681;
//const int minScanNum = 7251;
//const int maxScanNum = 7326;
//const double featureMass = 32347.18;
// const int minScanNum = 4451;
// const int maxScanNum = 4541;
// const double featureMass = 31267.95;
var tolerance = new Tolerance(10);
var relaxedTolerance = new Tolerance(20);
const int minTagLength = 5;
const int minMergedTagLength = 7;
const int minNumTagMatches = 1;
var rawFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".raw");
var run = PbfLcMsRun.GetLcMsRun(rawFileName);
var aminoAcidSet = AminoAcidSet.GetStandardAminoAcidSet();
var featureFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".ms1ft");
var filter = new Ms1FtFilter(run, tolerance, featureFileName);
var ms2ScanNums =
filter.GetMatchingMs2ScanNums(featureMass)
.Where(scanNum => scanNum > minScanNum && scanNum < maxScanNum)
.ToArray();
const string tagFileName = dataSet + ".seqtag"; //"_MinLength3.seqtag"; //Path.ChangeExtension(dataSet, ".seqtag");
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);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
var tagParser = new SequenceTagParser(tagFileName, minTagLength);
var proteinsToTags = new Dictionary <string, IList <MatchedTag> >();
foreach (var ms2ScanNum in ms2ScanNums)
{
var tags = tagParser.GetSequenceTags(ms2ScanNum);
foreach (var tag in tags)
{
var matchedIndices = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).ToArray();
foreach (var index in matchedIndices)
{
var protein = fastaDb.GetProteinName(index);
var startIndex = fastaDb.GetZeroBasedPositionInProtein(index);
var matchedTag = new MatchedTag(tag, startIndex, featureMass);
IList <MatchedTag> existingTags;
if (proteinsToTags.TryGetValue(protein, out existingTags))
{
existingTags.Add(matchedTag);
}
else
{
proteinsToTags.Add(protein, new List <MatchedTag> {
matchedTag
});
}
}
}
}
foreach (var entry in proteinsToTags.OrderByDescending(e => e.Value.Count))
{
if (entry.Value.Count < minNumTagMatches)
{
break;
}
var proteinName = entry.Key;
var proteinSequence = fastaDb.GetProteinSequence(proteinName);
var protein = new Sequence(proteinSequence, aminoAcidSet);
Console.WriteLine(proteinName + "\t" + entry.Value.Count);
var matchedTagSet = new MatchedTagSet(proteinSequence, aminoAcidSet,
tolerance, relaxedTolerance);
Console.WriteLine("********** Before merging");
foreach (var matchedTag in entry.Value)
{
var seq = proteinSequence.Substring(matchedTag.StartIndex,
matchedTag.EndIndex - matchedTag.StartIndex);
var nTermMass = protein.GetMass(0, matchedTag.StartIndex);
var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count);
Console.WriteLine("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}",
(matchedTag.NTermFlankingMass - nTermMass), seq, (matchedTag.CTermFlankingMass - cTermMass), matchedTag.StartIndex,
matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable);
matchedTagSet.Add(matchedTag);
}
Console.WriteLine("********** After merging");
foreach (var matchedTag in matchedTagSet.Tags)
{
if (matchedTag.Length < minMergedTagLength)
{
continue;
}
var seq = proteinSequence.Substring(matchedTag.StartIndex,
matchedTag.EndIndex - matchedTag.StartIndex);
var nTermMass = protein.GetMass(0, matchedTag.StartIndex);
var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count);
Console.WriteLine("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}",
(matchedTag.NTermFlankingMass - nTermMass), seq, (matchedTag.CTermFlankingMass - cTermMass), matchedTag.StartIndex,
matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable);
}
break;
}
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.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 isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && 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);
}
/// <summary>
/// Initializes a new instance of the <see cref="MsPfParameters"/> class, with the parameters specifying required options for a search
/// </summary>
/// <param name="specFilePath"></param>
/// <param name="dbFilePath"></param>
/// <param name="outputDir"></param>
/// <param name="aaSet"></param>
/// <param name="featureFilePath"></param>
public MsPfParameters(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet, string featureFilePath = null) : this()
{
SpecFilePath = specFilePath;
DatabaseFilePath = dbFilePath;
AminoAcidSet = aaSet;
OutputDir = outputDir;
FeatureFilePath = featureFilePath;
}
public void Test43KProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Configure amino acid set
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var dethiomethylM = new SearchModification(Modification.Dethiomethyl, 'M', SequenceLocation.Everywhere, false);
var deamidatedN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
var deamidatedQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
var pyroCarbamidomethylC = new SearchModification(Modification.PyroCarbamidomethyl, 'C',
SequenceLocation.ProteinNTerm, false);
var phosphoS = new SearchModification(Modification.Phosphorylation, 'S', SequenceLocation.Everywhere, false);
var phosphoT = new SearchModification(Modification.Phosphorylation, 'T', SequenceLocation.Everywhere, false);
var phosphoY = new SearchModification(Modification.Phosphorylation, 'Y', SequenceLocation.Everywhere, false);
var nitrosylC = new SearchModification(Modification.Nitrosyl, 'C', SequenceLocation.Everywhere, false);
var nethylmaleimideC = new SearchModification(Modification.Nethylmaleimide, 'C', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
glutathioneC,
oxM,
dethiomethylM,
acetylN,
//phosphoS,
//phosphoT,
//phosphoY,
deamidatedN,
// deamidatedQ,
glutathioneC,
pyroCarbamidomethylC,
nitrosylC,
nethylmaleimideC
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
// var aaSet = new AminoAcidSet();
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(aaSet, AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
var ms1Filter = new SimpleMs1Filter();
var ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(run);
foreach (var ms2ScanNum in Ms2ScanNums)
{
ms2ScorerFactory.GetScorer(ms2ScanNum);
}
for (var numNTermCleavages = 0; numNTermCleavages <= 0; numNTermCleavages++)
{
if (numNTermCleavages > 0)
{
seqGraph.CleaveNTerm();
}
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
var modCombinations = modCombs[modIndex];
foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass))
{
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
continue;
}
var charge =
(int)
Math.Round(sequenceMass /
(spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var scorer = ms2ScorerFactory.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
if (score <= 3)
{
continue;
}
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = protSequence.Substring(numNTermCleavages);
var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1];
var post = annotation[annotation.Length - 1];
Console.WriteLine("{0}.{1}.{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}", pre, sequence, post, ms2ScanNum, modCombinations,
precursorIon.GetMostAbundantIsotopeMz(), precursorIon.Charge, precursorIon.Composition.Mass, score);
}
}
}
}
/// <summary>
/// Initializes a new instance of the <see cref="MsPfParameters"/> class, with the parameters specifying required options for a search
/// </summary>
/// <param name="specFilePath"></param>
/// <param name="dbFilePath"></param>
/// <param name="outputDir"></param>
/// <param name="aaSet"></param>
/// <param name="featureFilePath"></param>
public MsPfParameters(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet, string featureFilePath = null) : this()
{
// ReSharper disable VirtualMemberCallInConstructor
SpecFilePath = specFilePath;
DatabaseFilePath = dbFilePath;
AminoAcidSet = aaSet;
OutputDir = outputDir;
FeatureFilePath = featureFilePath;
// ReSharper restore VirtualMemberCallInConstructor
}
public IcRescorer(string specFilePath, string icResultFilePath, string outputFilePath, AminoAcidSet aaSet, Tolerance tolerance, double ms2CorrThreshold = 0.7
, int minProductIonCharge = 1, int maxProductIonCharge = 10)
{
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
_topDownScorer = new InformedTopDownScorer(run, aaSet, minProductIonCharge, maxProductIonCharge, tolerance, ms2CorrThreshold);
Rescore(icResultFilePath, outputFilePath);
}
public void FindProteinDeltaMass()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string folderPath = @"D:\MassSpecFiles\Glyco\";
if (!Directory.Exists(folderPath))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, folderPath);
}
var fileSet = new string[]
{
"User_sample_test_02252015", "User_sample_test_MWCO_02262016", "User_sample_test_SEC_F3_03022105",
"User_sample_test_SEC_F1_02272015", "User_sample_test_SEC_F2_02282015"
};
const string fastaFilePath = folderPath + "ID_003836_DA9CC1E4.fasta";
for (var i = 0; i < fileSet.Length; i++)
{
var datasetName = fileSet[i];
var tagFilePath = folderPath + datasetName + ".seqtag";
//var outputFilePath = folderPath + datasetName + ".matchedtag";
var outputFilePath = folderPath + datasetName + ".dmass";
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
using (var writer = new StreamWriter(outputFilePath))
{
var isHeader = true;
var nReadSeqTag = 0;
Console.WriteLine(@"Reading {0} file", tagFilePath);
var nColumn = 0;
foreach (var line in File.ReadAllLines(tagFilePath))
{
if (isHeader)
{
isHeader = false;
nColumn = line.Split('\t').Length;
writer.WriteLine(line + "\t" + "Protein" + "\t" + "DetectedFlankingMass" + "\t" + "ExpectedFlankingMass" + "\t" + "DeltaMass");
continue;
}
var token = line.Split('\t');
if (token.Length != nColumn)
{
continue;
}
var tag = token[1];
//var scan = Convert.ToInt32(token[0]);
if (tag.Length < 6)
{
continue;
}
var nTerminal = token[2].Equals("1");
var detectedFlankingMass = Double.Parse(token[3]);
if (!nTerminal)
{
detectedFlankingMass -= Composition.H2O.Mass;
}
nReadSeqTag++;
var matchedProteins =
searchableDb.FindAllMatchedSequenceIndices(tag)
.Select(index => fastaDb.GetProteinName(index))
.Distinct().ToArray();
if (matchedProteins.Length < 1)
{
continue;
}
foreach (var protName in matchedProteins)
{
var seqStr = fastaDb.GetProteinSequence(protName);
var oriSeq = new Sequence(seqStr, AminoAcidSet.GetStandardAminoAcidSet());
var startIdx = 0;
while (true)
{
var idx = seqStr.IndexOf(tag, startIdx);
if (idx < 0)
{
break; //no matching
}
//var nClv = (nTerminal) ? idx : seqStr.Length - idx - tag.Length;
var nClv = (nTerminal) ? 2 : 1;
for (var j = 0; j < nClv; j++)
{
var flankComposition = (nTerminal)
? oriSeq.GetComposition(j, idx)
: oriSeq.GetComposition(idx + tag.Length, oriSeq.Count - j);
var massDiff = (detectedFlankingMass - flankComposition.Mass);
if (massDiff > -500 && massDiff < 2000)
{
//writer.WriteLine(massDiff);
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", line, protName, detectedFlankingMass, flankComposition.Mass, massDiff);
}
if (massDiff > 2000)
{
break;
}
}
startIdx = idx + tag.Length;
}
}
//var matchedProteinStr = string.Join(",", matchedProteins);
//var massDiffStr = string.Join(",", massDiffList);
//writer.WriteLine("{0}\t{1}\t{2}\t{3}", line, matchedProteins.Length, matchedProteinStr, massDiffStr);
}
Console.WriteLine(@"{0} seq tags are processed", nReadSeqTag);
}
Console.WriteLine(@"Done");
}
}
public string Parse(Dictionary <string, string> parameters)
{
var message = CheckIsValid(parameters);
if (message != null)
{
return(message);
}
var specFilePath = parameters["-s"];
if (Directory.Exists(specFilePath)) // Directory
{
SpecFilePaths = Directory.GetFiles(specFilePath, "*.raw");
}
else
{
SpecFilePaths = new[] { specFilePath };
}
DatabaseFilePath = parameters["-d"];
var outputDir = parameters["-o"] ?? Environment.CurrentDirectory;
if (outputDir[outputDir.Length - 1] == Path.DirectorySeparatorChar)
{
outputDir = outputDir.Remove(outputDir.Length - 1);
}
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
return("OutputDir " + outputDir + " is not a directory!");
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
var modFilePath = parameters["-mod"];
if (modFilePath != null)
{
var parser = new ModFileParser(modFilePath);
_searchModifications = parser.SearchModifications;
_maxNumDynModsPerSequence = parser.MaxNumDynModsPerSequence;
if (_searchModifications == null)
{
return("Error while parsing " + modFilePath + "!");
}
AminoAcidSet = new AminoAcidSet(_searchModifications, _maxNumDynModsPerSequence);
}
else
{
AminoAcidSet = new AminoAcidSet();
_searchModifications = new SearchModification[0];
}
var enzymeId = Convert.ToInt32(parameters["-e"]);
Enzyme enzyme;
switch (enzymeId)
{
case 0:
enzyme = Enzyme.UnspecificCleavage;
break;
case 1:
enzyme = Enzyme.Trypsin;
break;
case 2:
enzyme = Enzyme.Chymotrypsin;
break;
case 3:
enzyme = Enzyme.LysC;
break;
case 4:
enzyme = Enzyme.LysN;
break;
case 5:
enzyme = Enzyme.GluC;
break;
case 6:
enzyme = Enzyme.ArgC;
break;
case 7:
enzyme = Enzyme.AspN;
break;
case 8:
enzyme = Enzyme.Alp;
break;
case 9:
enzyme = Enzyme.NoCleavage;
break;
default:
return("Invalid enzyme ID (" + enzymeId + ") for parameter -e");
}
Enzyme = enzyme;
NumTolerableTermini = Convert.ToInt32(parameters["-ntt"]);
if (NumTolerableTermini < 0 || NumTolerableTermini > 2)
{
return("Invalid value (" + NumTolerableTermini + ") for parameter -m");
}
PrecursorIonTolerancePpm = Convert.ToDouble(parameters["-t"]);
ProductIonTolerancePpm = Convert.ToDouble(parameters["-f"]);
var tdaVal = Convert.ToInt32(parameters["-tda"]);
if (tdaVal != 0 && tdaVal != 1)
{
return("Invalid value (" + tdaVal + ") for parameter -tda");
}
Tda = (tdaVal == 1);
MinSequenceLength = Convert.ToInt32(parameters["-minLength"]);
MaxSequenceLength = Convert.ToInt32(parameters["-maxLength"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinSequenceLength (" + MinSequenceLength + ") is larger than MaxSequenceLength (" + MaxSequenceLength + ")!");
}
MinPrecursorIonCharge = Convert.ToInt32(parameters["-minCharge"]);
MaxPrecursorIonCharge = Convert.ToInt32(parameters["-maxCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinPrecursorCharge (" + MinPrecursorIonCharge + ") is larger than MaxPrecursorCharge (" + MaxPrecursorIonCharge + ")!");
}
MinProductIonCharge = Convert.ToInt32(parameters["-minFragCharge"]);
MaxProductIonCharge = Convert.ToInt32(parameters["-maxFragCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return("MinFragmentCharge (" + MinProductIonCharge + ") is larger than MaxFragmentCharge (" + MaxProductIonCharge + ")!");
}
return(null);
}
public void TestGetScoreDistribution(int scanNum, string protSequence)
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
if (!pbfFile.Exists)
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, pbfFile);
}
const string modStr = "";
const int maxCharge = 20;
const int minCharge = 1;
const double filteringWindowSize = 1.1;
const int isotopeOffsetTolerance = 2;
var tolerance = new Tolerance(10);
var run = PbfLcMsRun.GetLcMsRun(pbfFile.FullName);
// Configure amino acid set
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
oxM,
acetylN
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var comparer = new FilteredProteinMassBinning(aaSet, 50000, 28);
//Console.WriteLine("{0}\t{1}", comparer.NumberOfBins, comparer.GetBinNumber(proteinMass));
var stopwatch = Stopwatch.StartNew();
var graphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
stopwatch.Stop();
Console.WriteLine(@"edge generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var stopwatch2 = Stopwatch.StartNew();
var sequence = Sequence.CreateSequence(protSequence, modStr, aaSet);
var proteinMass = sequence.Mass + Composition.H2O.Mass;
Console.WriteLine("Mass = {0}", proteinMass);
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
var deconvSpec = Deconvoluter.GetDeconvolutedSpectrum(spectrum, minCharge, maxCharge,
isotopeOffsetTolerance, filteringWindowSize, tolerance, 0.7);
stopwatch.Restart();
var scorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconvSpec, spectrum, tolerance, comparer);
var graph = graphFactory.CreateScoringGraph(scorer, proteinMass);
stopwatch.Stop();
Console.WriteLine(@"node generation elapsed time = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
stopwatch.Reset();
stopwatch.Start();
var gf = new GeneratingFunction(graph);
gf.ComputeGeneratingFunction();
//gf.ComputeGeneratingFunction(graph);
stopwatch.Stop();
Console.WriteLine(@"computing generation function = {0:0.000} sec", (stopwatch.ElapsedMilliseconds) / 1000.0d);
var scoreDist = gf.GetScoreDistribution();
Console.WriteLine("{0}-{1}", scoreDist.MinScore, scoreDist.MaxScore);
Console.WriteLine("{0} : {1}", "score", "specEValue");
for (var score = 15; score <= gf.MaximumScore; score++)
{
var specEvalue = gf.GetSpectralEValue(score);
Console.WriteLine("{0} : {1}", score, specEvalue);
}
stopwatch2.Stop();
Console.WriteLine(@"TOTAL computing generation function = {0:0.000} sec", stopwatch2.ElapsedMilliseconds / 1000.0d);
}
public FilteredProteinMassBinning(AminoAcidSet aaSet, double maxProteinMass = 50000, int numBits = 27)
{
_aminoAcidSet = aaSet;
var terminalModifications = GetTerminalModifications(aaSet);
var extendedAminoAcidArray = GetExtendedAminoAcidArray(aaSet);
MaxMass = maxProteinMass;
MinMass = MaxMass;
foreach (var aa in extendedAminoAcidArray)
{
if (aa.Mass < MinMass)
{
MinMass = aa.Mass;
}
foreach (var mod in terminalModifications)
{
var modAa = new ModifiedAminoAcid(aa, mod);
if (modAa.Mass < MinMass)
{
MinMass = modAa.Mass;
}
}
}
_mzComparer = new MzComparerWithBinning(numBits);
_minMzBinIndex = _mzComparer.GetBinNumber(MinMass);
_maxMzBinIndex = _mzComparer.GetBinNumber(MaxMass);
var numberOfMzBins = _maxMzBinIndex - _minMzBinIndex + 2; // pad zero mass bin
_mzBinToFilteredBinMap = new int[numberOfMzBins];
for (var i = 0; i < numberOfMzBins; i++)
{
_mzBinToFilteredBinMap[i] = -1;
}
var tempMap = new int[numberOfMzBins];
var fineNodes = new BitArray(Constants.GetBinNumHighPrecision(MaxMass));
fineNodes[0] = true;
var effectiveBinCounter = 0;
for (var fineBinIdx = 0; fineBinIdx < fineNodes.Length; fineBinIdx++)
{
if (!fineNodes[fineBinIdx])
{
continue;
}
var fineNodeMass = fineBinIdx / Constants.RescalingConstantHighPrecision;
foreach (var aa in extendedAminoAcidArray)
{
var validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + aa.Mass);
if (validFineNodeIndex >= fineNodes.Length)
{
break;
}
fineNodes[validFineNodeIndex] = true;
if (fineBinIdx == 0 && !(aa is ModifiedAminoAcid)) // include terminal modifications
{
foreach (var terminalMod in terminalModifications)
{
var modifiedAa = new ModifiedAminoAcid(aa, terminalMod);
validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + modifiedAa.Mass);
if (validFineNodeIndex >= fineNodes.Length)
{
break;
}
fineNodes[validFineNodeIndex] = true;
}
}
}
/*foreach (var m in massList)
* {
* var validFineNodeIndex = Constants.GetBinNumHighPrecision(fineNodeMass + m);
* if (validFineNodeIndex >= fineNodes.Length) break;
* fineNodes[validFineNodeIndex] = true;
* }*/
var binNum = _mzComparer.GetBinNumber(fineNodeMass);
if (fineBinIdx == 0 || (binNum >= _minMzBinIndex && binNum <= _maxMzBinIndex && _mzBinToFilteredBinMap[binNum - _minMzBinIndex + 1] < 0))
{
_mzBinToFilteredBinMap[binNum == 0 ? 0 : binNum - _minMzBinIndex + 1] = effectiveBinCounter;
tempMap[effectiveBinCounter] = binNum;
effectiveBinCounter++;
}
}
_filteredBinToMzBinMap = new int[effectiveBinCounter];
Array.Copy(tempMap, _filteredBinToMzBinMap, effectiveBinCounter);
}
public void TestBottomUpSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet, bool?tda, int ntt, double corrThreshold = 0.3)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Search parameters
const int minSequenceLength = 6; // 7
const int maxSequenceLength = 40; // 1000
const int minPrecursorIonCharge = 1; // 3
const int maxPrecursorIonCharge = 4; // 67
const int minProductIonCharge = 1; // 1
const int maxProductIonCharge = 2; // 15
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var enzyme = Enzyme.Trypsin;
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
dbFilePath,
outputDir,
aaSet,
enzyme)
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
RunTargetDecoyAnalysisBool = tda,
NumTolerableTermini = ntt
};
bottomUpLauncher.RunSearch(corrThreshold);
//topDownLauncher.RunIntactProteinSearch();
}
public void TestGetProteinsWithTagMatchingSingleSpec()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataSet = @"H:\Research\Lewy\raw\Lewy_intact_07";
// const int scanNum = 5158;
const int minTagLength = 7;
const int minNumTagMatches = 1;
var aminoAcidSet = AminoAcidSet.GetStandardAminoAcidSet();
const int scanNum = 2;
// Parse sequence tags
//const string tagFileName = dataSet + ".seqtag"; //"_MinLength3.seqtag"; //Path.ChangeExtension(dataSet, ".seqtag");
const string rawFilePath = "";
const string fastaFilePath = @"H:\Research\Lewy\ID_004858_0EE8CF61.fasta";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
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 tags = tagParser.GetSequenceTags(scanNum);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spec = run.GetSpectrum(scanNum) as ProductSpectrum;
var tagFinder = new SequenceTagFinder(spec, new Tolerance(5));
var tags = tagFinder.GetAllSequenceTagString();
var proteinsToTags = new Dictionary <string, IList <MatchedTag> >();
foreach (var tag in tags)
{
var matchedIndices = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).ToArray();
foreach (var index in matchedIndices)
{
var protein = fastaDb.GetProteinName(index);
var startIndex = fastaDb.GetOneBasedPositionInProtein(index);
var matchedTag = new MatchedTag(tag, startIndex, 0.0);
IList <MatchedTag> existingTags;
if (proteinsToTags.TryGetValue(protein, out existingTags))
{
existingTags.Add(matchedTag);
}
else
{
proteinsToTags.Add(protein, new List <MatchedTag> {
matchedTag
});
}
}
}
foreach (var entry in proteinsToTags.OrderByDescending(e => e.Value.Count))
{
if (entry.Value.Count < minNumTagMatches)
{
break;
}
var proteinName = entry.Key;
var proteinSequence = fastaDb.GetProteinSequence(proteinName);
var protein = new Sequence(proteinSequence, aminoAcidSet);
Console.WriteLine(proteinName + "\t" + entry.Value.Count);
foreach (var matchedTag in entry.Value)
{
var seq = proteinSequence.Substring(matchedTag.StartIndex,
matchedTag.EndIndex - matchedTag.StartIndex);
var nTermMass = protein.GetMass(0, matchedTag.StartIndex);
var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count);
Console.WriteLine("\t{0} ({1})\t{2}\t{3} ({4})\t{5}\t{6}\t{7}",
matchedTag.NTermFlankingMass, (matchedTag.NTermFlankingMass - nTermMass),
seq,
matchedTag.CTermFlankingMass, (matchedTag.CTermFlankingMass - cTermMass),
matchedTag.StartIndex,
matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable);
}
}
}
public void TestChaoChao(string specFilePath)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
const string dbFilePath = @"D:\Research\Data\ChaoChao\database\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
const string outputDir = @"D:\Research\Data\ChaoChao\Ic\";
// Configure amino acid set
//var carbamidomethylC = new SearchModification(Modification.Carbamidomethylation, 'C', SequenceLocation.Everywhere, true);
//var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
//var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 0;
var searchModifications = new List <SearchModification>
{
//carbamidomethylC,
//acetylN,
//oxM
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
bool?tda = true; // true: target & decoy, false: target, null: decoy
const int minSequenceLength = 7; // 7
const int maxSequenceLength = 150; // 1000
const int minPrecursorIonCharge = 1; // 3
const int maxPrecursorIonCharge = 30; // 67
const int minProductIonCharge = 1; // 1
const int maxProductIonCharge = 15; // 15
const double precursorIonTolerancePpm = 10;
const double productIonTolerancePpm = 10;
const double corrThreshold = 0.7;
var bottomUpLauncher = new IcBottomUpLauncher(
specFilePath,
dbFilePath,
outputDir,
aaSet,
null)
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
RunTargetDecoyAnalysisBool = tda,
NumTolerableTermini = 0
};
bottomUpLauncher.RunSearch(corrThreshold);
}
public void TestRunningTimeChromGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var numPeptides = 0;
foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin))
{
++numPeptides;
var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length - 4), aaSet).Composition + Composition.H2O;
var mz = new Ion(comp, 2).GetMonoIsotopicMz();
//Console.WriteLine(peptide.Annotation + " " + mz);
rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//Assert.True(xic1.Count == xic2.Count);
//for (var i = 0; i < xic1.Count; i++)
//{
// if (!xic1[i].Equals(xic2[i]))
// {
// Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]);
// }
// Assert.True(xic1[i].Equals(xic2[i]));
//}
if (numPeptides == 100000)
{
break;
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestCompositeScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
// 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(pbfFile.FullName);
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);
if (pbfFile.DirectoryName == null)
{
Assert.Ignore("Ignoring test since cannot determine the parent directory of " + pbfFile.FullName);
}
var fileExt = new[] { "IcTarget", "IcDecoy" };
foreach (var ext in fileExt)
{
var resultFileName = Path.Combine(pbfFile.DirectoryName, Path.GetFileNameWithoutExtension(pbfFile.Name)) + string.Format("_{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 = Path.Combine(pbfFile.DirectoryName, Path.GetFileNameWithoutExtension(pbfFile.Name)) + string.Format("_{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, 30, 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));
if (!(run.GetSpectrum(scan) is ProductSpectrum ms2Spec))
{
Console.WriteLine("Could not get the spectrum datafor scan {0}", scan);
}
public void TestNominalMassErrors()
{
const int MAX_RUNTIME_SECONDS = 60;
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const int minLength = 300;
const int maxLength = 400;
var sw = new System.Diagnostics.Stopwatch();
var fastaFile = Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"MSPathFinderT\ID_003962_71E1A1D4.fasta"));
var db = new FastaDatabase(fastaFile.FullName);
db.Read();
var indexedDb = new IndexedDatabase(db);
var numSequences = 0L;
sw.Start();
var hist = new long[11];
var aaSet = new AminoAcidSet();
foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsetsNoEnzyme(minLength, maxLength))
{
++numSequences;
var annotation = peptideAnnotationAndOffset.Annotation;
var sequenceStr = annotation.Substring(2, annotation.Length - 4);
var sequenceComp = aaSet.GetComposition(sequenceStr);
var mass = sequenceComp.Mass;
var nominalMass = sequenceComp.NominalMass;
var error = (int)Math.Round(mass * Constants.RescalingConstant) - nominalMass;
var errorBin = error + hist.Length / 2;
if (errorBin < 0)
{
errorBin = 0;
}
if (errorBin >= hist.Length)
{
errorBin = hist.Length - 1;
}
hist[errorBin]++;
if (numSequences % 100 == 0 && sw.Elapsed.TotalSeconds > MAX_RUNTIME_SECONDS)
{
break;
}
}
Console.WriteLine("Sequence count: {0:N0}", numSequences);
Console.WriteLine("{0,10} {1,10} {2,10}", "Bin ", "Count", "Fraction");
for (var i = 0; i < hist.Length; i++)
{
Console.WriteLine("{0,10:F1} {1,10:N0} {2,10:F1}%", i - hist.Length / 2, hist[i], hist[i] / (double)numSequences * 100);
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:F1} sec", sw.Elapsed.TotalSeconds);
}
public void TestMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(15);
var productIonTolerance = new Tolerance(15);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.MFQQEVTITAPNGLHTRPAAQFVKEAKGFTSEITVTSNGKSASAKSLFKLQTLGLTQGTVVTISAEGEDEQKAVEHLVKLMAELE._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
var specFilePath = Base.Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_SPEC_FILES_FOLDER, "SBEP_STM_001_02272012_Aragon.pbf"));
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath.FullName, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 6;
const int modIndex = 0;
const int ms2ScanNum = 4448;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestForYufeng()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// QC_Shew
const string specFilePath = @"H:\Research\Yufeng\TopDownYufeng\raw\yufeng_column_test2.raw";
//const string dbFilePath = @"H:\Research\Yufeng\TopDownYufeng\database\ID_002216_235ACCEA.fasta";
const string dbFilePath = @"H:\Research\Yufeng\TopDownYufeng\database\SO_3942_Truncated.fasta";
const string outputDir = @"H:\Research\Yufeng\TopDownYufeng\Debug";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// 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 glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
//var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
//var pyroGluQ = new SearchModification(Modification.PTeyroGluQ, 'Q', SequenceLocation.Everywhere, false);
//var cysteinylC = new SearchModification(Modification.Cysteinyl, 'C', SequenceLocation.Everywhere, false);
//var deamdN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
//var deamdQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
//const int numMaxModsPerProtein = 0;
//var searchModifications = new List<SearchModification>
//{
// dehydroC,
// oxM,
// acetylN
//};
//var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
var aaSet = new AminoAcidSet();
const int searchMode = 2; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = false; // true: target & decoy, false: target, null: decoy
const int minSequenceLength = 21; // 7
const int maxSequenceLength = 500; // 1000
const int minPrecursorIonCharge = 2; // 3
const int maxPrecursorIonCharge = 50; // 67
const int minProductIonCharge = 1; // 1
const int maxProductIonCharge = 20; // 15
const double minSequenceMass = 3000.0;
const double maxSequenceMass = 50000.0;
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet,
minSequenceLength, maxSequenceLength,
minPrecursorIonCharge, maxPrecursorIonCharge,
minProductIonCharge, maxProductIonCharge,
minSequenceMass, maxSequenceMass,
tda, searchMode
);
}
} // true: target and decoy, false: target only, null: decoy only
public void QuickId()
{
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 1;
const int maxCharge = 20;
var tolerance = new Tolerance(10);
const double corrThreshold = 0.7;
var comparer = new MzComparerWithBinning(numBits);
const double minFragmentMass = 200.0;
const double maxFragmentMass = 50000.0;
var minFragMassBin = comparer.GetBinNumber(minFragmentMass);
var maxFragMassBin = comparer.GetBinNumber(maxFragmentMass);
var aminoAcidSet = new AminoAcidSet(modFilePath);
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ms2ScanNumArr = run.GetScanNumbers(2).ToArray();
var sw = new Stopwatch();
sw.Start();
Console.Write("Building Spectrum Arrays...");
var massVectors = new BitArray[maxFragMassBin - minFragMassBin + 1];
for (var i = minFragMassBin; i <= maxFragMassBin; i++)
{
massVectors[i - minFragMassBin] = new BitArray(run.MaxLcScan + 1);
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
var productSpec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (productSpec == null)
{
continue;
}
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec.Peaks, minCharge, maxCharge, 2, 1.1, tolerance, corrThreshold);
if (deconvolutedPeaks == null)
{
continue;
}
foreach (var p in deconvolutedPeaks)
{
var mass = p.Mass;
var deltaMass = tolerance.GetToleranceAsDa(mass, 1);
var minMass = mass - deltaMass;
var maxMass = mass + deltaMass;
var minBinNum = comparer.GetBinNumber(minMass);
var maxBinNum = comparer.GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (binNum >= minFragMassBin && binNum <= maxFragMassBin)
{
massVectors[binNum - minFragMassBin][ms2ScanNum] = true;
}
}
}
}
sw.Stop();
Console.WriteLine(@"{0:f1} sec.", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
var fastaDb = new FastaDatabase(fastaFilePath);
fastaDb.Read();
var indexedDb = new IndexedDatabase(fastaDb);
var numProteins = 0;
var intactProteinAnnotationAndOffsets =
indexedDb.IntactSequenceAnnotationsAndOffsets(0, int.MaxValue);
var bestProtein = new string[run.MaxLcScan + 1];
var bestScore = new int[run.MaxLcScan + 1];
foreach (var annotationAndOffset in intactProteinAnnotationAndOffsets)
{
if (++numProteins % 10 == 0)
{
Console.WriteLine(@"Processing, {0} proteins done, {1:f1} sec elapsed",
numProteins,
sw.Elapsed.TotalSeconds);
}
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var protSequence = annotation.Substring(2, annotation.Length - 4);
// suffix
var seqGraph = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
continue;
}
for (var numNTermCleavage = 0; numNTermCleavage <= 1; numNTermCleavage++)
{
if (numNTermCleavage > 0)
{
seqGraph.CleaveNTerm();
}
var allCompositions = seqGraph.GetAllFragmentNodeCompositions();
var scoreArr = new int[run.MaxLcScan + 1];
foreach (var fragComp in allCompositions)
{
var suffixMass = fragComp.Mass + BaseIonType.Y.OffsetComposition.Mass;
var binNum = comparer.GetBinNumber(suffixMass);
if (binNum < minFragMassBin || binNum > maxFragMassBin)
{
continue;
}
var vector = massVectors[binNum - minFragMassBin];
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (vector[ms2ScanNum])
{
++scoreArr[ms2ScanNum];
}
}
}
foreach (var ms2ScanNum in ms2ScanNumArr)
{
if (scoreArr[ms2ScanNum] > bestScore[ms2ScanNum])
{
bestScore[ms2ScanNum] = scoreArr[ms2ScanNum];
var proteinName = fastaDb.GetProteinName(offset);
bestProtein[ms2ScanNum] = proteinName + (numNTermCleavage == 1 ? "'" : "");
}
}
}
// prefix
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestScore[ms2ScanNum], bestProtein[ms2ScanNum] ?? "");
}
}
public void TestTopDownSearch(string specFilePath, string dbFilePath, string outputDir, AminoAcidSet aaSet,
int minSequenceLength, int maxSequenceLength,
int minPrecursorIonCharge, int maxPrecursorIonCharge,
int minProductIonCharge, int maxProductIonCharge,
double minSequenceMass, double maxSequenceMass,
bool?tda, int searchMode)
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Search parameters
const int maxNumNTermCleavages = 1; // 30
const int maxNumCTermCleavages = 0;
const int precursorIonTolerancePpm = 10;
const int productIonTolerancePpm = 10;
var topDownLauncher = new IcTopDownLauncher(
specFilePath,
dbFilePath,
outputDir,
aaSet, "")
{
MinSequenceLength = minSequenceLength,
MaxSequenceLength = maxSequenceLength,
MaxNumNTermCleavages = maxNumNTermCleavages,
MaxNumCTermCleavages = maxNumCTermCleavages,
MinPrecursorIonCharge = minPrecursorIonCharge,
MaxPrecursorIonCharge = maxPrecursorIonCharge,
MinProductIonCharge = minProductIonCharge,
MaxProductIonCharge = maxProductIonCharge,
MinSequenceMass = minSequenceMass,
MaxSequenceMass = maxSequenceMass,
PrecursorIonTolerancePpm = precursorIonTolerancePpm,
ProductIonTolerancePpm = productIonTolerancePpm,
RunTargetDecoyAnalysisBool = tda,
SearchModeInt = searchMode,
};
//topDownLauncher.ForceParallel = true;
//topDownLauncher.MaxNumThreads = -1;
topDownLauncher.RunSearch(0.7);
//topDownLauncher.RunIntactProteinSearch();
}
static MgfSequenceReader()
{
StandardAminoAcidSet = new AminoAcidSet(Modification.Carbamidomethylation);
Modifications = new Dictionary <string, Tuple <AminoAcid, List <Modification> > >();
Modifications.Add("99.032",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('G'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("113.048",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('A'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("129.043",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('S'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("141.079",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('V'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("143.059",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('T'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("147.035",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('M'),
new List <Modification> {
Modification.Oxidation
}));
Modifications.Add("157.038",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('D'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("160.03",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('C'),
new List <Modification> {
Modification.Carbamidomethylation
}));
Modifications.Add("171.054",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('E'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("173.051",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('M'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("189.046",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('F'),
new List <Modification> {
Modification.Acetylation
}));
Modifications.Add("202.041",
new Tuple <AminoAcid, List <Modification> >(StandardAminoAcidSet.GetAminoAcid('C'),
new List <Modification> {
Modification.Carbamidomethylation,
Modification.Acetylation
}));
}
public void TestForVlad()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string specFilePath = @"D:\Research\Data\Vlad\raw\Alz_RA_C1_HCD_11012013_SW_03Nov2013.raw";
const string dbFilePath = @"D:\Research\Data\Vlad\database\ID_004221_1C042A1F.fasta";
//const string dbFilePath = @"D:\Research\Data\Vlad\database\HBA_MOUSE.fasta";
const string outputDir = @"D:\Research\Data\Vlad\Ic\POPSICLETest_M1";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
if (!File.Exists(dbFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFilePath);
}
// Configure amino acid set
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var dehydroC = new SearchModification(Modification.Dehydro, 'C', SequenceLocation.Everywhere, false);
var glutathioneC = new SearchModification(Modification.Glutathione, 'C', SequenceLocation.Everywhere, false);
var thrToAla = new SearchModification(Modification.ThrToAla, 'T', SequenceLocation.Everywhere, false);
var dethiomethylM = new SearchModification(Modification.Dethiomethyl, 'M', SequenceLocation.Everywhere, false);
var deamidatedN = new SearchModification(Modification.Deamidation, 'N', SequenceLocation.Everywhere, false);
var deamidatedQ = new SearchModification(Modification.Deamidation, 'Q', SequenceLocation.Everywhere, false);
var serToAsn = new SearchModification(Modification.SerToAsn, 'S', SequenceLocation.Everywhere, false);
var pyroCarbamidomethylC = new SearchModification(Modification.PyroCarbamidomethyl, 'C',
SequenceLocation.ProteinNTerm, false);
var phosphoS = new SearchModification(Modification.Phosphorylation, 'S', SequenceLocation.Everywhere, false);
var phosphoT = new SearchModification(Modification.Phosphorylation, 'T', SequenceLocation.Everywhere, false);
var phosphoY = new SearchModification(Modification.Phosphorylation, 'Y', SequenceLocation.Everywhere, false);
const int numMaxModsPerProtein = 4;
var searchModifications = new List <SearchModification>
{
dehydroC,
// glutathioneC,
oxM,
// dethiomethylM,
acetylN,
phosphoS,
phosphoT,
phosphoY
// thrToAla,
// serToAsn,
// deamidatedN,
// deamidatedQ,
// pyroCarbamidomethylC
};
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
const int searchMode = 1; // 0: all subsequences, 1: close to N- or C-term, 2: close to N- and C-term
bool? tda = false; // true: target & decoy, false: target, null: decoy
TestTopDownSearch(specFilePath, dbFilePath, outputDir, aaSet, tda, searchMode);
}
public void CreatePeptideAbundanceTableWithSkyline()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// Reading Henry's results
var pepKeySet = new HashSet <string>();
var resultDic = new Dictionary <string, Tuple <double, double> >();
const string henryResultPath = @"H:\Research\IPRG2015\Henry_results\tsv";
if (!Directory.Exists(henryResultPath))
{
Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, henryResultPath);
}
var aaSet = new AminoAcidSet();
foreach (var resultFile in Directory.GetFiles(henryResultPath, "*.tsv"))
{
var fileName = Path.GetFileName(resultFile);
if (fileName == null)
{
continue;
}
var sample = fileName.Substring(0, 2);
Console.WriteLine("Processing {0}", sample);
var tsvReader = new TsvFileParser(resultFile);
var peptides = tsvReader.GetData("Peptide").ToArray();
var charge = tsvReader.GetData("Charge").Select(c => Convert.ToInt32(c)).ToArray();
var prob = tsvReader.GetData("Prob").Select(Convert.ToDouble).ToArray();
var qValue = tsvReader.GetData("QValue").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < tsvReader.NumData; i++)
{
var peptide = peptides[i];
var nominalMass = GetNominalMass(aaSet, peptide);
var key = sample + ":" + GetPeptide(peptides[i]) + ":" + nominalMass + ":" + charge[i];
var pepKey = GetPeptide(peptides[i]) + ":" + nominalMass;
pepKeySet.Add(pepKey);
Tuple <double, double> existingScores;
if (resultDic.TryGetValue(key, out existingScores))
{
if (prob[i] > existingScores.Item1)
{
resultDic[key] = new Tuple <double, double>(prob[i], qValue[i]);
}
}
else
{
resultDic.Add(key, new Tuple <double, double>(prob[i], qValue[i]));
}
}
}
const string skylineFilePath = @"H:\Research\IPRG2015\MySkyline\TransitionResults.csv";
if (!File.Exists(skylineFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, skylineFilePath);
}
var skylineTable = new TsvFileParser(skylineFilePath, ',');
const string outputFilePath = @"H:\Research\IPRG2015\MySkyline\SkylineTransitionResultsWithScores3.tsv";
using (var writer = new StreamWriter(outputFilePath))
{
var peptides = skylineTable.GetData("Peptide Sequence").ToArray();
var samples = skylineTable.GetData("Replicate Name").Select(s => "" + s[0] + s[2]).ToArray();
var charges = skylineTable.GetData("Precursor Charge").Select(c => Convert.ToInt32(c)).ToArray();
var precursorMzs = skylineTable.GetData("Precursor Mz").Select(Convert.ToDouble).ToArray();
writer.WriteLine("{0}\tProbability\tQValue", string.Join("\t", skylineTable.GetHeaders().Take(skylineTable.GetHeaders().Count - 2)));
for (var i = 0; i < skylineTable.NumData; i++)
{
var precursorMz = precursorMzs[i];
var charge = charges[i];
var nominalMass = (int)Math.Round(((precursorMz - Constants.Proton) * charge - Composition.H2O.Mass) *
Constants.RescalingConstant);
var pepKey = peptides[i] + ":" + nominalMass;
if (!pepKeySet.Contains(pepKey))
{
//Console.WriteLine("Removing {0}", pepKey);
continue;
}
var key = samples[i] + ":" + peptides[i] + ":" + nominalMass + ":" + charge;
double?prob = null, qValue = null;
Tuple <double, double> scores;
if (resultDic.TryGetValue(key, out scores))
{
prob = scores.Item1;
qValue = scores.Item2;
}
var skylineData = skylineTable.GetRows()[i].Split(',');
for (var j = 0; j < skylineData.Length - 2; j++)
{
if (j != 2)
{
writer.Write(skylineData[j] + "\t");
}
else
{
writer.Write("" + skylineData[j][0] + skylineData[j][2] + "\t");
}
}
writer.WriteLine("{0}\t{1}",
prob != null ? prob.ToString() : "NA",
qValue != null ? qValue.ToString() : "NA");
}
}
Console.WriteLine("Done");
}
public IcBottomUpRescorer(string specFilePath, string icResultFilePath, string outputFilePath, AminoAcidSet aaSet, Tolerance tolerance)
{
_run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 0.0);
Rescore(icResultFilePath, outputFilePath);
}
public void TestCompositeScoring()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var pbfFilePath = Utils.GetPbfTestFilePath(false);
var pbfFile = Utils.GetTestFile(methodName, pbfFilePath);
// 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(pbfFile.FullName);
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);
if (pbfFile.DirectoryName == null)
{
Assert.Ignore("Ignoring test since cannot determine the parent directory of " + pbfFile.FullName);
}
var fileExt = new string[] { "IcTarget", "IcDecoy" };
foreach (var ext in fileExt)
{
var resultFileName = Path.Combine(pbfFile.DirectoryName, Path.GetFileNameWithoutExtension(pbfFile.Name)) + string.Format("_{0}.tsv", ext);
var parser = new TsvFileParser(resultFileName);
var scans = parser.GetData("Scan").Select(s => Convert.ToInt32((string)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 = Path.Combine(pbfFile.DirectoryName, Path.GetFileNameWithoutExtension(pbfFile.Name)) + string.Format("_{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, 30, 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;
if (ms2Spec == null)
{
Console.WriteLine("Could not get the spectrum datafor scan {0}", scan);
}
else
{
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);
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 (from item in lines where !string.IsNullOrWhiteSpace(item) select item).Take(20))
{
Console.WriteLine(line);
}
}
Console.WriteLine("Done");
}
}
