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");
}
}
private void WriteResultsToFile(SortedSet<DatabaseSequenceSpectrumMatch>[] matches, string outputFilePath, FastaDatabase database)
{
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Scan\tPre\tSequence\tPost\tModifications\tComposition\tProteinName\tProteinDesc" +
"\tProteinLength\tStart\tEnd\tCharge\tMostAbundantIsotopeMz\tMass\t#MatchedFragments\tIcScore"
);
for (var scanNum = _run.MinLcScan; scanNum <= _run.MaxLcScan; scanNum++)
{
if (matches[scanNum] == null) continue;
foreach (var match in matches[scanNum].Reverse())
{
var sequence = match.Sequence;
var offset = match.Offset;
var start = database.GetOneBasedPositionInProtein(offset) + 1 + match.NumNTermCleavages;
var end = start + sequence.Length - 1;
var proteinName = database.GetProteinName(match.Offset);
var protLength = database.GetProteinLength(proteinName);
var ion = match.Ion;
var scores = _bottomUpScorer.GetScores(match, ion.Composition, ion.Charge, scanNum);
if (ion == null)
{
Console.WriteLine(@"Null ion!");
}
if (scores == null)
{
Console.WriteLine(@"Null scores");
}
// Note for DblToString(value, 9, true), by having "9" and "true",
// values between 100 and 999 Da will have 7 digits after the decimal place, and
// values between 1000 and 9999 will have 6 digits after the decimal place
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}",
scanNum,
match.Pre,
sequence, // Sequence
match.Post,
scores.Modifications, // Modifications
ion.Composition, // Composition
proteinName, // ProteinName
database.GetProteinDescription(match.Offset), // ProteinDescription
protLength, // ProteinLength
start, // Start
end, // End
ion.Charge, // precursorCharge
StringUtilities.DblToString(ion.GetMostAbundantIsotopeMz(), 9, true), // MostAbundantIsotopeMz
StringUtilities.DblToString(ion.Composition.Mass, 9, true), // Mass
match.Score,
scores.Score // Score (re-scored)
);
}
}
}
}
public void CountMatchedProteins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int minTagLength = 3;
var scanToProtein = new Dictionary<int, string>();
var idTag = new Dictionary<int, bool>();
const string resultFilePath = @"H:\Research\ProMex\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var parser = new TsvFileParser(resultFilePath);
var scans = parser.GetData("Scan").Select(s => Convert.ToInt32(s)).ToArray();
var proteinNames = parser.GetData("ProteinName").ToArray();
var qValues = parser.GetData("QValue").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < qValues.Length; i++)
{
if (qValues[i] > 0.01) break;
scanToProtein.Add(scans[i], proteinNames[i]);
idTag.Add(scans[i], false);
}
const string rawFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(rawFilePath);
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
// const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.icsfldecoy.fasta";
// const string fastaFilePath =
// @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
Console.WriteLine("Sequence length: {0}", fastaDb.GetSequence().Length);
const string tagFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3.seqtag";
if (!File.Exists(tagFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFilePath);
}
var hist = new Dictionary<int, int>();
var scanSet = new HashSet<int>();
HashSet<string> proteinSetForThisScan = null;
var prevScan = -1;
var totalNumMatches = 0L;
var isHeader = true;
foreach (var line in File.ReadAllLines(tagFilePath))
{
if (isHeader)
{
isHeader = false;
continue;
}
var token = line.Split('\t');
if (token.Length < 3) continue;
var scan = Convert.ToInt32(token[0]);
var proteinId = scanToProtein.ContainsKey(scan) ? scanToProtein[scan] : null;
if (scan != prevScan)
{
if (proteinSetForThisScan != null)
{
var numMatches = proteinSetForThisScan.Count;
int numOcc;
if (hist.TryGetValue(numMatches, out numOcc)) hist[numMatches] = numOcc + 1;
else hist.Add(numMatches, 1);
}
prevScan = scan;
proteinSetForThisScan = new HashSet<string>();
}
scanSet.Add(scan);
var tag = token[1];
if (tag.Length < minTagLength) continue;
if (proteinSetForThisScan == null) continue;
var numMatchesForThisTag = 0;
foreach (var matchedProtein in searchableDb.FindAllMatchedSequenceIndices(tag)
.Select(index => fastaDb.GetProteinName(index)))
{
proteinSetForThisScan.Add(matchedProtein);
++numMatchesForThisTag;
if (proteinId != null && matchedProtein.Equals(proteinId))
{
idTag[scan] = true;
}
}
totalNumMatches += numMatchesForThisTag;
// if (numMatchesForThisTag > 10)
// {
// Console.WriteLine("{0}\t{1}", tag, numMatchesForThisTag);
// }
}
if (proteinSetForThisScan != null)
{
var numMatches = proteinSetForThisScan.Count;
int numOcc;
if (hist.TryGetValue(numMatches, out numOcc)) hist[numMatches] = numOcc + 1;
else hist.Add(numMatches, 1);
}
Console.WriteLine("AvgNumMatches: {0}", totalNumMatches/(float)scanSet.Count);
Console.WriteLine("Histogram:");
foreach (var entry in hist.OrderBy(e => e.Key))
{
Console.WriteLine("{0}\t{1}", entry.Key, entry.Value);
}
Console.WriteLine("NumId: {0}", idTag.Count);
Console.WriteLine("NumIdByTag: {0}", idTag.Select(e => e.Value).Count(v => v));
}
public void CountMatchedScansPerProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int minTagLength = 6;
var proteinToScan = new Dictionary<string, HashSet<int>>();
const string fastaFilePath = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.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);
Console.WriteLine(@"Sequence length: {0}", fastaDb.GetSequence().Length);
//const string tagFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3_seqtag.tsv";
//const string tagFilePath = @"\\protoapps\UserData\Jungkap\Co_culture\23B_pellet_TD_3Feb14_Bane_PL011402.seqtag";
const string tagFilePath = @"D:\MassSpecFiles\co_culture\23A_pellet_TD_3Feb14_Bane_PL011402.seqtag";
if (!File.Exists(tagFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFilePath);
}
var isHeader = true;
var numMatchedPairs = 0;
foreach (var line in File.ReadAllLines(tagFilePath))
{
if (isHeader)
{
isHeader = false;
continue;
}
var token = line.Split('\t');
if (token.Length != 3) continue;
var scan = Convert.ToInt32(token[0]);
var tag = token[1];
if (tag.Length < minTagLength) continue;
foreach (var matchedProtein in searchableDb.FindAllMatchedSequenceIndices(tag)
.Select(index => fastaDb.GetProteinName(index)))
{
++numMatchedPairs;
HashSet<int> matchedScans;
if (proteinToScan.TryGetValue(matchedProtein, out matchedScans))
{
matchedScans.Add(scan);
}
else
{
matchedScans = new HashSet<int> {scan};
proteinToScan.Add(matchedProtein, matchedScans);
}
}
}
var numMatchedProteins = proteinToScan.Keys.Count;
var numAllProteins = fastaDb.GetNumEntries();
Console.WriteLine("NumAllProteins: {0}", numAllProteins);
Console.WriteLine("NumMatchedProteins: {0}", numMatchedProteins);
Console.WriteLine("AvgMatchedScansPerProtein: {0}", numMatchedPairs / (float)numAllProteins);
}
private void WriteResultsToFile(DatabaseSequenceSpectrumMatch[] matches, string outputFilePath, FastaDatabase database)
{
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Scan\tPre\tSequence\tPost\tModifications\tComposition\tProteinName\tProteinDesc" +
"\tProteinLength\tStart\tEnd\tCharge\tMostAbundantIsotopeMz\tMass\t#MatchedFragments\tProbability\tSpecEValue\tEValue");
foreach(var scanNum in _ms2ScanNums)
{
var match = matches[scanNum];
if (match == null) continue;
var sequence = match.Sequence;
var offset = match.Offset;
var start = database.GetOneBasedPositionInProtein(offset) + 1 + match.NumNTermCleavages;
var end = start + sequence.Length - 1;
var proteinName = database.GetProteinName(match.Offset);
var protLength = database.GetProteinLength(proteinName);
var ion = match.Ion;
var proteinDescription = database.GetProteinDescription(match.Offset);
var probability = CompositeScorer.GetProbability(match.Score);
// Note for DblToString(value, 9, true), by having "9" and "true",
// values between 100 and 999 Da will have 7 digits after the decimal place, and
// values between 1000 and 9999 will have 6 digits after the decimal place
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}\t{16}\t{17}",
scanNum,
match.Pre, // Pre
sequence, // Sequence
match.Post, // Post
match.ModificationText, // Modifications
ion.Composition, // Composition
proteinName, // ProteinName
proteinDescription, // ProteinDescription
protLength, // ProteinLength
start, // Start position in protein
end, // End position in protein
ion.Charge, // precursorCharge
StringUtilities.DblToString(ion.GetMostAbundantIsotopeMz(), 9, true), // MostAbundantIsotopeMz
StringUtilities.DblToString(ion.Composition.Mass, 9, true), // Mass
match.NumMatchedFragments, // (Number of matched fragments)
StringUtilities.DblToString(probability, 4), // Probability
StringUtilities.DblToString(ExcelMinValue(match.SpecEvalue), 6, true, 0.001), // EValue; will be displayed using scientific notation if the value is less than 0.001
StringUtilities.DblToString(ExcelMinValue(match.SpecEvalue * database.GetNumEntries()), 6, true, 0.001) // SpecEValue; will be displayed using scientific notation if the value is less than 0.001
);
}
}
}
public void FindProteins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
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);
const string tagFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3_seqtag.tsv";
if (!File.Exists(tagFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFilePath);
}
const string outputFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3_matchedtag.tsv";
using (var writer = new StreamWriter(outputFilePath))
{
var isHeader = true;
foreach (var line in File.ReadAllLines(tagFilePath))
{
if (isHeader)
{
isHeader = false;
writer.WriteLine(line+"\t"+"Proteins");
continue;
}
var token = line.Split('\t');
if (token.Length != 3) continue;
var tag = token[1];
var matchedProteins =
searchableDb.FindAllMatchedSequenceIndices(tag)
.Select(index => fastaDb.GetProteinName(index))
.Distinct().ToArray();
var matchedProteinStr = string.Join(",", matchedProteins);
writer.WriteLine("{0}\t{1}\t{2}", line, matchedProteins.Length, matchedProteinStr);
}
}
Console.WriteLine(@"Done");
}
public void TestGettingProteinLengthAndPosition()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\Short.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
db.Read();
var indexedDb = new IndexedDatabase(db);
foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsets(6, 20, 2, 0, Enzyme.Trypsin))
{
var annotation = peptideAnnotationAndOffset.Annotation;
var offset = peptideAnnotationAndOffset.Offset;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}",
annotation,
offset,
db.GetProteinName(offset),
db.GetProteinLength(db.GetProteinName(offset)),
db.GetOneBasedPositionInProtein(offset)+1);
}
}
public void TestId()
{
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.icsfldecoy.fasta";
//const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\Decoy_SO4280.fasta";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\SO2312.fasta";
const string modFilePath = @"H:\Research\QCShew_TopDown\Production\Mods.txt";
const int numBits = 29; // max error: 4ppm
const int minCharge = 2;
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 ms2ScanNumArr = new[] {4130};
var ms2ScanNumArr = new[] { 5189 };
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;
productSpec.FilterNoise();
var deconvolutedPeaks = Deconvoluter.GetDeconvolutedPeaks(productSpec, 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:f4} 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}{1} proteins...", numProteins,
numProteins == 1 ? "st" : numProteins == 2 ? "nd" : numProteins == 3 ? "rd" : "th");
if (numProteins != 0)
{
sw.Stop();
Console.WriteLine("Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
sw.Reset();
sw.Start();
}
}
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 <= 0; numNTermCleavage++)
{
if (numNTermCleavage > 0) seqGraph.CleaveNTerm();
var allCompositions = seqGraph.GetAllFragmentNodeCompositions().ToArray();
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];
Console.WriteLine(suffixMass);
}
}
}
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
//var seqGraphPrefix = SequenceGraph.CreateGraph(aminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
// AminoAcid.ProteinCTerm);
//if (seqGraphPrefix == null) continue;
//{
// 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 ? "'" : "");
// }
// }
//}
}
Console.WriteLine("ScanNum\tBestProtein\tScore");
foreach (var ms2ScanNum in ms2ScanNumArr)
{
Console.WriteLine("{0}\t{1}\t{2}", ms2ScanNum, bestProtein[ms2ScanNum] ?? "", bestScore[ms2ScanNum]);
}
//sw.Stop();
//Console.WriteLine(@"Scoring: {0:f4} sec.", sw.Elapsed.TotalSeconds);
}
public void TestFeatureIdMatching()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string resultFilePath = @"H:\Research\QCShew_TopDown\Production\M1_V092\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var resultParser = new MsPathFinderParser(resultFilePath);
const double qValueThreshold = 0.01;
const double tolerancePpm = 13;
const string dataSet = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3";
var rawFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".raw");
if (!File.Exists(rawFileName))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFileName);
}
var run = PbfLcMsRun.GetLcMsRun(rawFileName);
var idList =
resultParser.GetIdList().TakeWhile(id => id.QValue <= qValueThreshold).OrderBy(id => id.Mass).ToList();
var idMassList = idList.Select(id => id.Mass).ToList();
var idFlag = new bool[idList.Count];
// Parse sequence tags
var tagFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".seqtag");
const int minTagLength = 6;
const int numProtMatches = 4;
// const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.icsfldecoy.fasta";
if (!File.Exists(tagFileName))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFileName);
}
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
var tagParser = new SequenceTagParser(tagFileName, minTagLength);
var featureFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".ms1ft");
var featureParser = new TsvFileParser(featureFileName);
var minScan = featureParser.GetData("MinScan").Select(s => Convert.ToInt32(s)).ToArray();
var maxScan = featureParser.GetData("MaxScan").Select(s => Convert.ToInt32(s)).ToArray();
var minCharge = featureParser.GetData("MinCharge").Select(s => Convert.ToInt32(s)).ToArray();
var maxCharge = featureParser.GetData("MaxCharge").Select(s => Convert.ToInt32(s)).ToArray();
var monoMass = featureParser.GetData("MonoMass").Select(Convert.ToDouble).ToArray();
var numFeaturesWithId = 0;
var numFeaturesWithMs2 = 0;
var numFeaturesWithTags = 0;
var numFeaturesWithMatchingTags = 0;
var numFeaturesWithTwoOrMoreMatchingTags = 0;
var numFeaturesWithNoIdAndMatchingTags = 0;
for (var i = 0; i < featureParser.NumData; i++)
{
var mass = monoMass[i];
// Find Id
var tolDa = new Tolerance(tolerancePpm).GetToleranceAsDa(mass, 1);
var minMass = mass - tolDa;
var maxMass = mass + tolDa;
var index = idMassList.BinarySearch(mass);
if (index < 0) index = ~index;
var matchedId = new List<MsPathFinderId>();
// go down
var curIndex = index - 1;
while (curIndex >= 0)
{
var curId = idList[curIndex];
if (curId.Mass < minMass) break;
if (curId.Scan > minScan[i] && curId.Scan < maxScan[i]
&& curId.Charge >= minCharge[i] && curId.Charge <= maxCharge[i])
{
matchedId.Add(curId);
idFlag[curIndex] = true;
}
--curIndex;
}
// go up
curIndex = index;
while (curIndex < idList.Count)
{
var curId = idList[curIndex];
if (curId.Mass > maxMass) break;
if (curId.Scan >= minScan[i] && curId.Scan <= maxScan[i]
&& curId.Charge >= minCharge[i] && curId.Charge <= maxCharge[i])
{
matchedId.Add(curId);
idFlag[curIndex] = true;
}
++curIndex;
}
var hasId = false;
if (matchedId.Any())
{
++numFeaturesWithId;
hasId = true;
}
// Find MS2 scans
// var numMs2Scans = 0;
var tags = new List<SequenceTag>();
var hasMs2 = false;
for (var scanNum = minScan[i]; scanNum <= maxScan[i]; scanNum++)
{
var isolationWindow = run.GetIsolationWindow(scanNum);
if (isolationWindow == null) continue;
var isolationWindowTargetMz = isolationWindow.IsolationWindowTargetMz;
var charge = (int)Math.Round(mass / isolationWindowTargetMz);
if (charge < minCharge[i] || charge > maxCharge[i]) continue;
var mz = Ion.GetIsotopeMz(mass, charge,
Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex);
if (isolationWindow.Contains(mz))
{
// ++numMs2Scans;
tags.AddRange(tagParser.GetSequenceTags(scanNum));
hasMs2 = true;
}
}
if (hasMs2) ++numFeaturesWithMs2;
if (tags.Any()) ++numFeaturesWithTags;
var protHist = new Dictionary<string, int>();
var hasMatchedTag = false;
foreach (var tag in tags)
{
var matchedProteins = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).Select(idx => fastaDb.GetProteinName(idx)).ToArray();
if (matchedProteins.Any())
{
hasMatchedTag = true;
foreach (var protein in matchedProteins)
{
int num;
if (protHist.TryGetValue(protein, out num)) protHist[protein] = num + 1;
else protHist[protein] = 1;
}
}
}
if (hasMatchedTag)
{
++numFeaturesWithMatchingTags;
if (!hasId) ++numFeaturesWithNoIdAndMatchingTags;
}
if (protHist.Any())
{
var maxOcc = protHist.Values.Max();
if (maxOcc >= numProtMatches) ++numFeaturesWithTwoOrMoreMatchingTags;
}
}
Console.WriteLine("NumFeatures: {0}", featureParser.NumData);
Console.WriteLine("NumId: {0}", idList.Count);
Console.WriteLine("NumFeaturesWithId: {0} ({1})", numFeaturesWithId, numFeaturesWithId / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithMs2: {0} ({1})", numFeaturesWithMs2, numFeaturesWithMs2 / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithTag: {0} ({1})", numFeaturesWithTags, numFeaturesWithTags / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithMatchedTag: {0} ({1})", numFeaturesWithMatchingTags, numFeaturesWithMatchingTags / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithMoreThanOneMatchedTag: {0} ({1})", numFeaturesWithTwoOrMoreMatchingTags, numFeaturesWithTwoOrMoreMatchingTags / (float)featureParser.NumData);
Console.WriteLine("NumFeaturesWithNoIdAndMatchedTag: {0} ({1})", numFeaturesWithNoIdAndMatchingTags, numFeaturesWithNoIdAndMatchingTags / (float)featureParser.NumData);
for (var i = 0; i < idFlag.Length; i++)
{
if (!idFlag[i])
{
Console.WriteLine(idList[i].Scan);
}
}
// Console.WriteLine(string.Join(",", filter.GetMatchingMs2ScanNums(8115.973001)));
//
// Console.WriteLine(featureFileName);
}
public void 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 TestTagMatchingSingleSpec()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataSet = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3";
const int scanNum = 4533;
// Parse sequence tags
var tagFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".seqtag");
const int minTagLength = 8;
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
if (!File.Exists(tagFileName))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFileName);
}
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
var tagParser = new SequenceTagParser(tagFileName, minTagLength);
var tags = tagParser.GetSequenceTags(scanNum);
foreach (var tag in tags)
{
var matchedProteins = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence)
.Select(index => fastaDb.GetProteinName(index)).ToArray();
if (matchedProteins.Any())
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}", tag.Sequence, tag.IsPrefix, tag.FlankingMass, string.Join("\t", matchedProteins));
}
}
}
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 CreateTargetList()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string databaseFilePath = @"D:\Research\Data\IPRG2014\database\SpikedInPeptides.fasta";
if (!File.Exists(databaseFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, databaseFilePath);
}
var database = new FastaDatabase(databaseFilePath);
database.Read();
var indexedDatabase = new IndexedDatabase(database);
var numTargets = 0;
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
Console.WriteLine("Peptide\tFormula\tProtein");
foreach (var annotationAndOffset in indexedDatabase.AnnotationsAndOffsets(6, 30, 1, 1, Enzyme.Trypsin))
{
var annotation = annotationAndOffset.Annotation;
var peptide = annotation.Substring(2, annotation.Length - 4);
var offset = annotationAndOffset.Offset;
Console.WriteLine("{0}\t{1}\t{2}", peptide, (aaSet.GetComposition(peptide) + Composition.H2O).ToPlainString(), database.GetProteinName(offset));
numTargets++;
}
Console.WriteLine("NumTargets: {0}", numTargets);
}
