public IList <SequenceTag> GetAllSequenceTagString(int ms2ScanNum)
{
IList <SequenceTag> tags;
lock (_ms2ScanToTagMap)
{
if (_ms2ScanToTagMap.TryGetValue(ms2ScanNum, out tags))
{
return(tags);
}
}
var spec = _run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
return(new List <SequenceTag>());
}
var tagFinder = new SequenceTagFinder(spec, _tolerance, _minTagLen, _maxTagLen, _aminoAcids);
tags = tagFinder.GetAllSequenceTagString();
lock (_ms2ScanToTagMap)
{
_ms2ScanToTagMap[ms2ScanNum] = tags;
}
return(tags);
}
public void Generate(int ms2ScanNum)
{
var spec = _run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null) return;
var tagFinder = new SequenceTagFinder(spec, _tolerance, _minTagLen, _maxTagLen, _aminoAcids);
var tags = tagFinder.GetAllSequenceTagString();
lock (_ms2ScanToTagMap)
{
_ms2ScanToTagMap[ms2ScanNum] = tags;
}
}
public void Generate(int ms2ScanNum)
{
var spec = _run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
return;
}
var tagFinder = new SequenceTagFinder(spec, _tolerance, _minTagLen, _maxTagLen, _aminoAcids);
var tags = tagFinder.GetAllSequenceTagString();
lock (_ms2ScanToTagMap)
{
_ms2ScanToTagMap[ms2ScanNum] = tags;
}
}
private List <SequenceTag> GetTags(List <ProductSpectrum> spectrums)
{
var tagDict = new Dictionary <string, SequenceTag>();
if (spectrums.Count == 0)
{
return(tagDict.Values.ToList());
}
foreach (var spect in spectrums)
{
var tagFinder = new SequenceTagFinder(spect, new Tolerance(10), 4);
var tags = tagFinder.GetAllSequenceTagString();
foreach (var t in tags)
{
if (tagDict.ContainsKey(t.Sequence))
{
continue;
}
tagDict.Add(t.Sequence, t);
}
}
return(tagDict.Values.ToList());
}
public IList<SequenceTag> GetAllSequenceTagString(int ms2ScanNum)
{
IList<SequenceTag> tags;
lock (_ms2ScanToTagMap)
{
if (_ms2ScanToTagMap.TryGetValue(ms2ScanNum, out tags))
{
return tags;
}
}
var spec = _run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null) return new List<SequenceTag>();
var tagFinder = new SequenceTagFinder(spec, _tolerance, _minTagLen, _maxTagLen, _aminoAcids);
tags = tagFinder.GetAllSequenceTagString();
lock (_ms2ScanToTagMap)
{
_ms2ScanToTagMap[ms2ScanNum] = tags;
}
return tags;
}
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);
}
}
}
private List<SequenceTag> GetTags(List<ProductSpectrum> spectrums)
{
var tagDict = new Dictionary<string,SequenceTag>();
if (spectrums.Count == 0) return tagDict.Values.ToList();
foreach (var spect in spectrums)
{
var tagFinder = new SequenceTagFinder(spect, new Tolerance(10), 4);
var tags = tagFinder.GetAllSequenceTagString();
foreach (var t in tags)
{
if (tagDict.ContainsKey(t.Sequence)) continue;
tagDict.Add(t.Sequence,t);
}
}
return tagDict.Values.ToList();
}
public void TestSequenceTag()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//const string TestRawFile = @"D:\\Vlad_TopDown\\raw\\yufeng_column_test2.raw";
//const string TestResultFile = @"D:\\Vlad_TopDown\\results\\yufeng_column_test2_IcTda.tsv";
const string TestRawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string TestResultFile = @"D:\MassSpecFiles\training\IdResult\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
//const string TestRawFile = @"D:\MassSpecFiles\Lewy\Lewy_intact_01.raw";
//const string TestResultFile = @"D:\MassSpecFiles\Lewy\Lewy_intact_01_IcTda.tsv";
if (!File.Exists(TestRawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFile);
}
if (!File.Exists(TestResultFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestResultFile);
}
// Configure amino acid set
var aminoAcidList = new List<AminoAcid>();
foreach (var aa in AminoAcid.StandardAminoAcidArr)
{
aminoAcidList.Add(aa);
aminoAcidList.Add(new ModifiedAminoAcid(aa, Modification.Acetylation));
aminoAcidList.Add(new ModifiedAminoAcid(aa, Modification.Oxidation));
}
//const int MaxTags = 100000;
var tsvParser = new TsvFileParser(TestResultFile);
var headerList = tsvParser.GetHeaders();
var tsvData = tsvParser.GetAllData();
var ms2ScanNumbers = tsvData["Scan"];
var run = PbfLcMsRun.GetLcMsRun(TestRawFile);
var nSpec = 0;
var nHitSpec = 0;
for (var i = 0; i < ms2ScanNumbers.Count; i++)
//foreach(var scanNum in targetScans)
{
var scanNum = Int32.Parse(ms2ScanNumbers[i]);
//if (scanNum != 4672) continue;
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
int tsvIndex = ms2ScanNumbers.FindIndex(x => Int32.Parse(x) == scanNum);
var qValue = double.Parse(tsvData["QValue"].ElementAt(tsvIndex));
if (qValue > 0.01) break;
var seqStr = tsvData["Sequence"].ElementAt(tsvIndex).Trim();
var modStr = tsvData["Modifications"].ElementAt(tsvIndex).Trim();
var tolerance = new Tolerance(5);
var tagFinder = new SequenceTagFinder(spectrum, tolerance, 5, 8, aminoAcidList.ToArray());
var nTags = 0;
var nHit = 0;
var seqOjb = Sequence.CreateSequence(seqStr, modStr, new AminoAcidSet());
var compWithoutH2O = seqOjb.Composition - Composition.H2O;
//Console.WriteLine(compWithoutH2O.Mass);
foreach (var seqTagStr in tagFinder.GetAllSequenceTagString())
{
if (seqStr.Contains(seqTagStr.Sequence)) //|| seqStr.Contains(Reverse(tagStr)))
{
//var idx = seqStr.IndexOf(seqTagStr.Sequence);
//seqStr.Substring(0, idx)
/*var comp2 = seqOjb.GetComposition(0, idx);
Console.Write(comp2.Mass);
Console.Write("\t");
Console.Write(seqTagStr.FlankingMass);
Console.Write("\t");
Console.Write(seqTagStr.Sequence);
Console.Write("\t");
Console.Write(seqTagStr.IsPrefix);
Console.WriteLine("");
*/
if (seqStr.Contains(seqTagStr.Sequence)) nHit++;
}
nTags++;
}
nSpec++;
if (nHit > 0) nHitSpec++;
Console.WriteLine(@"[{0}]seqLen = {1}: {2}/{3}", scanNum, seqStr.Length, nHit, nTags);
}
//var existingTags = tagFinder.ExtractExistingSequneceTags(sequence);
Console.Write("{0}/{1}", nHitSpec, nSpec);
}
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 TestSequenceTag()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
//const string TestRawFile = @"D:\\Vlad_TopDown\\raw\\yufeng_column_test2.raw";
//const string TestResultFile = @"D:\\Vlad_TopDown\\results\\yufeng_column_test2_IcTda.tsv";
const string TestRawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
const string TestResultFile = @"D:\MassSpecFiles\training\IdResult\QC_Shew_Intact_26Sep14_Bane_C2Column3_IcTda.tsv";
//const string TestRawFile = @"D:\MassSpecFiles\Lewy\Lewy_intact_01.raw";
//const string TestResultFile = @"D:\MassSpecFiles\Lewy\Lewy_intact_01_IcTda.tsv";
if (!File.Exists(TestRawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFile);
}
if (!File.Exists(TestResultFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestResultFile);
}
// Configure amino acid set
var aminoAcidList = new List <AminoAcid>();
foreach (var aa in AminoAcid.StandardAminoAcidArr)
{
aminoAcidList.Add(aa);
aminoAcidList.Add(new ModifiedAminoAcid(aa, Modification.Acetylation));
aminoAcidList.Add(new ModifiedAminoAcid(aa, Modification.Oxidation));
}
//const int MaxTags = 100000;
var tsvParser = new TsvFileParser(TestResultFile);
var headerList = tsvParser.GetHeaders();
var tsvData = tsvParser.GetAllData();
var ms2ScanNumbers = tsvData["Scan"];
var run = PbfLcMsRun.GetLcMsRun(TestRawFile);
var nSpec = 0;
var nHitSpec = 0;
for (var i = 0; i < ms2ScanNumbers.Count; i++)
//foreach(var scanNum in targetScans)
{
var scanNum = Int32.Parse(ms2ScanNumbers[i]);
//if (scanNum != 4672) continue;
var spectrum = run.GetSpectrum(scanNum) as ProductSpectrum;
int tsvIndex = ms2ScanNumbers.FindIndex(x => Int32.Parse(x) == scanNum);
var qValue = double.Parse(tsvData["QValue"].ElementAt(tsvIndex));
if (qValue > 0.01)
{
break;
}
var seqStr = tsvData["Sequence"].ElementAt(tsvIndex).Trim();
var modStr = tsvData["Modifications"].ElementAt(tsvIndex).Trim();
var tolerance = new Tolerance(5);
var tagFinder = new SequenceTagFinder(spectrum, tolerance, 5, 8, aminoAcidList.ToArray());
var nTags = 0;
var nHit = 0;
var seqOjb = Sequence.CreateSequence(seqStr, modStr, new AminoAcidSet());
var compWithoutH2O = seqOjb.Composition - Composition.H2O;
//Console.WriteLine(compWithoutH2O.Mass);
foreach (var seqTagStr in tagFinder.GetAllSequenceTagString())
{
if (seqStr.Contains(seqTagStr.Sequence)) //|| seqStr.Contains(Reverse(tagStr)))
{
//var idx = seqStr.IndexOf(seqTagStr.Sequence);
//seqStr.Substring(0, idx)
/*var comp2 = seqOjb.GetComposition(0, idx);
*
* Console.Write(comp2.Mass);
* Console.Write("\t");
*
* Console.Write(seqTagStr.FlankingMass);
* Console.Write("\t");
* Console.Write(seqTagStr.Sequence);
* Console.Write("\t");
* Console.Write(seqTagStr.IsPrefix);
* Console.WriteLine("");
*/
if (seqStr.Contains(seqTagStr.Sequence))
{
nHit++;
}
}
nTags++;
}
nSpec++;
if (nHit > 0)
{
nHitSpec++;
}
Console.WriteLine(@"[{0}]seqLen = {1}: {2}/{3}", scanNum, seqStr.Length, nHit, nTags);
}
//var existingTags = tagFinder.ExtractExistingSequneceTags(sequence);
Console.Write("{0}/{1}", nHitSpec, nSpec);
}
