public List<ProteinSpectrumMatch> LoadIdentificationResult(string path, ProteinSpectrumMatch.SearchTool tool = ProteinSpectrumMatch.SearchTool.Unknown, int maxPrsm = int.MaxValue)
{
List<ProteinSpectrumMatch> prsmList = null;
if (tool == ProteinSpectrumMatch.SearchTool.Unknown)
{
if (path.EndsWith("IcTda.tsv")) tool = ProteinSpectrumMatch.SearchTool.MsPathFinder;
else if (path.EndsWith("MSAlign_ResultTable.txt")) tool = ProteinSpectrumMatch.SearchTool.MsAlign;
else if (path.EndsWith("msgfdb_syn.txt")) tool = ProteinSpectrumMatch.SearchTool.MsGfPlus;
}
if (tool == ProteinSpectrumMatch.SearchTool.MsAlign)
prsmList = ReadMsAlignResult(path, maxPrsm);
else if (tool == ProteinSpectrumMatch.SearchTool.MsPathFinder)
prsmList = ReadMsPathFinderResult(path, maxPrsm);
else if (tool == ProteinSpectrumMatch.SearchTool.MsGfPlus)
prsmList = ReadMsGfPlusResult(path, maxPrsm);
return prsmList;
}
public List<ProteinSpectrumMatch> ReadMsAlignResult(string msAlignResultTablePath, int maxPrsm)
{
var parser = new TsvFileParser(msAlignResultTablePath);
var prsmList = new List<ProteinSpectrumMatch>();
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Peptide")[i];
var scanNum = int.Parse(parser.GetData("Scan(s)")[i]);
var mass = double.Parse(parser.GetData("Precursor_mass")[i]);
var protNameDesc = parser.GetData("Protein_name")[i];
var k = protNameDesc.IndexOf(' ');
var protName = (k < 0) ? protNameDesc : protNameDesc.Substring(0, k);
var protDesc = (k < 0) ? protNameDesc : protNameDesc.Substring(k+1);
var firstResId = int.Parse(parser.GetData("First_residue")[i]);
var lastResId = int.Parse(parser.GetData("Last_residue")[i]);
var score = double.Parse(parser.GetData("#matched_fragment_ions")[i]);
var sequenceText = parser.GetData("Peptide")[i];
var charge = int.Parse(parser.GetData("Charge")[i]);
var evalue = double.Parse(parser.GetData("E-value")[i]);
var fdr = Double.Parse(parser.GetData("FDR")[i]);
if (fdr > FdrCutoff) continue;
var prsm = new ProteinSpectrumMatch(sequence, scanNum, mass, charge, protName, protDesc, firstResId, lastResId, score, ProteinSpectrumMatch.SearchTool.MsAlign)
{
SequenceText = sequenceText,
SpectralEvalue = evalue,
};
prsmList.Add(prsm);
if (prsmList.Count >= maxPrsm) break;
}
return prsmList;
}
private List<ProteinSpectrumMatch> MergePrsm(List<ProteinSpectrumMatch> targetList)
{
//var sortedList = targetList.OrderBy(prsm => prsm.ScanNum).ToList();
//var minScan = sortedList.First().ScanNum;
var maxScan = targetList.Max(prsm => prsm.ScanNum);
var ret = new ProteinSpectrumMatch[maxScan + 1];
foreach (var prsm in targetList)
{
var scan = prsm.ScanNum;
if (ret[scan] == null)
{
ret[scan] = prsm;
}
else
{
if (prsm.SpectralEvalue < ret[scan].SpectralEvalue)
ret[scan] = prsm;
}
}
return ret.Where(prsm => prsm != null).ToList();
}
public List<ProteinSpectrumMatch> ReadMsGfPlusResult(string msgfResultPath, int maxPrsm)
{
var parser = new TsvFileParser(msgfResultPath);
var prsmList = new List<ProteinSpectrumMatch>();
var prevScanNum = -1;
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Peptide")[i];
var scanNum = int.Parse(parser.GetData("Scan")[i]);
if (prevScanNum == scanNum) continue;
prevScanNum = scanNum;
var mz = double.Parse(parser.GetData("PrecursorMZ")[i]);
var protName = parser.GetData("Protein")[i];
var protDesc = "";
var score = double.Parse(parser.GetData("MSGFScore")[i]);
var charge = int.Parse(parser.GetData("Charge")[i]);
var seq = Sequence.GetSequenceFromMsGfPlusPeptideStr(sequence);
var sequenceText = GetSequenceText(seq);
var mass = (mz - Constants.Proton)*charge;
var firstResId = 0;
var lastResId = 0;
var fdr = Double.Parse(parser.GetData("QValue")[i]);
if (fdr > FdrCutoff) continue;
var prsm = new ProteinSpectrumMatch(sequence, scanNum, mass, charge, protName, protDesc, firstResId, lastResId, score, ProteinSpectrumMatch.SearchTool.MsGfPlus)
{
SequenceText = sequenceText,
};
prsmList.Add(prsm);
if (prsmList.Count >= maxPrsm) break;
}
return prsmList;
}
public List<ProteinSpectrumMatch> ReadMsPathFinderResult(string msPathFinderResultPath, int maxPrsm, double minScore = 3, double maxScore = int.MaxValue)
{
var parser = new TsvFileParser(msPathFinderResultPath);
var prsmList = new List<ProteinSpectrumMatch>();
var scoreColumn = parser.GetData("#MatchedFragments") ?? parser.GetData("Score");
var qValColumn = parser.GetData("QValue");
var evalueColumn = parser.GetData("SpecEValue");
for (var i = 0; i < parser.NumData; i++)
{
var sequence = parser.GetData("Sequence")[i];
var scanNum = int.Parse(parser.GetData("Scan")[i]);
var mass = double.Parse(parser.GetData("Mass")[i]);
var protName = parser.GetData("ProteinName")[i];
var protDesc = parser.GetData("ProteinDesc")[i];
var charge = int.Parse(parser.GetData("Charge")[i]);
var firstResId = int.Parse(parser.GetData("Start")[i]);
var lastResId = int.Parse(parser.GetData("End")[i]);
var score = double.Parse(scoreColumn[i]);
var mod = parser.GetData("Modifications")[i];
var evalue = (evalueColumn != null) ? double.Parse(parser.GetData("SpecEValue")[i]) : 0;
var pre = parser.GetData("Pre")[i];
var post = parser.GetData("Post")[i];
var proteinLen = int.Parse(parser.GetData("ProteinLength")[i]);
if (score < minScore || score > maxScore) continue;
if (qValColumn != null)
{
var fdr = double.Parse(qValColumn[i]);
if (fdr > FdrCutoff) continue;
}
var sequenceText = GetSequenceText(sequence, mod);
var prsm = new ProteinSpectrumMatch(sequence, scanNum, mass, charge, protName, protDesc, firstResId, lastResId, score, ProteinSpectrumMatch.SearchTool.MsPathFinder)
{
SequenceText = sequenceText,
Modifications = mod,
Pre = pre,
Post = post,
ProteinLength = proteinLen,
SpectralEvalue = evalue,
};
prsmList.Add(prsm);
if (prsmList.Count >= maxPrsm) break;
}
return prsmList;
}
