private void btnLoad_Click(object sender, EventArgs e)
{
if (rawFile.Exists)
{
if (reader != null)
{
reader.Close();
}
reader = RawFileFactory.GetRawFileReader(rawFile.FullName);
lastScan = reader.GetLastSpectrumNumber();
}
if (ms3MatchedFile.Exists)
{
items = (from line in File.ReadAllLines(ms3MatchedFile.FullName).Skip(1)
let parts = line.Split('\t')
let pm = int.Parse(parts[6])
where pm > 0
select new MS3MatchItem()
{
Category = parts[0],
Sequence1 = parts[1],
Scan1 = int.Parse(parts[2]),
Sequence2 = parts[3],
Scan2 = int.Parse(parts[4]),
MinMz = parts[5].StringAfter(">=").Trim(),
PrecursorMatched = pm,
MS3Matched = int.Parse(parts[7])
}).ToList();
gvPeptides.DataSource = items;
}
}
public FileData3 ReadFromFile(string fileName)
{
FileData3 result = new FileData3();
result.FileName = new FileInfo(fileName).Name;
rawFile.Open(fileName);
try
{
for (int scan = rawFile.GetFirstSpectrumNumber(); scan <= rawFile.GetLastSpectrumNumber(); scan++)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan, minPeakMz - 1, maxPeakMz + 1);
result.AddPeaks(minPeakMz, maxPeakMz, scan, pkl);
}
}
finally
{
rawFile.Close();
}
return(result);
}
private void btnLoad_Click(object sender, EventArgs e)
{
if (rawFile.Exists)
{
if (reader != null)
{
reader.Close();
}
reader = RawFileFactory.GetRawFileReader(rawFile.FullName);
lastScan = reader.GetLastSpectrumNumber();
}
if (ms3xcorrFile.Exists)
{
items = (from line in File.ReadAllLines(ms3xcorrFile.FullName).Skip(1)
let parts = line.Split('\t')
select new MS3XcorrItem()
{
Category = parts[0],
Sequence1 = parts[1],
MS2Scan1 = int.Parse(parts[2]),
MS2Precursor1 = double.Parse(parts[3]),
MS3Scan1 = int.Parse(parts[4]),
MS3Precursor1 = double.Parse(parts[5]),
Sequence2 = parts[6],
MS2Scan2 = int.Parse(parts[7]),
MS2Precursor2 = double.Parse(parts[8]),
MS3Scan2 = int.Parse(parts[9]),
MS3Precursor2 = double.Parse(parts[10]),
Xcorr = double.Parse(parts[11])
}).ToList();
items.RemoveAll(m => m.MS3Precursor1 < 250);
items = items.OrderBy(m => m.Category).ThenBy(m => m.Sequence1).ThenBy(m => m.MS3Precursor1).ToList();
gvPeptides.DataSource = items;
}
}
public override IEnumerable <string> Process(string fileName)
{
string resultFile = new FileInfo(targetDir + "\\" + FileUtils.ChangeExtension(new FileInfo(fileName).Name, ".txt")).FullName;
reader.Open(fileName);
try
{
using (StreamWriter sw = new StreamWriter(resultFile))
{
sw.NewLine = "\n";
sw.WriteLine();
sw.WriteLine("FUNCTION 1");
int firstScan = reader.GetFirstSpectrumNumber();
int lastScan = reader.GetLastSpectrumNumber();
for (int i = firstScan; i <= lastScan; i++)
{
var pkl = reader.GetPeakList(i);
sw.WriteLine("");
sw.WriteLine("Scan\t\t{0}", i);
sw.WriteLine("Retention Time\t{0:0.000}", reader.ScanToRetentionTime(i));
sw.WriteLine("");
foreach (var peak in pkl)
{
sw.WriteLine("{0:0.0000}\t{1:0}", peak.Mz, peak.Intensity);
}
}
}
}
finally
{
reader.Close();
}
return(new string[] { resultFile });
}
private List <SrmScan> GetMRMScans(string directory)
{
var fileName = GetPeakFileName(directory);
if (File.Exists(fileName))
{
SetProgressMessage("Reading scan from " + fileName + " ...");
return(new SrmScanFileFormat().ReadFromFile(fileName));
}
else
{
List <PeakList <Peak> > pkls = new List <PeakList <Peak> >();
SetProgressMessage("Reading scan from " + directory + " ...");
IRawFile reader = RawFileFactory.GetRawFileReader(directory);
try
{
var firstCount = reader.GetFirstSpectrumNumber();
var lastCount = reader.GetLastSpectrumNumber();
Progress.SetRange(firstCount, lastCount);
Progress.SetPosition(firstCount);
for (int i = firstCount; i <= lastCount; i++)
{
if (reader.GetMsLevel(i) != 2)
{
continue;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.Increment(1);
var pkl = reader.GetPeakList(i);
var precursor = reader.GetPrecursorPeak(i);
if (precursor != null)
{
pkl.PrecursorMZ = precursor.Mz;
pkl.PrecursorCharge = precursor.Charge;
}
pkl.ScanTimes.Add(new ScanTime(i, reader.ScanToRetentionTime(i)));
pkls.Add(pkl);
}
List <SrmScan> result = new List <SrmScan>();
pkls.ForEach(m => m.ForEach(n => result.Add(new SrmScan(m.PrecursorMZ, n.Mz, m.ScanTimes[0].RetentionTime, n.Intensity, true))));
new SrmScanFileFormat().WriteToFile(fileName, result);
SetProgressMessage("finished.");
return(result);
}
finally
{
reader.Close();
}
}
}
public void Quantify(string rawFileName, List <IIdentifiedSpectrum> spectra, string detailDir)
{
if (!Directory.Exists(detailDir))
{
Directory.CreateDirectory(detailDir);
}
var experimental = RawFileFactory.GetExperimental(rawFileName);
Dictionary <string, DifferentRetentionTimeEnvelopes> spectrumKeyMap = new Dictionary <string, DifferentRetentionTimeEnvelopes>();
Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> > envelopeSpectrumGroup = new Dictionary <SilacEnvelopes, List <IIdentifiedSpectrum> >();
double precursorPPM = GetPrecursorPPM(spectra);
try
{
_rawReader.Open(rawFileName);
int firstScanNumber = _rawReader.GetFirstSpectrumNumber();
int lastScanNumber = _rawReader.GetLastSpectrumNumber();
Progress.SetRange(1, spectra.Count);
int pepCount = 0;
for (int s = 0; s < spectra.Count; s++)
{
Console.WriteLine(s);
IIdentifiedSpectrum spectrum = spectra[s];
SilacQuantificationSummaryItem.ClearAnnotation(spectrum);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
int startScan = spectrum.Query.FileScan.FirstScan;
if (startScan > lastScanNumber)
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "OUT_OF_RANGE";
continue;
}
Progress.SetPosition(pepCount++);
IIdentifiedPeptide sp = spectrum.Peptide;
string seq = GetMatchSequence(spectrum);
IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(seq, spectrum.TheoreticalMH, spectrum.Query.Charge);
SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo);
//如果轻重离子理论质荷比一样，忽略
if (!sci.IsSilacData())
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "NOT_SILAC";
continue;
}
//如果轻重离子理论质荷比与观测值不一致，忽略
if (!sci.IsMzEquals(spectrum.ObservedMz, MAX_DELTA_MZ))
{
ValidateModifications(seq);
spectrum.GetOrCreateQuantificationItem().RatioStr = "WRONG_IDENTIFICATION";
continue;
}
//如果没有找到相应的FullScan，忽略
int identifiedFullScan = _rawReader.FindPreviousFullScan(startScan, firstScanNumber);
if (-1 == identifiedFullScan)
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE";
continue;
}
DifferentRetentionTimeEnvelopes pkls = FindEnvelopes(spectrumKeyMap, spectrum, sci);
SilacEnvelopes envelope = pkls.FindSilacEnvelope(identifiedFullScan);
//如果该scan被包含在已经被定量的结果中，忽略
if (envelope != null)
{
envelope.SetScanIdentified(identifiedFullScan, spectrum.IsExtendedIdentification());
envelopeSpectrumGroup[envelope].Add(spectrum);
continue;
}
//从原始文件中找出该spectrum的定量信息
int maxIndex = Math.Min(option.ProfileLength - 1, pkls.LightProfile.FindMaxIndex());
double mzTolerance = PrecursorUtils.ppm2mz(sci.Light.Mz, option.PPMTolerance);
//如果FullScan没有相应的离子，忽略。（鉴定错误或者扩展定量时候，会出现找不到pair的现象）
SilacPeakListPair splp = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, identifiedFullScan);
if (null == splp)
{
spectrum.GetOrCreateQuantificationItem().RatioStr = "NO_PROFILE";
continue;
}
splp.IsIdentified = true;
splp.IsExtendedIdentification = spectrum.IsExtendedIdentification();
SilacEnvelopes envelopes = new SilacEnvelopes();
envelopes.Add(splp);
//向前查找定量信息
int fullScan = identifiedFullScan;
int scanNumber = 0;
while ((fullScan = _rawReader.FindPreviousFullScan(fullScan - 1, firstScanNumber)) != -1)
{
if (_rawReader.IsBadDataScan(fullScan))
{
continue;
}
scanNumber++;
var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber);
if (null == item)
{
break;
}
envelopes.Add(item);
}
envelopes.Reverse();
//向后查找定量信息
fullScan = identifiedFullScan;
scanNumber = 0;
while ((fullScan = _rawReader.FindNextFullScan(fullScan + 1, lastScanNumber)) != -1)
{
if (_rawReader.IsBadDataScan(fullScan))
{
continue;
}
scanNumber++;
var item = GetLightHeavyPeakList(_rawReader, sci, maxIndex, mzTolerance, fullScan, scanNumber <= MinScanNumber);
if (null == item)
{
break;
}
envelopes.Add(item);
}
//对每个scan计算轻重的离子丰度
envelopes.ForEach(m => m.CalculateIntensity(pkls.LightProfile, pkls.HeavyProfile));
pkls.Add(envelopes);
envelopeSpectrumGroup.Add(envelopes, new List <IIdentifiedSpectrum>());
envelopeSpectrumGroup[envelopes].Add(spectrum);
}
}
finally
{
_rawReader.Close();
}
foreach (string key in spectrumKeyMap.Keys)
{
DifferentRetentionTimeEnvelopes pkls = spectrumKeyMap[key];
foreach (SilacEnvelopes envelopes in pkls)
{
if (0 == envelopes.Count)
{
continue;
}
List <IIdentifiedSpectrum> mps = envelopeSpectrumGroup[envelopes];
double mzTolerance = PrecursorUtils.ppm2mz(mps[0].Query.ObservedMz, option.PPMTolerance);
string scanStr = GetScanRange(envelopes);
string resultFilename = detailDir + "\\" + mps[0].Query.FileScan.Experimental + "." + PeptideUtils.GetPureSequence(mps[0].Sequence) + "." + mps[0].Query.Charge + scanStr + ".silac";
IPeptideInfo peptideInfo = new IdentifiedPeptideInfo(mps[0].GetMatchSequence(), mps[0].TheoreticalMH, mps[0].Query.Charge);
SilacCompoundInfo sci = GetSilacCompoundInfo(peptideInfo);
SilacQuantificationSummaryItem item = new SilacQuantificationSummaryItem(sci.Light.IsSample);
item.RawFilename = rawFileName;
item.SoftwareVersion = this.SoftwareVersion;
item.PeptideSequence = mps[0].Sequence;
item.Charge = mps[0].Charge;
item.LightAtomComposition = sci.Light.Composition.ToString();
item.HeavyAtomComposition = sci.Heavy.Composition.ToString();
item.LightProfile = pkls.LightProfile;
item.HeavyProfile = pkls.HeavyProfile;
item.ObservedEnvelopes = envelopes;
item.ValidateScans(sci, precursorPPM);
item.Smoothing();
item.CalculateRatio();
new SilacQuantificationSummaryItemXmlFormat().WriteToFile(resultFilename, item);
int maxScoreItemIndex = FindMaxScoreItemIndex(mps);
for (int i = 0; i < mps.Count; i++)
{
if (maxScoreItemIndex == i)
{
item.AssignToAnnotation(mps[i], resultFilename);
}
else
{
item.AssignDuplicationToAnnotation(mps[i], resultFilename);
}
}
}
}
foreach (IIdentifiedSpectrum mph in spectra)
{
mph.InitializeRatioEnabled();
}
}
public override IEnumerable <string> Process(string targetDir)
{
foreach (var raw in rawFiles)
{
List <SimplePeakChro> waitingPeaks = new List <SimplePeakChro>();
foreach (var peak in targetPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
else
{
var p = new SimplePeakChroXmlFormat().ReadFromFile(file);
peak.MaxRetentionTime = p.MaxRetentionTime;
peak.Peaks = p.Peaks;
}
}
if (waitingPeaks.Count == 0)
{
continue;
}
rawReader.Open(raw);
try
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
var lastRt = rawReader.ScanToRetentionTime(lastScan);
waitingPeaks.ForEach(m =>
{
m.Peaks.Clear();
m.MaxRetentionTime = lastRt;
});
Progress.SetMessage("Processing chromotograph extracting...");
Progress.SetRange(firstScan, lastScan);
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (rawReader.GetMsLevel(scan) != 1)
{
continue;
}
Progress.SetPosition(scan);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawReader.GetPeakList(scan);
double rt = rawReader.ScanToRetentionTime(scan);
foreach (var peak in waitingPeaks)
{
var env = pkl.FindPeak(peak.Mz, peak.MzTolerance);
Peak findPeak = new Peak(peak.Mz, 0.0, 0);
if (env.Count > 0)
{
if (env.Count == 1)
{
findPeak = env[0];
}
else
{
var charge = env.FindCharge(peak.Charge);
if (charge.Count > 0)
{
if (charge.Count == 1)
{
findPeak = charge[0];
}
else
{
findPeak = charge.FindMaxIntensityPeak();
}
}
else
{
findPeak = env.FindMaxIntensityPeak();
}
}
}
peak.Peaks.Add(new ScanPeak()
{
Mz = findPeak.Mz,
Intensity = findPeak.Intensity,
Scan = scan,
RetentionTime = rt,
Charge = findPeak.Charge,
PPMDistance = PrecursorUtils.mz2ppm(peak.Mz, findPeak.Mz - peak.Mz)
});
}
}
waitingPeaks.ForEach(m => m.TrimPeaks(minRetentionTime));
}
finally
{
rawReader.Close();
}
Progress.SetMessage("Saving ... ");
foreach (var peak in waitingPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
new SimplePeakChroXmlFormat().WriteToFile(file, peak);
}
Progress.SetMessage("Finished.");
Progress.End();
}
return(new string[] { targetDir });
}
public override IEnumerable <string> Process(string rawFilename)
{
string ms1Filename = GetResultFilename(rawFilename);
string ms1IndexFilename = ms1Filename + ".index";
rawFile.Open(rawFilename);
try
{
int firstScan = rawFile.GetFirstSpectrumNumber();
int lastScan = rawFile.GetLastSpectrumNumber();
int firstFullScan = 0;
for (firstFullScan = firstScan; firstFullScan < lastScan; firstFullScan++)
{
if (rawFile.GetMsLevel(firstFullScan) == 1)
{
break;
}
}
if (firstFullScan >= lastScan)
{
return(new List <string>());
}
Progress.SetRange(firstScan, lastScan);
using (var sw = new StreamWriter(ms1Filename))
{
//write header
sw.Write("H\tCreationDate\t{0:m/dd/yyyy HH:mm:ss}\n", DateTime.Now);
sw.Write("H\tExtractor\t{0}\n", GetProgramName());
sw.Write("H\tExtractorVersion\t{0}\n", GetProgramVersion());
sw.Write("H\tComments\t{0} written by Quanhu Sheng, 2008-2009\n", GetProgramName());
sw.Write("H\tExtractorOptions\tMS1\n");
sw.Write("H\tAcquisitionMethod\tData-Dependent\n");
sw.Write("H\tDataType\tCentriod\n");
sw.Write("H\tScanType\tMS1\n");
sw.Write("H\tFirstScan\t{0}\n", firstScan);
sw.Write("H\tLastScan\t{0}\n", lastScan);
using (var swIndex = new StreamWriter(ms1IndexFilename))
{
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetPosition(scan);
if (rawFile.GetMsLevel(scan) == 1)
{
sw.Flush();
swIndex.Write("{0}\t{1}\n", scan, sw.BaseStream.Position);
sw.Write("S\t{0}\t{0}\n", scan);
sw.Write("I\tRetTime\t{0:0.####}\n", rawFile.ScanToRetentionTime(scan));
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
foreach (Peak p in pkl)
{
sw.Write("{0:0.0000} {1:0.0} {2}\n", p.Mz, p.Intensity, p.Charge);
}
}
}
}
}
}
finally
{
rawFile.Close();
}
Progress.End();
return(new[] { ms1Filename });
}
public void CloseFile()
{
reader.Close();
}
public override IEnumerable <string> Process(string targetDir)
{
foreach (var raw in rawFiles)
{
List <RetentionTimePeak> waitingPeaks = new List <RetentionTimePeak>();
foreach (var peak in targetPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
}
if (waitingPeaks.Count == 0)
{
continue;
}
rawReader.Open(raw);
try
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
waitingPeaks.ForEach(m => m.Chromotographs.Clear());
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (rawReader.GetMsLevel(scan) != 1)
{
continue;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawReader.GetPeakList(scan);
double rt = rawReader.ScanToRetentionTime(scan);
var st = new ScanTime(scan, rt);
foreach (var peak in waitingPeaks)
{
var env = pkl.FindEnvelopeDirectly(peak.PeakEnvelope, peak.MzTolerance, () => new Peak());
env.ScanTimes.Add(st);
peak.Chromotographs.Add(env);
}
}
waitingPeaks.ForEach(m => m.TrimPeaks());
}
finally
{
rawReader.Close();
}
foreach (var peak in waitingPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
new RetentionTimePeakXmlFormat().WriteToFile(file, peak);
}
}
return(new string[] { targetDir });
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.InitGraphPane(this.title, "m/z", "Intensity", true, 0.0);
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
panel.InitGraphPane(this.title + ", Scan=" + envelope.Scan.ToString(), "m/z", "Intensity", true, 0.0);
double minMz = envelope[0].Mz - 1.0;
double maxMz = envelope[envelope.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var ppl = new PointPairList();
envelope.ForEach(p => { if (p.Intensity > 0)
{
ppl.Add(p.Mz, p.Intensity);
}
});
panel.AddIndividualLine("Isotopic Envelope", ppl, Color.Red);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
var halfMax = (from env in envelope
select env.Intensity).Max() / 2;
ppl.Clear();
envelope.ForEach(p => { if (p.Intensity == 0)
{
ppl.Add(p.Mz, halfMax);
}
});
panel.AddIndividualLine("", ppl, defaultColor: Color.Red, dStyle: DashStyle.Dash);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Close();
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
panel.AddIndividualLine("PeakList From RawFile", pplRaw, Color.Blue);
panel.AddTextDown(pplRaw, 5, (m => m.X.ToString("0.0000")));
/*
* foreach (var p in ppl)
* {
* if (p.Y == 0)
* {
* double ppm = double.MaxValue;
* double ppmAbs = Math.Abs(ppm);
* foreach (var pp in pplRaw)
* {
* double ppmCur = PrecursorUtils.mz2ppm(pp.X, pp.X - p.X);
* double ppmCurAbs = Math.Abs(ppmCur);
* if (Math.Abs(ppmCur) < ppmAbs)
* {
* ppm = ppmCur;
* ppmAbs = ppmCurAbs;
* }
*
* if (pp.X > p.X)
* {
* break;
* }
* }
*
* p.Z = ppm;
* }
* }
*/
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
