//public void ExportCompoundModeHtml(string targetDir)
//{
// if (pairedResults == null)
// {
// return;
// }
// btnCompoundMode.PerformClick();
// var oldViewDecoy = ViewDecoy;
// ViewDecoy = true;
// try
// {
// var mainFile = new FileInfo(targetDir + "\\compound.html").FullName;
// var imageDir = FileUtils.ChangeExtension(mainFile, ".images");
// try
// {
// var imageDirName = new DirectoryInfo(imageDir).Name;
// if (!Directory.Exists(imageDir))
// {
// Directory.CreateDirectory(imageDir);
// }
// using (StreamWriter sw = new StreamWriter(mainFile))
// {
// sw.WriteLine("<html>");
// sw.WriteLine("<head>");
// sw.WriteLine("<title>Compound Quantification Result</title>");
// sw.WriteLine("</head>");
// sw.WriteLine("<body>");
// Predicate<CompoundItem> accept = m => m.IsDecoy && m.Enabled;
// var validDecoy = GetCompoundCount(visibleCompounds, accept);
// if (validDecoy > 0)
// {
// sw.WriteLine("{0} valid decoy entries (blue highlighted)<br>", validDecoy);
// OutputCompound(sw, visibleCompounds, accept, imageDir, imageDirName, Color.Blue);
// }
// GC.Collect();
// GC.WaitForFullGCComplete();
// accept = pep => !pep.IsDecoy && !pep.Enabled;
// var invalidTarget = GetCount(pr, accept);
// if (invalidTarget > 0)
// {
// sw.WriteLine("{0} invalid target entries (red highlighted)<br>", invalidTarget);
// Output(sw, pr, accept, imageDir, imageDirName, Color.Red);
// }
// GC.Collect();
// GC.WaitForFullGCComplete();
// accept = pep => !pep.IsDecoy && pep.Enabled;
// var validTarget = GetCount(pr, accept);
// if (validTarget > 0)
// {
// sw.WriteLine("{0} valid target entries<br>", validTarget);
// Output(sw, pr, accept, imageDir, imageDirName, Color.Black);
// }
// GC.Collect();
// GC.WaitForFullGCComplete();
// sw.WriteLine("</body>");
// sw.WriteLine("</html>");
// }
// }
// catch (Exception ex)
// {
// Console.WriteLine(ex.StackTrace);
// MessageBox.Show(this, MyConvert.Format("Error when saving {0} : {1}", mainFile, ex.Message), "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
// return;
// }
// }
// finally
// {
// ViewDecoy = oldViewDecoy;
// }
// MessageBox.Show(this, "Srm result html format saved.", "Info", MessageBoxButtons.OK, MessageBoxIcon.Information);
//}
//private void OutputCompound(StreamWriter sw, List<CompoundItem> list, Predicate<CompoundItem> accept, string imageDir, string imageDirName, Color color)
//{
// CurrencyManager cm = (CurrencyManager)this.BindingContext[visibleCompounds];
// var valid = new HashSet<CompoundItem>(from p in list
// where accept(p)
// select p);
// for (int index = 0; index < visibleCompounds.Count; index++)
// {
// var comp = visibleCompounds[index];
// if (valid.Contains(comp))
// {
// cm.Position = index;
// //gvCompounds.Refresh();
// //gvCompounds_SelectionChanged(null, null);
// //gvProductPair.Refresh();
// //gvProductPair_SelectionChanged(null, null);
// //MessageBox.Show(comp.ObjectName + " " + comp.PrecursurFormula);
// WritePeptide(sw, pep, color);
// WriteImage(imageDir, imageDirName, sw, pep);
// }
// }
//}
//private int GetCompoundCount(List<CompoundItem> list, Predicate<CompoundItem> accept)
//{
// return list.Count(m => accept(m));
//}
private void Output(StreamWriter sw, SrmPairedResult node, Predicate <SrmPairedPeptideItem> accept, string imageDir, string imageDirName, Color color)
{
CurrencyManager cm = (CurrencyManager)this.BindingContext[visibleCompounds];
var valid = new HashSet <SrmPairedPeptideItem>(from p in node
where accept(p)
select p);
for (int index = 0; index < visibleCompounds.Count; index++)
{
var comp = visibleCompounds[index];
var pep = comp.GetPeptideItem(node.PureFileName);
if (valid.Contains(pep))
{
cm.Position = index;
//gvCompounds.Refresh();
//gvCompounds_SelectionChanged(null, null);
//gvProductPair.Refresh();
//gvProductPair_SelectionChanged(null, null);
//MessageBox.Show(comp.ObjectName + " " + comp.PrecursurFormula);
WritePeptide(sw, pep, color);
WriteImage(imageDir, imageDirName, sw, pep);
}
}
}
public SrmFileItem(SrmPairedResult result, SrmPairedPeptideItem peptide, SrmPairedProductIon production)
{
this.PairedResult = result;
this.PairedPeptide = peptide;
this.PairedProductIon = production;
_precursorMz = new Pair <double, double>(peptide.LightPrecursorMZ, peptide.HeavyPrecursorMZ);
_productIonMz = new Pair <double, double>(production.LightProductIon, production.HeavyProductIon);
}
public static SrmPairedResult ToPairedResult(this List <SrmTransition> transList)
{
SrmPairedResult result = new SrmPairedResult();
//所有母离子有相同名称、相同质荷比认为是来自相同precursor，合并为一个peptide。
var pepgroup = transList.GroupBy(m => m.PrecursorFormula + MyConvert.Format("{0:0.0000}", m.PrecursorMZ));
var peptides = new List <SrmPeptideItem>();
foreach (var g in pepgroup)
{
var pep = new SrmPeptideItem();
pep.PrecursorMZ = g.First().PrecursorMZ;
pep.ProductIons = new List <SrmTransition>(g);
peptides.Add(pep);
}
//具有相同母离子名称和电荷的transition认为是轻重标。
var lhgroup = peptides.GroupBy(m => m.ProductIons[0].PrecursorFormula + "_" + m.ProductIons[0].PrecursorCharge.ToString()).ToList();
// var lhgroup = peptides.GroupBy(m => m.ProductIons[0].PrecursorFormula + "_" + m.ProductIons[0].PrecursorCharge.ToString()).ToList();
foreach (var g in lhgroup)
{
if (g.Count() > 2)
{
throw new Exception(string.Format("There are {0} transition with same precursor formula and precursor charge: {1}, {2}", g.Count(), g.First().ProductIons[0].PrecursorFormula, g.First().ProductIons[0].PrecursorCharge));
}
else if (g.Count() > 1)
{
var items = g.ToList();
items.Sort((m1, m2) => m1.PrecursorMZ.CompareTo(m2.PrecursorMZ));
SrmPairedPeptideItem light = new SrmPairedPeptideItem(items[0]);
SrmPairedPeptideItem heavy = new SrmPairedPeptideItem(items[1]);
if (!string.IsNullOrEmpty(light.ProductIonPairs[0].Light.Ion))
{
light.SetHeavyPeptideItemByIon(heavy);
}
else
{
light.SetHeavyPeptideItem(heavy);
}
result.Add(light);
}
else
{
SrmPairedPeptideItem light = new SrmPairedPeptideItem(g.First());
result.Add(light);
}
}
return(result);
}
protected override void DoRealGo()
{
mrmFileName = GetOriginFile();
btnGo.Enabled = false;
try
{
lblProgress.Text = "Reading MRM Scans ...";
mrmPairs = new SrmPairedResultXmlFormat().ReadFromFile(mrmFileName);
lblProgress.Text = "Finished.";
DisplayMRMTree();
}
finally
{
btnGo.Enabled = true;
}
}
public override IEnumerable <string> Process(string optionFile)
{
var targetDirectory = Path.GetDirectoryName(optionFile);
options = new SrmOptions();
options.FromXml(XElement.Load(optionFile));
var keys = options.RawFiles.Keys.ToList();
foreach (var key in keys)
{
if (string.IsNullOrEmpty(options.RawFiles[key]))
{
this.options.RawFiles[key] = key;
}
}
List <string> result = new List <string>();
bool ignoreWarning = false;
Dictionary <string, List <string> > map = GetGroupMap();
int totalCount = options.RawFiles.Count;
int curIndex = 0;
foreach (var groupKey in map.Keys)
{
var mrmFile = GetMrmFileName(targetDirectory, groupKey);
SrmPairedResult taskResult = new SrmPairedResult()
{
Options = this.options
};
var files = map[groupKey];
foreach (var rawFile in files)
{
curIndex++;
this.prefix = MyConvert.Format("Processing {0}/{1}", curIndex, totalCount);
SetProgressMessage(rawFile);
Console.WriteLine(rawFile);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
//读取所有scan信息
List <SrmScan> mrmIntensities = GetMRMScans(rawFile);
//mrmIntensities.RemoveAll(m => !( Math.Abs(m.PrecursorMz - 767.4) < 0.1 || Math.Abs(m.PrecursorMz - 770.9) < 0.1));
SetProgressMessage("building mrm groups ...");
var mrms = ScanToTransaction(mrmIntensities);
//将MRMPeptideItem转换为MRMPairedPeptideItem对象
SrmPairedResult mrmPairs;
if (File.Exists(options.DefinitionFile))
{
mrmPairs = BuildResultBasedOnDefinedFile(ref ignoreWarning, mrms);
}
else
{
mrmPairs = BuildResultBasedOnRealData(mrms);
}
mrmPairs.Options = this.options;
mrmPairs.PeakPicking();
//固定阈值筛选。
var filter = mrmPairs.Options.GetFilter();
mrmPairs.ForEach(m =>
{
m.ProductIonPairs.ForEach(n => n.Enabled = filter.Accept(n));
});
taskResult.AddRange(mrmPairs);
}
if (options.HasDecoy)
{
//设置decoy标签
taskResult.AssignDecoy();
//是否有真实的decoy transition
var hasDecoy = taskResult.Any(m => m.ProductIonPairs.Any(n => n.IsDecoy));
if (hasDecoy)
{
//选取所有transition pairs，这些transition pairs有线性回归比值和回归系数
var pairs = (from m in taskResult
from n in m.ProductIonPairs
where n.IsPaired && n.Enabled
orderby n.RegressionCorrelation descending
select n).ToList();
//如果有这些pair，那么，那些不成pair的transition全部设置为disabled
if (pairs.Count > 0)
{
taskResult.ForEach(m => m.ProductIonPairs.ForEach(n => n.Enabled = n.Enabled && n.IsPaired));
}
//计算每个pair的qvalue
TargetFalseDiscoveryRateCalculator calc = new TargetFalseDiscoveryRateCalculator();
var decoyCount = pairs.Count(m => m.IsDecoy);
var targetCount = pairs.Count - decoyCount;
for (int d = pairs.Count - 1; d >= 0; d--)
{
pairs[d].Qvalue = calc.Calculate(decoyCount, targetCount);
if (pairs[d].IsDecoy)
{
decoyCount--;
}
else
{
targetCount--;
}
}
//找到qvalue小于给定fdr的pair，qvalue大于该pair的全部设置为disable
for (int d = pairs.Count - 1; d >= 0; d--)
{
if (!pairs[d].IsDecoy && pairs[d].Qvalue <= options.TransitionFdr)
{
for (int d2 = d + 1; d2 < pairs.Count - 1; d2++)
{
pairs[d2].Enabled = false;
}
break;
}
}
}
}
taskResult.ForEach(m =>
{
m.CheckEnabled(this.options.OutlierEvalue, this.options.MinValidTransitionPair);
});
taskResult.CalculatePeptideRatio();
taskResult.Sort((m1, m2) => m1.LightPrecursorMZ.CompareTo(m2.LightPrecursorMZ));
new SrmPairedResultXmlFormat().WriteToFile(mrmFile, taskResult);
result.Add(mrmFile);
}
Progress.End();
return(result);
}
private SrmPairedResult BuildResultBasedOnRealData(List <SrmTransition> mrms)
{
SrmPairedResult mrmPairs;
//将Transaction转换为MRMPeptideItem
var peptides = new List <SrmPeptideItem>();
foreach (var mrm in mrms)
{
bool bFound = false;
foreach (var pep in peptides)
{
if (mrm.IsBrother(pep.ProductIons[0], this.options.RetentionTimeToleranceInSecond, 0.0001))
{
pep.ProductIons.Add(mrm);
bFound = true;
break;
}
}
if (!bFound)
{
SrmPeptideItem item = new SrmPeptideItem();
item.PrecursorMZ = mrm.PrecursorMZ;
item.ProductIons.Add(mrm);
peptides.Add(item);
}
}
//按照precursormz排序
foreach (var pep in peptides)
{
pep.ProductIons.Sort((m1, m2) => m1.ProductIon.CompareTo(m2.ProductIon));
}
mrmPairs = new SrmPairedResult();
mrmPairs.AddRange(from p in peptides
orderby p.PrecursorMZ
select new SrmPairedPeptideItem(p));
//合并ProductIon完全一样或者差距相同的Item
for (int i = 0; i < mrmPairs.Count; i++)
{
var iLight = mrmPairs[i];
for (int j = i + 1; j < mrmPairs.Count; j++)
{
var jLight = mrmPairs[j];
if (Math.Abs(iLight.LightPrecursorMZ - jLight.LightPrecursorMZ) > this.options.MaxPrecursorDistance)
{
continue;
}
if (iLight.AddPerfectPairedPeptideItem(jLight, this.options.AllowedGaps, this.options.MzTolerance, this.options.RetentionTimeToleranceInSecond))
{
mrmPairs.RemoveAt(j);
break;
}
}
}
//容错情况下，合并ProductIon完全一样或者差距相同的Item
for (int i = 0; i < mrmPairs.Count; i++)
{
var iLight = mrmPairs[i];
if (iLight.IsPaired)
{
continue;
}
for (int j = i + 1; j < mrmPairs.Count; j++)
{
var jLight = mrmPairs[j];
if (jLight.IsPaired)
{
continue;
}
if (Math.Abs(iLight.LightPrecursorMZ - jLight.LightPrecursorMZ) > this.options.MaxPrecursorDistance)
{
continue;
}
if (iLight.AddErrorPairedPeptideItem(jLight, this.options.AllowedGaps, this.options.MzTolerance, this.options.RetentionTimeToleranceInSecond))
{
mrmPairs.RemoveAt(j);
break;
}
}
}
return(mrmPairs);
}
private int GetCount(SrmPairedResult node, Predicate <SrmPairedPeptideItem> pred)
{
return(node.Count(m => pred(m)));
}
