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);
}
