public static IdentificationSummary Parse(string proteinFile, string defaultDecoyPattern, IFalseDiscoveryRateCalculator defaultCalc)
{
IdentificationSummary result = new IdentificationSummary();
result.FileName = FileUtils.ChangeExtension(new FileInfo(proteinFile).Name, "");
Regex decoyReg = new Regex(defaultDecoyPattern);
IIdentifiedProteinGroupFilter decoyFilter = null;
IFalseDiscoveryRateCalculator curCalc = null;
var paramFile = FileUtils.ChangeExtension(proteinFile, ".param");
if (File.Exists(paramFile))
{
BuildSummaryOptions options = BuildSummaryOptionsUtils.LoadFromFile(paramFile);
if (options.FalseDiscoveryRate.FilterByFdr)
{
decoyFilter = options.GetDecoyGroupFilter();
curCalc = options.FalseDiscoveryRate.GetFalseDiscoveryRateCalculator();
}
}
if (decoyFilter == null)
{
decoyFilter = new IdentifiedProteinGroupNameRegexFilter(defaultDecoyPattern, false);
curCalc = defaultCalc;
}
var peptideFile = FileUtils.ChangeExtension(proteinFile, ".peptides");
if (File.Exists(peptideFile))
{
var peptides = new MascotPeptideTextFormat().ReadFromFile(peptideFile);
var fullSpectra = GetSpectraByNPT(peptides, 2);
var fullTargetSpectra = GetTargetSpectra(decoyReg, fullSpectra);
var semiSpectra = GetSpectraByNPT(peptides, 1);
var semiTargetSpectra = GetTargetSpectra(decoyReg, semiSpectra);
result.FullSpectrumCount = GetSpectrumCount(fullSpectra);
result.FullTargetSpectrumCount = GetSpectrumCount(fullTargetSpectra);
result.SemiSpectrumCount = GetSpectrumCount(semiSpectra);
result.SemiTargetSpectrumCount = GetSpectrumCount(semiTargetSpectra);
result.FullPeptideCount = IdentifiedSpectrumUtils.GetUniquePeptideCount(fullSpectra);
result.FullTargetPeptideCount = IdentifiedSpectrumUtils.GetUniquePeptideCount(fullTargetSpectra);
result.SemiPeptideCount = IdentifiedSpectrumUtils.GetUniquePeptideCount(semiSpectra);
result.SemiTargetPeptideCount = IdentifiedSpectrumUtils.GetUniquePeptideCount(semiTargetSpectra);
result.FullSpectrumFdr = curCalc.Calculate(result.FullSpectrumCount - result.FullTargetSpectrumCount, result.FullTargetSpectrumCount);
result.SemiSpectrumFdr = curCalc.Calculate(result.SemiSpectrumCount - result.SemiTargetSpectrumCount, result.SemiTargetSpectrumCount);
result.FullPeptideFdr = curCalc.Calculate(result.FullPeptideCount - result.FullTargetPeptideCount, result.FullTargetPeptideCount);
result.SemiPeptideFdr = curCalc.Calculate(result.SemiPeptideCount - result.SemiTargetPeptideCount, result.SemiTargetPeptideCount);
}
if (File.Exists(proteinFile))
{
var ir = new MascotResultTextFormat().ReadFromFile(proteinFile);
ir.InitUniquePeptideCount();
var u2proteins = (from p in ir
where p[0].UniquePeptideCount > 1
select p).ToList();
var u1proteins = (from p in ir
where p[0].UniquePeptideCount == 1
select p).ToList();
result.ProteinGroupCount = ir.Count;
result.Unique2ProteinGroupCount = u2proteins.Count;
int targetCount;
result.Unique2ProteinFdr = CalculateProteinFdr(u2proteins, decoyFilter, defaultCalc, out targetCount);
result.Unique2ProteinGroupTargetCount = (int)targetCount;
result.Unique1ProteinFdr = CalculateProteinFdr(u1proteins, decoyFilter, defaultCalc, out targetCount);
result.Unique1ProteinGroupTargetCount = (int)targetCount;
}
return(result);
}
private void RunCurrentParameter(string parameterFile, List <string> result, BuildSummaryOptions conf)
{
IStringParser <string> acParser = conf.Database.GetAccessNumberParser();
IIdentifiedProteinBuilder proteinBuilder = new IdentifiedProteinBuilder();
IIdentifiedProteinGroupBuilder groupBuilder = new IdentifiedProteinGroupBuilder()
{
Progress = this.Progress
};
IdentifiedSpectrumBuilderResult isbr;
List <IIdentifiedSpectrum> finalPeptides;
if (string.IsNullOrEmpty(options.PeptideFile))
{ //parse from configuration
//build spectrum list
IIdentifiedSpectrumBuilder spectrumBuilder = conf.GetSpectrumBuilder();
if (spectrumBuilder is IProgress)
{
(spectrumBuilder as IProgress).Progress = this.Progress;
}
isbr = spectrumBuilder.Build(parameterFile);
finalPeptides = isbr.Spectra;
}
else
{
Progress.SetMessage("Reading peptides from {0} ...", options.PeptideFile);
finalPeptides = new MascotPeptideTextFormat().ReadFromFile(options.PeptideFile);
conf.SavePeptidesFile = false;
isbr = null;
}
CalculateIsoelectricPoint(finalPeptides);
//如果需要通过蛋白质注释去除contamination，首先需要在肽段水平删除
if (conf.Database.HasContaminationDescriptionFilter() && (conf.FalseDiscoveryRate.FdrLevel != FalseDiscoveryRateLevel.Protein))
{
Progress.SetMessage("Removing contamination by description ...");
var notConGroupFilter = conf.Database.GetNotContaminationDescriptionFilter(Progress);
var tempResultBuilder = new IdentifiedResultBuilder(null, null);
while (true)
{
List <IIdentifiedProtein> proteins = proteinBuilder.Build(finalPeptides);
List <IIdentifiedProteinGroup> groups = groupBuilder.Build(proteins);
IIdentifiedResult tmpResult = tempResultBuilder.Build(groups);
HashSet <IIdentifiedSpectrum> notConSpectra = new HashSet <IIdentifiedSpectrum>();
foreach (var group in tmpResult)
{
if (notConGroupFilter.Accept(group))
{
notConSpectra.UnionWith(group[0].GetSpectra());
}
}
if (notConSpectra.Count == finalPeptides.Count)
{
break;
}
finalPeptides = notConSpectra.ToList();
}
}
if (conf.FalseDiscoveryRate.FilterOneHitWonder && conf.FalseDiscoveryRate.MinOneHitWonderPeptideCount > 1)
{
Progress.SetMessage("Filtering single wonders ...");
var proteinFilter = new IdentifiedProteinSingleWonderPeptideCountFilter(conf.FalseDiscoveryRate.MinOneHitWonderPeptideCount);
List <IIdentifiedProtein> proteins = proteinBuilder.Build(finalPeptides);
int oldProteinCount = proteins.Count;
proteins.RemoveAll(l => !proteinFilter.Accept(l));
if (oldProteinCount != proteins.Count)
{
HashSet <IIdentifiedSpectrum> newspectra = new HashSet <IIdentifiedSpectrum>();
foreach (var protein in proteins)
{
newspectra.UnionWith(protein.GetSpectra());
}
finalPeptides = newspectra.ToList();
}
}
//if (conf.SavePeptidesFile && !(conf.FalseDiscoveryRate.FilterOneHitWonder && conf.FalseDiscoveryRate.MinOneHitWonderPeptideCount > 1))
if (conf.SavePeptidesFile)
{
if (conf.Database.RemovePeptideFromDecoyDB)
{
DecoyPeptideBuilder.AssignDecoy(finalPeptides, conf.GetDecoySpectrumFilter());
for (int i = finalPeptides.Count - 1; i >= 0; i--)
{
if (finalPeptides[i].FromDecoy)
{
finalPeptides.RemoveAt(i);
}
}
}
finalPeptides.Sort();
//保存肽段文件
IFileFormat <List <IIdentifiedSpectrum> > peptideFormat = conf.GetIdentifiedSpectrumFormat();
string peptideFile = FileUtils.ChangeExtension(parameterFile, ".peptides");
Progress.SetMessage("Writing peptides file...");
peptideFormat.WriteToFile(peptideFile, finalPeptides);
result.Add(peptideFile);
if (!conf.FalseDiscoveryRate.FilterByFdr && conf.Database.DecoyPatternDefined)
{
WriteFdrFile(parameterFile, conf, finalPeptides);
}
Progress.SetMessage("Calculating precursor offset...");
result.AddRange(new PrecursorOffsetCalculator(finalPeptides).Process(peptideFile));
}
Progress.SetMessage("Building protein...");
//构建蛋白质列表
List <IIdentifiedProtein> finalProteins = proteinBuilder.Build(finalPeptides);
Progress.SetMessage("Building protein group...");
//构建蛋白质群列表
List <IIdentifiedProteinGroup> finalGroups = groupBuilder.Build(finalProteins);
if (conf.Database.HasContaminationDescriptionFilter())
{
var notConGroupFilter = conf.Database.GetNotContaminationDescriptionFilter(Progress);
for (int i = finalGroups.Count - 1; i >= 0; i--)
{
if (!notConGroupFilter.Accept(finalGroups[i]))
{
finalGroups.RemoveAt(i);
}
}
}
//构建最终鉴定结果
var resultBuilder = conf.GetIdentifiedResultBuilder();
resultBuilder.Progress = Progress;
IIdentifiedResult finalResult = resultBuilder.Build(finalGroups);
finalResult.BuildGroupIndex();
if (conf.FalseDiscoveryRate.FilterByFdr)
{
var decoyGroupFilter = conf.GetDecoyGroupFilter();
foreach (var group in finalResult)
{
group.FromDecoy = decoyGroupFilter.Accept(group);
foreach (var protein in group)
{
protein.FromDecoy = group.FromDecoy;
}
}
finalResult.ProteinFDR = conf.FalseDiscoveryRate.GetFalseDiscoveryRateCalculator().Calculate(finalResult.Count(l => l[0].FromDecoy), finalResult.Count(l => !l[0].FromDecoy));
}
CalculateIsoelectricPoint(finalResult.GetProteins());
if (isbr != null)
{
finalResult.PeptideFDR = isbr.PeptideFDR;
}
//保存非冗余蛋白质列表文件
var resultFormat = conf.GetIdetifiedResultFormat(finalResult, this.Progress);
string noredundantFile = FileUtils.ChangeExtension(parameterFile, ".noredundant");
Progress.SetMessage("Writing noredundant file...");
resultFormat.WriteToFile(noredundantFile, finalResult);
result.Add(noredundantFile);
Progress.SetMessage("Finished!");
}
