public override void WriteToFile(string filename, List <IIdentifiedSpectrum> t)
{
using (var sw = new StreamWriter(filename))
{
sw.WriteLine(PeptideFormat.GetHeader());
foreach (IIdentifiedSpectrum mph in t)
{
sw.WriteLine(PeptideFormat.GetString(mph));
}
if (!NotExportSummary)
{
sw.WriteLine();
sw.WriteLine("----- summary -----");
var totalCount = IdentifiedSpectrumUtils.GetSpectrumCount(t);
var totalUniqueCount = IdentifiedSpectrumUtils.GetUniquePeptideCount(t);
sw.WriteLine("Total spectra: " + totalCount);
sw.WriteLine("Total peptides: " + totalUniqueCount);
var tags = (from s in t
select s.Tag).Distinct().ToList();
if (tags.Count > 1)
{
tags.Sort();
sw.WriteLine();
sw.WriteLine("Tag\tSpectra\tPeptides");
sw.WriteLine("All\t{0}\t{1}", totalCount, totalUniqueCount);
foreach (var tag in tags)
{
var tagspectra = from s in t
where s.Tag == tag
select s;
sw.WriteLine("{0}\t{1}\t{2}", tag, IdentifiedSpectrumUtils.GetSpectrumCount(tagspectra), IdentifiedSpectrumUtils.GetUniquePeptideCount(tagspectra));
}
}
}
}
string enzymeFile = filename + ".enzyme";
new ProteaseFile().Write(enzymeFile, t);
}
public override List <IIdentifiedSpectrum> ReadFromFile(string filename)
{
var result = new List <IIdentifiedSpectrum>();
using (var sr = new StreamReader(filename))
{
string line = sr.ReadLine();
if (IgnoreComments)
{
while (line != null && line.StartsWith("#"))
{
line = sr.ReadLine();
}
}
this.PeptideFormat = new PeptideLineFormat(line);
while ((line = sr.ReadLine()) != null)
{
if (line.Trim().Length == 0)
{
break;
}
result.Add(PeptideFormat.ParseString(line));
}
}
string enzymeFile = filename + ".enzyme";
if (File.Exists(enzymeFile))
{
new ProteaseFile().Fill(enzymeFile, result);
}
DoAfterRead(result);
return(result);
}
private IIdentifiedProteinGroup ReadNextProteinGroup(StreamReader filein, Dictionary <string, IIdentifiedSpectrum> peptideMap, ref string lastLine)
{
Progress.SetPosition(filein.BaseStream.Position);
while (!IdentifiedResultUtils.IsProteinLine(lastLine) && (lastLine = filein.ReadLine()) != null)
{
}
if (lastLine == null)
{
return(null);
}
IIdentifiedProteinGroup result = new IdentifiedProteinGroup();
while (IdentifiedResultUtils.IsProteinLine(lastLine))
{
IIdentifiedProtein protein = ProteinFormat.ParseString(lastLine);
result.Add(protein);
protein.GroupIndex = IdentifiedResultUtils.GetGroupIndex(lastLine);
lastLine = filein.ReadLine();
}
List <IIdentifiedSpectrum> peptides = new List <IIdentifiedSpectrum>();
while (!IdentifiedResultUtils.IsProteinLine(lastLine))
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
IIdentifiedSpectrum mphit = PeptideFormat.ParseString(lastLine);
string id = string.Format("{0}-{1}-{2}-{3}", mphit.Query.FileScan.LongFileName, mphit.Rank, mphit.Engine, mphit.Tag);
if (!peptideMap.ContainsKey(id))
{
peptideMap[id] = mphit;
}
else
{
mphit = peptideMap[id];
}
peptides.Add(mphit);
lastLine = filein.ReadLine();
if (lastLine == null || lastLine.Trim().Length == 0)
{
break;
}
}
foreach (IIdentifiedSpectrum hit in peptides)
{
result.AddIdentifiedSpectrum(hit);
}
return(result);
}
public void Initialize(List <IIdentifiedSpectrum> spectra)
{
string oldPeptideHeader = PeptideFormat == null?GetDefaultPeptideHeader() : PeptideFormat.GetHeader();
List <string> pepAnnotations = AnnotationUtils.GetAnnotationKeys(spectra);
string newPeptideHeader = StringUtils.GetMergedHeader(oldPeptideHeader, pepAnnotations, '\t');
PeptideFormat = new PeptideLineFormat(newPeptideHeader, GetEngineName(), spectra);
}
protected virtual void WritePeptideHeader(StreamWriter sw)
{
sw.WriteLine(PeptideFormat.GetHeader());
}
protected virtual void WritePeptide(StreamWriter sw, IIdentifiedSpectrum mph)
{
sw.WriteLine(PeptideFormat.GetString(mph));
}
public void InitializeByResult(IIdentifiedResult identifiedResult)
{
string oldProteinHeader = ProteinFormat == null?GetDefaultProteinHeader() : ProteinFormat.GetHeader();
InitializeProteinFormat(identifiedResult, oldProteinHeader);
string oldPeptideHeader = PeptideFormat == null?GetDefaultPeptideHeader() : PeptideFormat.GetHeader();
InitializePeptideFormat(identifiedResult, oldPeptideHeader);
}
public override void WriteToFile(string fileName, IIdentifiedResult identifiedResult)
{
CheckFormat(identifiedResult);
List <IIdentifiedSpectrum> allSpectra = identifiedResult.GetSpectra();
for (int i = 0; i < allSpectra.Count; i++)
{
allSpectra[i].Id = i.ToString();
}
string linkFilename = GetLinkFileName(fileName);
HashSet <IIdentifiedSpectrum> spectra = new HashSet <IIdentifiedSpectrum>();
using (var linkWriter = new StreamWriter(linkFilename))
{
linkWriter.WriteLine("PeptideId\tGroupId");
using (var sw = new StreamWriter(fileName))
{
sw.WriteLine(ProteinFormat.GetHeader());
var groups = GetValidGroups(identifiedResult);
foreach (IIdentifiedProteinGroup mpg in groups)
{
GroupWriter.WriteToStream(sw, mpg);
var validSpectra = GetValidSpectra(mpg.GetSortedPeptides());
foreach (var spectrum in validSpectra)
{
linkWriter.WriteLine(spectrum.Id + "\t" + mpg.Index);
}
spectra.UnionWith(validSpectra);
}
}
}
var finalSpectra = from s in spectra
orderby s.Id
select s;
string peptideFile = GetPeptideFileName(fileName);
if (!PeptideFormat.GetHeader().Contains("Id\t"))
{
PeptideFormat = new PeptideLineFormat("Id\t" + PeptideFormat.GetHeader());
}
using (var sw = new StreamWriter(peptideFile))
{
WritePeptideHeader(sw);
foreach (IIdentifiedSpectrum mph in finalSpectra)
{
WritePeptide(sw, mph);
}
}
if (identifiedResult.Count > 0 && identifiedResult[0][0].Sequence != null)
{
string fastaFilename = fileName + ".fasta";
WriteFastaFile(fastaFilename, identifiedResult);
}
}
