public override IEnumerable <string> Process(string filename)
{
string resultFile = FileUtils.ChangeExtension(filename, "peptides");
using (IdentifiedProteinGroupEnumerator iter = new IdentifiedProteinGroupEnumerator(filename, true))
{
using (StreamWriter sw = new StreamWriter(resultFile))
{
sw.WriteLine(iter.PeptideFormat.GetHeader());
HashSet <string> saved = new HashSet <string>();
HashSet <string> uniquepeptides = new HashSet <string>();
while (iter.MoveNext())
{
IIdentifiedProteinGroup group = iter.Current;
List <IIdentifiedSpectrum> spectra = group[0].GetSpectra();
spectra.ForEach(delegate(IIdentifiedSpectrum spectrum)
{
string dta = spectrum.Query.FileScan.LongFileName;
if (!saved.Contains(dta))
{
saved.Add(dta);
uniquepeptides.Add(spectrum.Peptide.PureSequence);
sw.WriteLine(iter.PeptideFormat.GetString(spectrum));
}
});
}
sw.WriteLine();
sw.WriteLine("----- summary -----");
sw.WriteLine("Total peptides: {0}", saved.Count);
sw.WriteLine("Unique peptides: {0}", uniquepeptides.Count);
}
}
return(new [] { resultFile });
}
protected override IEnumerable <string> DoProcess(string filename, List <string> result, Dictionary <IFilter <IIdentifiedSpectrum>, SpectrumEntry> map)
{
string database = filename + ".fasta";
if (!File.Exists(database))
{
throw new Exception("Fasta file not exists : " + database);
}
IAccessNumberParser acParser = AccessNumberParserFactory.GuessParser(database);
Dictionary <string, Sequence> seqMap = DatabaseUtils.GetAccessNumberMap(database, acParser);
try
{
using (IdentifiedProteinGroupEnumerator iter = new IdentifiedProteinGroupEnumerator(filename))
{
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
entry.ResultWriter.WriteLine(iter.ProteinFormat.GetHeader());
entry.ResultWriter.WriteLine(iter.PeptideFormat.GetHeader());
}
while (iter.MoveNext())
{
IIdentifiedProteinGroup group = iter.Current;
List <IIdentifiedSpectrum> spectra = group[0].GetSpectra();
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
entry.Spectra.Clear();
foreach (IIdentifiedSpectrum spectrum in spectra)
{
if (filter.Accept(spectrum))
{
entry.Spectra.Add(spectrum);
}
}
if (entry.Spectra.Count > 0)
{
for (int i = 0; i < group.Count; i++)
{
entry.ResultWriter.WriteLine("${0}-{1}{2}", group.Index, i + 1, iter.ProteinFormat.GetString(group[i]));
string ac = acParser.GetValue(group[i].Name);
Sequence seq = seqMap[ac];
entry.FastaWriter.WriteLine(">" + seq.Reference);
entry.FastaWriter.WriteLine(seq.SeqString);
}
foreach (IIdentifiedSpectrum spectrum in entry.Spectra)
{
entry.ResultWriter.WriteLine(iter.PeptideFormat.GetString(spectrum));
}
}
}
}
return(result);
}
}
finally
{
foreach (SpectrumEntry entry in map.Values)
{
entry.Dispose();
}
}
}
