public override IEnumerable <string> Process(string filename)
{
var parser = new OutParser();
string resultFilename;
if (null == this.targetDir)
{
resultFilename = FileUtils.ChangeExtension(filename, ".xml");
}
else
{
resultFilename = targetDir + "/" + FileUtils.ChangeExtension(new FileInfo(filename).Name, ".xml");
}
using (PepXmlWriter writer = new PepXmlWriter("out"))
{
writer.Open(resultFilename);
writer.OpenMsmsRunSummary(filename);
SequestParam sp = new SequestParamFile().ReadFromFile(filename);
writer.WriteSequestParam(sp);
using (var reader = new OutsReader(filename))
{
int totalCount = reader.FileCount;
Progress.SetRange(0, totalCount);
int currentCount = 0;
while (reader.HasNext)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
List <string> contents = reader.NextContent();
IIdentifiedSpectrum sph = parser.Parse(contents);
if (sph == null)
{
continue;
}
writer.WriteSequestPeptideHit(sph);
currentCount++;
Progress.SetPosition(currentCount);
}
Progress.SetPosition(totalCount);
}
writer.CloseMsmsRunSummary();
}
return(new[] { resultFilename });
}
public void TestException()
{
using (var reader = new OutsReader(@"../../../data/20030428_4_29L_15.outs"))
{
for (int i = 0; i < 731; i++)
{
reader.NextContent();
}
//expect to throw exception
reader.NextContent();
}
}
public void TestAll()
{
using (var reader = new OutsReader(@"../../../data/20030428_4_29L_15.outs"))
{
Assert.AreEqual(731, reader.FileCount);
for (int i = 0; i < 731; i++)
{
Assert.AreEqual(true, reader.HasNext);
reader.NextContent();
}
Assert.AreEqual(false, reader.HasNext);
}
}
private void ExtractFileByPeptide(OutsReader reader, Dictionary <string, IIdentifiedSpectrum> outFilenamePeptideMap, string toDirectory)
{
Progress.SetRange(0, 1, reader.FileCount);
int count = 0;
while (outFilenamePeptideMap.Count > 0 && reader.HasNext)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
string filename = reader.NextFilename;
if (outFilenamePeptideMap.ContainsKey(filename))
{
List <string> content = reader.NextContent();
IIdentifiedSpectrum sph = outFilenamePeptideMap[filename];
IIdentifiedSpectrum parsed = parser.Parse(content);
if (sph.Sequence.Equals(parsed.Sequence))
{
string targetFilename = toDirectory + "/" + filename;
using (StreamWriter sw = new StreamWriter(targetFilename))
{
foreach (string line in content)
{
sw.WriteLine(line);
}
}
outFilenamePeptideMap.Remove(filename);
}
}
else
{
reader.SkipNextContent();
}
Progress.SetPosition(0, count++);
}
Progress.SetPosition(0, reader.FileCount);
}
private void ExtractMultipleRaw(string raw, List <string> rawFiles, List <IIdentifiedSpectrum> peptides)
{
string toDirectory = CreateToDirectory(raw);
List <string> dtaFilenames = GetDtaFilenames(peptides);
string dtasFile = new DtaOutFilenameConverter(rawFiles[0]).GetDtasFilename();
using (DtasReader dtas = new DtasReader(dtasFile))
{
Progress.SetMessage(0, "Extracting from " + dtasFile + " ...");
ExtractFile(dtas, dtaFilenames, toDirectory);
}
Dictionary <string, IIdentifiedSpectrum> outFilenamePeptideMap = GetOutFilenamePeptideMap(peptides);
foreach (string rawFile in rawFiles)
{
string outsFile = new DtaOutFilenameConverter(rawFiles[0]).GetOutsFilename();
Progress.SetMessage(0, "Extracting from " + outsFile + " ...");
using (OutsReader outs = new OutsReader(outsFile))
{
ExtractFileByPeptide(outs, outFilenamePeptideMap, toDirectory);
}
}
if (outFilenamePeptideMap.Count > 0)
{
StringBuilder sb;
if (outFilenamePeptideMap.Count == 1)
{
sb = new StringBuilder("There is a file not found in dtas/outs file");
}
else
{
sb = new StringBuilder("There are a few files not found in dtas/outs file");
}
foreach (string key in outFilenamePeptideMap.Keys)
{
sb.Append("\n" + key);
}
throw new Exception(sb.ToString());
}
}
private void ExtractSingleRaw(string raw, string rawFile, List <IIdentifiedSpectrum> peptides)
{
string toDirectory = CreateToDirectory(raw);
List <string> dtaFilenames = GetDtaFilenames(peptides);
string dtasFile = new DtaOutFilenameConverter(rawFile).GetDtasFilename();
using (DtasReader dtas = new DtasReader(dtasFile))
{
Progress.SetMessage(0, MyConvert.Format("Extracting dta from {0} ...", dtasFile));
ExtractFile(dtas, dtaFilenames, toDirectory);
}
List <string> outFilenames = GetOutFilenames(peptides);
string outsFile = new DtaOutFilenameConverter(rawFile).GetOutsFilename();
using (OutsReader outs = new OutsReader(outsFile))
{
Progress.SetMessage(0, MyConvert.Format("Extracting out from {0} ...", outsFile));
ExtractFile(outs, outFilenames, toDirectory);
}
}
