public PHRPReaderParser(string synopsisFilePath, FragmentLadderOptions fragLadderOptions)
{
m_fragLadderOptions = fragLadderOptions;
m_fragLadderOptions.modificationList.Clear();
using (var reader = new StreamReader(synopsisFilePath))
{
m_firstLine = reader.ReadLine().Split('\t');
for (int i = 0; i < m_firstLine.Length; i++)
{
if (m_firstLine[i] == "Peptide")
{
m_peptideColumnIndex = i;
break;
}
}
}
var oStartupOptions = new clsPHRPStartupOptions
{
LoadModsAndSeqInfo = true,
LoadMSGFResults = true,
LoadScanStatsData = false,
MaxProteinsPerPSM = 100
};
m_reader = new clsPHRPReader(synopsisFilePath, oStartupOptions);
//m_reader.FastReadMode = true;
m_reader.SkipDuplicatePSMs = true;
m_parser = m_reader.PHRPParser;
}
public async Task <IEnumerable <PrSm> > ReadAsync(IEnumerable <string> modIgnoreList = null, IProgress <double> progress = null)
{
var oStartupOptions = new clsPHRPStartupOptions {
LoadModsAndSeqInfo = true
};
var phrpReader = new clsPHRPReader(filePath, oStartupOptions);
if (!string.IsNullOrEmpty(phrpReader.ErrorMessage))
{
throw new Exception(phrpReader.ErrorMessage);
}
var identifications = await Task.Run(
() =>
{
var ids = new List <PrSm>();
while (phrpReader.MoveNext())
{
phrpReader.FinalizeCurrentPSM();
var psm = phrpReader.CurrentPSM;
var proteins = psm.Proteins;
var parsedSequence = ParseSequence(psm.PeptideCleanSequence, psm.ModifiedResidues);
foreach (var protein in proteins)
{
var prsm = new PrSm
{
Heavy = false,
ProteinName = protein,
ProteinDesc = string.Empty,
Charge = psm.Charge,
Sequence = parsedSequence,
Scan = psm.ScanNumber,
Score = Convert.ToDouble(psm.MSGFSpecProb),
UseGolfScoring = true,
QValue = 0,
};
prsm.SetSequence(GetSequenceText(parsedSequence), parsedSequence);
ids.Add(prsm);
}
}
return(ids);
});
return(identifications);
}
/// <summary>
/// PHRPReader configuration
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
protected clsPHRPReader InitializeReader(string path)
{
AbortRequested = false;
var oStartupOptions = new clsPHRPStartupOptions
{
LoadModsAndSeqInfo = true,
LoadMSGFResults = true,
LoadScanStatsData = false,
MaxProteinsPerPSM = 100
};
UpdateProgress(0, "Initializing reader");
var reader = new clsPHRPReader(path, oStartupOptions)
{
SkipDuplicatePSMs = true,
FastReadMode = true
};
return(reader);
}
