private void StoreResult(TextWriter writer, DartIdData groupData, string datasetName)
{
if (string.IsNullOrWhiteSpace(groupData.DataLine))
{
return;
}
var outputValues = new List <string>
{
datasetName,
groupData.Peptide,
groupData.SpecEValue,
groupData.Charge.ToString(),
groupData.Proteins.First(),
string.Join(";", groupData.Proteins.Distinct()),
groupData.ElutionTime,
groupData.PeakWidthMinutes
};
writer.WriteLine(string.Join("\t", outputValues));
}
public bool ConsolidatePSMs(string psmFilePath, bool multiJobFile)
{
try
{
var inputFile = new FileInfo(psmFilePath);
var outputFileName = Path.GetFileNameWithoutExtension(inputFile.Name) + "_ForDartID.txt";
string outputFilePath;
if (inputFile.DirectoryName != null)
{
outputFilePath = Path.Combine(inputFile.DirectoryName, outputFileName);
}
else
{
outputFilePath = outputFileName;
}
var msgfPlusColumns = new SortedDictionary <Enum, int>();
mScanTimeColIndex = -1;
mPeakWidthMinutesColIndex = -1;
var requiredColumns = new List <MSGFPlusSynFileColumns>
{
MSGFPlusSynFileColumns.Peptide,
MSGFPlusSynFileColumns.SpecEValue,
MSGFPlusSynFileColumns.Charge,
MSGFPlusSynFileColumns.Protein
};
string datasetName;
if (multiJobFile)
{
datasetName = "TBD";
throw new NotImplementedException(
"ConsolidatePSMs needs to be updated to support an input file where Job or Dataset is the first column");
}
// Obtain the dataset name from the filename
if (psmFilePath.EndsWith(MASICResultsMerger.RESULTS_SUFFIX, StringComparison.OrdinalIgnoreCase))
{
datasetName = Path.GetFileName(psmFilePath.Substring(0, psmFilePath.Length - MASICResultsMerger.RESULTS_SUFFIX.Length));
}
else
{
datasetName = Path.GetFileNameWithoutExtension(psmFilePath);
}
if (datasetName.EndsWith("_syn", StringComparison.OrdinalIgnoreCase) ||
datasetName.EndsWith("_fht", StringComparison.OrdinalIgnoreCase))
{
datasetName = datasetName.Substring(0, datasetName.Length - 4);
}
// ReSharper disable StringLiteralTypo
if (datasetName.EndsWith("_msgfplus", StringComparison.OrdinalIgnoreCase))
{
datasetName = datasetName.Substring(0, datasetName.Length - "_msgfplus".Length);
}
else if (datasetName.EndsWith("_msgfdb", StringComparison.OrdinalIgnoreCase))
{
datasetName = datasetName.Substring(0, datasetName.Length - "_msgfdb".Length);
}
// ReSharper restore StringLiteralTypo
var psmGroup = new DartIdData();
using var reader = new StreamReader(new FileStream(inputFile.FullName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
using var writer = new StreamWriter(new FileStream(outputFilePath, FileMode.Create, FileAccess.Write, FileShare.ReadWrite));
var headerLine = new List <string>
{
"Dataset",
"Peptide",
"MSGFDB_SpecEValue",
"Charge",
"LeadingProtein",
"Proteins",
"ElutionTime",
"PeakWidthMinutes"
};
writer.WriteLine(string.Join("\t", headerLine));
while (!reader.EndOfStream)
{
var dataLine = reader.ReadLine();
if (string.IsNullOrWhiteSpace(dataLine))
{
continue;
}
if (mScanTimeColIndex < 0)
{
var success = ParseMergedFileHeaderLine(dataLine, msgfPlusColumns);
if (!success)
{
return(false);
}
if (mScanTimeColIndex < 0)
{
OnErrorEvent(string.Format("File {0} is missing column {1} on the header line", inputFile.Name,
MASICResultsMerger.SCAN_STATS_ELUTION_TIME_COLUMN));
return(false);
}
if (mPeakWidthMinutesColIndex < 0)
{
OnErrorEvent(string.Format("File {0} is missing column {1} on the header line", inputFile.Name,
MASICResultsMerger.PEAK_WIDTH_MINUTES_COLUMN));
return(false);
}
// Validate that the required columns exist
foreach (var requiredColumn in requiredColumns)
{
if (ColumnExists(msgfPlusColumns, requiredColumn))
{
continue;
}
OnErrorEvent(string.Format("File {0} is missing column {1} on the header line", inputFile.Name, requiredColumn.ToString()));
return(false);
}
continue;
}
var dataColumns = dataLine.Split('\t');
var scanNumber = GetValueInt(dataColumns, msgfPlusColumns, MSGFPlusSynFileColumns.Scan);
var charge = GetValueInt(dataColumns, msgfPlusColumns, MSGFPlusSynFileColumns.Charge);
var peptide = GetValue(dataColumns, msgfPlusColumns, MSGFPlusSynFileColumns.Peptide);
var protein = GetValue(dataColumns, msgfPlusColumns, MSGFPlusSynFileColumns.Protein);
if (!PeptideCleavageStateCalculator.SplitPrefixAndSuffixFromSequence(peptide, out var primarySequence, out _, out _))
{
primarySequence = peptide;
}
if (scanNumber != psmGroup.ScanNumber ||
charge != psmGroup.Charge ||
!string.Equals(primarySequence, psmGroup.PrimarySequence))
{
StoreResult(writer, psmGroup, datasetName);
psmGroup = new DartIdData(dataLine, scanNumber, peptide, primarySequence, protein)
{
SpecEValue = GetValue(dataColumns, msgfPlusColumns, MSGFPlusSynFileColumns.SpecEValue),
Charge = charge,
ElutionTime = dataColumns[mScanTimeColIndex],
PeakWidthMinutes = dataColumns[mPeakWidthMinutesColIndex]
};
}
else
{
psmGroup.Proteins.Add(protein);
}
}
StoreResult(writer, psmGroup, datasetName);
return(true);
}
catch (Exception ex)
{
OnErrorEvent("Error in ConsolidatePSMs", ex);
return(false);
}
}
