public static ProteinProphetResult postProcessing(ExclusionProfile exclusionProfile, String experimentName,
Boolean keepResults)
{
String partialCometFileOutputFolder = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "PartialCometFile");
if (!Directory.Exists(partialCometFileOutputFolder))
{
Directory.CreateDirectory(partialCometFileOutputFolder);
}
String outputCometFile = Path.Combine(partialCometFileOutputFolder,
experimentName + "_partial" + InputFileOrganizer.PepXMLSuffix);
PartialPepXMLWriter.writePartialPepXMLFile(InputFileOrganizer.OriginalCometOutput, exclusionProfile.getSpectraUsed(),
outputCometFile, InputFileOrganizer.MS2SimulationTestFile, InputFileOrganizer.FASTA_FILE, outputCometFile); //TODO was using MZML instead of MS2
ProteinProphetResult ppr = RunProteinProphet(outputCometFile, InputFileOrganizer.OutputFolderOfTheRun, keepResults);
//PostProcessingScripts.deleteFile(outputCometFile);
// delete these files if this flag is false
//if (!keepResults)
//{
//}
return(ppr);
}
