public static void DoJob()
{
String comet = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\MS_QC_120min.pep.xml";
String output = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\";
ProteinProphetResult ppr = PostProcessingScripts.RunProteinProphet(comet, output, true);
Console.WriteLine(ppr.ToString());
}
public static void DoJob()
{
InputFileOrganizer.FASTA_FILE = "C:\\Coding\\2019LavalleeLab\\temp2\\ExampleDataSet\\uniprot_SwissProt_Human_1_11_2017.fasta";
//String outputCometFile = "C:\\Coding\\2019LavalleeLab\\temp2\\ModifiedDBSearchFiles\\Result\\ModdedSearch_MLGEGolden_nonCheat_peptideSearchResultIncluded\\PartialCometFile\\1ModdedSearch_MLGE_nonCheat_peptideSearchResultIncluded_partial.pep.xml";
String outputCometFile = "C:\\Coding\\2019LavalleeLab\\temp2\\ModifiedDBSearchFiles\\Result\\Modded_MLGEGolden_rtCheatpeptideSearchResultIncluded\\PartialCometFile\\1Modded_MLGEGolden_rtCheat_partial.pep.xml";
ProteinProphetResult ppr = PostProcessingScripts.RunProteinProphet(outputCometFile, InputFileOrganizer.OutputFolderOfTheRun, true);
//String proteinProphetFile = "C:\\Coding\\2019LavalleeLab\\temp2\\Output\\ProteinGroup_Combined_rtCheat\\protein_prophet_output\\ProteinGroup_Combined_rtCheat_partial_interact.prot.xml";
//ProteinProphetResult ppr = ProteinProphetEvaluator.getProteinProphetResult(proteinProphetFile);
Console.WriteLine(ppr.ToString());
Console.WriteLine("Protein groups " + ppr.getFilteredProteinGroups().Count);
}
