public static void DoJob() { String fastaFile = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\uniprot_SwissProt_Human_1_11_2017.fasta"; String outputFile = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\"; DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(fastaFile); }
private static void ConstructDecoyFasta() { if (!GlobalVar.useDecoyFastaComputedFile) { log.Debug("Generating decoy database for comet search validation"); InputFileOrganizer.DecoyFasta = DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(InputFileOrganizer.FASTA_FILE, InputFileOrganizer.preExperimentFilesFolder); log.Debug("Concacenated decoy database generated."); } }
private static void SimulationWithDecoyParamsSetUp() { GlobalVar.isSimulationForFeatureExtraction = true; String decoyConcatDB = DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(InputFileOrganizer.FASTA_FILE, InputFileOrganizer.OutputFolderOfTheRun); InputFileOrganizer.ExclusionDBFasta = decoyConcatDB; //sets the in-program databse to one that contains decoy protein - for feature generation only InputFileOrganizer.DecoyFasta = decoyConcatDB; GlobalVar.useDecoyFastaComputedFile = true; GlobalVar.useIDXComputedFile = false; GlobalVar.useChainsawComputedFile = false; GlobalVar.usePepXMLComputedFile = false; GlobalVar.useRTCalcComputedFile = false; //InputFileOrganizer.RTCalcResult = "C:\\Users\\LavalleeLab\\Documents\\JoshTemp\\RealTimeMS\\TestData\\PreComputedFiles\\tempOutputPeptideList_rtOutput_240min.txt"; }