private static Database databaseSetUp(String fasta_file_name) { FastaFile f = Loader.parseFasta(fasta_file_name); DigestedFastaFile df = PerformDigestion.performDigest(f, GlobalVar.NUM_MISSED_CLEAVAGES); int numberOfProteinsInFasta = f.getAccessionToFullSequence().Count; int numberOfPeptidesInDigestedFasta = df.getDigestedPeptideArray().Count; log.Info("Fasta file: " + fasta_file_name); log.Info("Num missed cleavages: " + GlobalVar.NUM_MISSED_CLEAVAGES); log.Info("Number of proteins: " + numberOfProteinsInFasta); log.Info("Number of peptides: " + numberOfPeptidesInDigestedFasta); log.Debug("Constructing graph..."); Database g; if (GlobalVar.isSimulationForFeatureExtraction == true) { g = new Database(f, df, true, false); } else { g = new Database(f, df, true, true); } log.Debug(g); return(g); }
//depricated public static String GenerateConcacenatedDecoyFasta_MimicCometInternal(String fastaFile, String outputFilePath) { StreamWriter sw = new StreamWriter(outputFilePath); DigestedFastaFile df = PerformDigestion.performDigest(fastaFile, GlobalVar.NUM_MISSED_CLEAVAGES, false); List <DigestedPeptide> targetSequences = df.getDigestedPeptideArray(); String line; foreach (DigestedPeptide targetSeq in targetSequences) { //write the target sequence line = ">" + targetSeq.getAccession(); sw.WriteLine(line); line = targetSeq.getSequence(); sw.WriteLine(line); //write the decoy sequence line = ">" + GlobalVar.DecoyPrefix + targetSeq.getAccession(); sw.WriteLine(line); line = ReverseSequence_keepCTerm(targetSeq.getSequence()); sw.WriteLine(line); } sw.Close(); return(outputFilePath); }
public static DigestedFastaFile performDigest(String fastaFilePath, int numMissedCleavages, Boolean keepFile) { if (GlobalVar.useChainsawComputedFile) { return(Loader.parseDigestedFasta(InputFileOrganizer.ChainSawResult)); } // These are the output file paths String outputTSVFile = fastaFilePath + "_digestedPeptides.tsv"; String outputIndexFile = fastaFilePath + ".index"; /* Peptide chainsaw parameters */ String chainsaw = InputFileOrganizer.ChainSaw; // tool location //String enzyme = "Trypsin/P"; String enzyme = "Trypsin"; String specificity = "fully"; int minimumPeptideLength = GlobalVar.MinimumPeptideLength; int maximumPeptideLength = 200; // minimum and maximum peptide length is what typically is analyzed well by the // mass spectrometer // This is the chainsaw command to be run on the terminal String chainsawCommand = chainsaw + " -c " + enzyme + " -s " + specificity + " -m " + minimumPeptideLength + " -M " + maximumPeptideLength + " -n " + numMissedCleavages + " " + fastaFilePath; log.Info("Digesting database using ChainSaw"); // perform in-silico digestion String chainsawOutput = ExecuteShellCommand.executeCommand(chainsawCommand); log.Info(chainsawCommand); log.Debug(chainsawOutput); // parse new tsv file DigestedFastaFile df = Loader.parseDigestedFasta(outputTSVFile); // this tool automatically outputs file in the same folder as the input database, move file to output folder, if (keepFile) { ExecuteShellCommand.executeCommand("move " + outputTSVFile + " " + InputFileOrganizer.preExperimentFilesFolder); InputFileOrganizer.ChainSawResult = InputFileOrganizer.preExperimentFilesFolder + "\\" + IOUtils.getBaseName(outputTSVFile); } else { ExecuteShellCommand.executeCommand("rm " + outputTSVFile); } //ExecuteShellCommand.executeCommand("rm " + outputIndexFile); return(df); }
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile, bool _includeCarbamidoModification, bool _includeRetentionTime, double _retentionTimeWindow) { includeCarbamidoModification = _includeCarbamidoModification; includeRetentionTime = _includeRetentionTime; retentionTimeWindow = _retentionTimeWindow; log.Debug("Constructing graph..."); SequenceToPeptide = new Dictionary <String, Peptide>(); peptides = new List <Peptide>(); AccesstionToProtein = fastaFile.getAccessionToFullSequence(); addPeptides(digestedFastaFile.getDigestedPeptideArray()); log.Debug("Done constructing graph."); }
public static Database loadExclusionDatabase(FastaFile fasta, DigestedFastaFile digestedFasta) { return(new Database(fasta, digestedFasta)); }
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile, bool _includeCarbamidoModification, bool _includeRetentionTime) : this(fastaFile, digestedFastaFile, _includeCarbamidoModification, _includeRetentionTime, DEFAULT_RETENTION_TIME_WINDOW) { }
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile) : this(fastaFile, digestedFastaFile, DEFAULT_INCLUDE_CARBAMIDO_MODIFICATION, DEFAULT_INCLUDE_RETENTION_TIME) { }