////Uses OpenMS to create a concacenated reversed database, reversed at each peptide segment with C terminus kept
//public static String CreateConcacenatedDecoyDB(String fastaFilePath, String outputFolder)
//{
// String DecoyDBGenerator= IOUtils.getAbsolutePath( InputFileOrganizer.DecoyDatabaseOpenMSEXE);
// String enzyme = "Trypsin";
// String outputFilePath = Path.Combine( outputFolder , IOUtils.getBaseName(fastaFilePath)+"_decoyConcacenated.fasta");
// String method = "reverse";
// String decoyString = GlobalVar.DecoyPrefix;
// String command = DecoyDBGenerator+" -in "+ fastaFilePath + " -out " +outputFilePath + " -enzyme "+ enzyme + " -decoy_string " + decoyString +" -decoy_string_position prefix "
// +" -method " +method +" -Decoy:keepPeptideNTerm false -Decoy:keepPeptideCTerm true";
// Logger.debug("Command: " +command);
// //Logger.debug("running OpenMS DecoyDatabase.exe to generate concacenated decoy database");
// ExecuteShellCommand.executeCommand(command);
// Logger.debug("DecoyDatabase at: "+outputFilePath);
// return outputFilePath;
//}
//public static String CreateConcacenatedDecoyDB_TPP(String fastaFilePath, String outputFolder)
//{
// String DecoyDBGenerator = IOUtils.getAbsolutePath(InputFileOrganizer.TPPDecoyGenerator);
// String outputFilePath = Path.Combine(outputFolder, IOUtils.getBaseName(fastaFilePath) + "_TPPDECOY.fasta");
// String decoyString = GlobalVar.DecoyPrefix;
// String command = "\""+DecoyDBGenerator + "\" -t \"" + decoyString + "\" \"" + fastaFilePath + "\" \"" + outputFilePath + "\"";
// Logger.debug("Command: " + command);
// //Logger.debug("running OpenMS DecoyDatabase.exe to generate concacenated decoy database");
// ExecuteShellCommand.executeCommand(command);
// Logger.debug("DecoyDatabase at: " + outputFilePath);
// return outputFilePath;
//}
//public static String CreateConcacenatedDecoyDB_improved(String fastaFilePath, String outputFolder)
//{
// //Fixes the problem of openMS-CometIDX chain.
// //in the faulty method, real sequences such as ABCDKEFGR
// //would be processed by openMS into DCBAKGFER
// //in comet idx that would turn into decoy peptide sequences: DCBAK, GFER, and DCBAKGFER
// //However, in an "offline" comet processing, the sequences with 1 misscleavage should be: DCBAK, GFER, and GFEKDCBAR
// //This new method ensures that happens.
// String outputFilePath = Path.Combine(outputFolder, IOUtils.getBaseName(fastaFilePath) + "_decoyConcacenated.fasta");
// outputFilePath = DecoyConcacenatedDatabaseGenerator.GenerateConcacenatedDecoyFasta(fastaFilePath, outputFilePath); //pretty redundant to re-set the outputFilePath, but it is what it is
// return outputFilePath;
//}
//Uses Comet to generate an IDX database file from a fasta file
public static String FastaToIDXConverter(String fastaFilePath, String outputFolder)
{
Logger.debug("Converting fasta to idx");
String cometEXE = InputFileOrganizer.CometExe;
String cometParams = InputFileOrganizer.CometParamsFile;
String command = cometEXE + " -D" + fastaFilePath + " -P" + cometParams + " -i";
Logger.debug("Command: " + command);
ExecuteShellCommand.executeCommand(command);
String outputfileName = IOUtils.getBaseName(fastaFilePath) + ".fasta.idx";
String currentOutputDirectory = Path.Combine(IOUtils.getDirectory(fastaFilePath), outputfileName); //because comet just generates the idx wherever the fasta originally is located
String targetOutputDirectory = Path.Combine(outputFolder, outputfileName);
if (File.Exists(targetOutputDirectory))
{
return(targetOutputDirectory);
}
else
{
ExecuteShellCommand.MoveFile(currentOutputDirectory, outputFolder);
}
Logger.debug("DecoyDatabase at: " + targetOutputDirectory);
return(targetOutputDirectory);
}
public static Dictionary <String, Double> calculateRetentionTime(String peptideList)
{
log.Debug("Calculating retention times using RTCalc...");
Console.WriteLine("Calculating peptide retention times using RTCalc... This might take a while");
// Dictionary<String, RetentionTime> rtmap = new Dictionary<String,
// RetentionTime>();
// This is the output file path
String rtOutput = InputFileOrganizer.preExperimentFilesFolder + "\\" + IOUtils.getBaseName(peptideList) + "_rtOutput.txt";
String rtCalc = InputFileOrganizer.RTCalc; // tool location
// This is the RTCalc command to be run on the terminal
String rtCalcCommand = rtCalc + " COEFF=" + InputFileOrganizer.RTCalcCoeff + " PEPS=" + peptideList + " OUTFILE=" + rtOutput;
// perform in-silico digestion
log.Debug(rtCalcCommand);
String rtTerminalOutput = ExecuteShellCommand.executeCommand(rtCalcCommand);
log.Debug(rtTerminalOutput);
// parse rtcalc output
Dictionary <String, Double> parsedOutput = Loader.parseRTCalcOutput(rtOutput);
// foreach (String peptideSequence in parsedOutput.Keys) {
// // unsure whether or not d is a rt peak or rt start
// double d = parsedOutput[&*peptideSequence);
// rtmap.Add(peptideSequence, convertDoubleToRetentionTime(d));
// }
log.Debug("Parsed " + parsedOutput.Count + " retention times");
// remove files
//ExecuteShellCommand.executeCommand("rm " + rtOutput);
log.Debug("Done calculating retention times using RTCalc.");
return(parsedOutput);
}
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 static void deleteFile(String fileName)
{
String command = "rm " + fileName;
ExecuteShellCommand.executeCommand(command);
}