Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data: X!Tandem

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2012 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 25 June 2012
// Yassene

String stdout = "beanshell \n";

String fullcommand = "java -jar " + mzxmlDecomposerExe + " " + mzxmlFile + " " + nrOfDaughters + " " + outputDirectory;
stdout = stdout + "running " + fullcommand + "\n";		
exec(fullcommand);

class FileExtFilter implements FileFilter {
public FileExtFilter(String ext) {
this.ext = ext;
}
public boolean accept(File file) {
return file.getName().endsWith(ext);
}
String ext = null;
}

File dirObj = new File(outputDirectory);
String extension = "zip";
File[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));
List filelist = new ArrayList();
for (int i = 0; i < fileObjList.length; i++) {
	filelist.add(fileObjList[i].getAbsolutePath());
}

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2012 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 25 June 2012
// Yassene

String stdout = "beanshell \n";

File folder = new File(outputDirectory);
String fileslist= " ";
File[] listOfFiles = folder.listFiles(); 
for (int i = 0; i < listOfFiles.length; i++) 
{
   if (listOfFiles[i].isFile() && listOfFiles[i].getName().endsWith("pep.xml")) 
   {
   fileslist = fileslist + " " + listOfFiles[i].getAbsolutePath();
   }
}
String fullcommand = "java -jar " + pepxmlComposerExe + fileslist;
stdout = stdout + "running " + fullcommand + "\n";
exec(fullcommand);


for (int i = 0; i < listOfFiles.length; i++) 
{
   if (listOfFiles[i].isFile() && !(listOfFiles[i].getName().contains("composed"))) 
   {
   	rm(listOfFiles[i].getAbsolutePath());
   }
}

File folder = new File(outputDirectory);
String fileslist;
File[] listOfFiles = folder.listFiles(); 
for (int i = 0; i < listOfFiles.length; i++) 
{
   if (listOfFiles[i].isFile()) 
   {
   fileslist = listOfFiles[i].getName();
	stdout= stdout + "\n" + fileslist;
   }
}

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2012 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 25 June 2012
// Yassene

String nrOfDaughters = nrOfDaughters;
String mzxmlFile = mzxmlFile;
String mzxmlDecomposerExe = mzxmlDecomposerExe;
File fastaFileZipped = new File(fastaFileZipped);
File tandemExe = new File(tandemExe);
File runTandemExe = new File(runTandemExe);
String outputDirectory = mzxmlFile+"_xtandemResults";
String pepxmlComposerExe = pepxmlComposerExe;
File tandem2xmlExe = new File(tandem2xmlExe);

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