Generate Spectral Library

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2013 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 14 May 2013
// Yassene

File file = new File(directory);
File[] fileObjList = file.listFiles();
ArrayList list = new ArrayList();
for (int i = 0; i < fileObjList.length; i++) {
	if (fileObjList[i].isFile()){
		list.add(fileObjList[i].getAbsolutePath());				
	}		
} 

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2013 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 14 May 2013
// Yassene

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

//String pathToSpectrastExe = "C:\\Inetpub\\tpp-bin\\spectrast.exe"; 
//String libraryName = "lib"; 
//String pThreshold="0.9"
// spectrast -cNraw -cP0.9 dataset1.xml

String filesList = "";
for (i = pathToPepXML.iterator(); i.hasNext();) {
	element = i.next();
	filesList = filesList + " " + element;	
}

String fullcommand = pathToTPPBinDir + "/spectrast -cN" + outputDirectory + "/" + libraryName + " -cP" + pThreshold + filesList;
System.out.print(fullcommand);					
Process p = null;
BufferedReader br = null;
		
p = Runtime.getRuntime().exec(fullcommand);
		
br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
int c;
StringBuffer sb = new StringBuffer();
while ((c = br.read()) != -1) {
	sb.append((char) c);
	}
br.close();

String stdout = fullcommand + "/n" + sb.toString();

String outputFile = outputDirectory + "/" + libraryName + ".splib";
File outputFileObject = new File(outputFile);

Value

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
// 14 November 2012
// Yassene

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.File;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.lang.ProcessBuilder;

//String pathToRunTandemJar = "C:\\workflows\\exe\\runTandem.jar"; 
String pathToTandemExe = pathToTPPBinDir + "/tandem";
String pathToTandem2xmlExe = pathToTPPBinDir + "/Tandem2XML";

String mzxml_file=mzxmlFile;
String fasta_file=fastaFile;

String fullcommand = "java -jar " + pathToRunTandemJar + " " + pathToTandemExe + " " + mzxml_file + " " + fasta_file;
System.out.print(fullcommand);				
Process p = null;
BufferedReader br = null;

p = Runtime.getRuntime().exec(fullcommand);

br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
int c;
StringBuffer sb = new StringBuffer();
while ((c = br.read()) != -1) {
	sb.append((char) c);
	}
br.close();
String stdout1 = fullcommand + "\n" + sb.toString();

String tandem_output_file = mzxml_file.substring(0, mzxml_file.toLowerCase().lastIndexOf(".")) + ".tandem";
String output_file = mzxml_file.substring(0, mzxml_file.toLowerCase().lastIndexOf(".")) + ".tandem.pep.xml";

//String fullcommand = pathToTandem2xmlExe + " " + tandem_output_file + " " + output_file;
//System.out.print(fullcommand);

ArrayList fullcommand2 = new ArrayList();

fullcommand2.add(pathToTandem2xmlExe);
fullcommand2.add(tandem_output_file);
fullcommand2.add(output_file);

ProcessBuilder builder = new ProcessBuilder(fullcommand2);
builder.redirectErrorStream(true);
Process pr = builder.start();

InputStream is = pr.getInputStream();
InputStreamReader isr = new InputStreamReader(is);
BufferedReader br = new BufferedReader(isr);
String line=null;
String stdout2=null; 
while ((line = br.readLine()) != null) {
	stdout2 = stdout2+line;
	//System.out.println(line);
}

String stdout = stdout1 + "\n-------------------------\n" + stdout2;
//String stdout = stdout1 + "\n" + fullcommand ;
String outputFile = output_file;
File outputFileObject = new File(outputFile);

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
// 14 May 2012
// Yassene

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

String interactfile = pepxmlFile + ".interact.pep.xml";
String fullcommand = pathToTPPBinDir + "//InteractParser " + interactfile + " " + pepxmlFile + " -L" + minPeptideLength;
System.out.print(fullcommand);				
Process p = null;
BufferedReader br = null;
p = Runtime.getRuntime().exec(fullcommand);
br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
int c;
StringBuffer sb = new StringBuffer();
while ((c = br.read()) != -1) {
	sb.append((char) c);
	}
br.close();
String stdout1 = fullcommand + "\n" + sb.toString();

String fullcommand = pathToTPPBinDir + "//DatabaseParser " + interactfile ;
System.out.print(fullcommand);
Process p = null;
BufferedReader br = null;
p = Runtime.getRuntime().exec(fullcommand);
br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
int c;
StringBuffer sb = new StringBuffer();
while ((c = br.read()) != -1) {
	sb.append((char) c);
	}
br.close();
String stdout2 = fullcommand + "\n" + sb.toString();

String fullcommand = pathToTPPBinDir + "//RefreshParser " + interactfile + " " + fastaFile;
System.out.print(fullcommand);
Process p = null;
BufferedReader br = null;
p = Runtime.getRuntime().exec(fullcommand);
br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
int c;
StringBuffer sb = new StringBuffer();
while ((c = br.read()) != -1) {
	sb.append((char) c);
	}
br.close();
String stdout3 = fullcommand + "\n" + sb.toString();

String fullcommand = pathToTPPBinDir + "//PeptideProphetParser " + interactfile + " MINPROB=" + minProbability;
System.out.print(fullcommand);
Process p = null;
BufferedReader br = null;
p = Runtime.getRuntime().exec(fullcommand);
br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
int c;
StringBuffer sb = new StringBuffer();
while ((c = br.read()) != -1) {
	sb.append((char) c);
	}
br.close();
String stdout4 = fullcommand + "\n" + sb.toString();

////running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
//String fullcommand = pathToTPPBinDir + "//ProphetModels.pl -i " + interactfile;
//System.out.print(fullcommand);
//Process p = null;
//BufferedReader br = null;
//p = Runtime.getRuntime().exec(fullcommand);
//br = new BufferedReader(new InputStreamReader( p.getInputStream() ));
//int c;
//StringBuffer sb = new StringBuffer();
//while ((c = br.read()) != -1) {
//	sb.append((char) c);
//	}
//br.close();
//String stdout5 = fullcommand + "\n" + sb.toString();

String stdout = stdout1 + "\n-------\n" + stdout2+ 
                      "\n-------\n" + stdout3 + "\n-------\n" + stdout4;

outputFile=interactfile;
File outputFileObject = new File(outputFile);

Value

Value

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