BioJava:Tutorial:MultiAlignClustalW

From BioJava

by Dickson S. Guedes

There are many questions in the mailing lists about "How to perform a Multiple Sequence Alignment using BioJava", but Biojava DOESN'T make multi-alignments by itself, so I'll post some code that I've created in my theses.

Ok. Let's Go...

First, this is how you call methods from ClustalWAlign's class.

MultAlignTest.java

/**
 * MultAlignTest.java
 * 
 * @author Dickson S. Guedes (guedes@unisul.br)
 * @author Israel S. de Medeiros (israelbrz@gmail.com)
 * @version 1.0	
 * @serialData 20060120 
 * 
 * Copyright (c) 2006.
 * 
 */
 
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
 
 
 
public class MultAlignTest {
 
	public static void main(String[] args) {
		try {
			// First create an instance for ClustalWAlign
			ClustalWAlign alSequences = new ClustalWAlign("FakeSequencesFile");
			
			// Now only add Sequences to alSequences
			alSequences.addSequence(DNATools.createDNASequence("atttagatgatatatcggccactagcatcgactacgactgacatcgt","Sequence1"));
			alSequences.addSequence(DNATools.createDNASequence("atagatgatggccatcgatcgagacgggatgactgacgtacgt","Sequence2"));
			alSequences.addSequence(DNATools.createDNASequence("atagatgatggccatcgatcgaagacggatgactgacgtacgt","Sequence3"));
			alSequences.addSequence(DNATools.createDNASequence("atagatgatggccatggatgactgacgtacgt","Sequence4"));
			alSequences.addSequence(DNATools.createDNASequence("atagatgatggccatccgatgaggacgtacgt","Sequence5"));
 
			// Here you are calling the core of class - The Multi-Alignment!
			alSequences.doMultAlign();
 
			// Now, you want to see results. Well...
			SequenceIterator it = alSequences.getIterator();
			
			while (it.hasNext()) {
				Sequence seq = it.nextSequence();
				System.out.println(seq.getName() + ": " + seq.seqString());
			}
			
			System.out.print("GUIDE TREE:" + alSequences.getGuideTree());
			
		} catch (Throwable t) {
			t.printStackTrace();
		}
	}
}

Now, the class that calls ClustalW as a external process:

ClustalWAlign.java

/**
 * ClustalWAlign.java
 * 
 * @author Dickson S. Guedes (guedes@unisul.br)
 * @author Israel S. de Medeiros (israelbrz@gmail.com)
 * @version 1.0	
 * @serialData 20060120 
 * 
 * Copyright (c) 2006.
 * 
 */
 
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
 
import org.biojava.bio.BioException;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.db.HashSequenceDB;
import org.biojava.bio.seq.db.SequenceDB;
import org.biojava.bio.seq.io.SeqIOTools;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.utils.ChangeVetoException;
 
public class ClustalWAlign {
	
	// This are Constants, but I'll change...
	private static final String fileFormat = "fasta";
	private static final String clustalwPath = "C:\\JAVA\\Workspace\\clustalw\\";
	
	private SequenceDB 		dbSequences;
	private String			strAlfa;
	private String 			fileName;
	private String			guideTree;
	
 
	public ClustalWAlign () {
		
		this.dbSequences = new HashSequenceDB();
		this.strAlfa = "DNA";
		
	}
	
	public ClustalWAlign (String fileName) {
		
		this.dbSequences = new HashSequenceDB();
		this.strAlfa = "DNA";
		this.fileName = fileName;
		
	}
	
	
	public ClustalWAlign (SequenceIterator itSequences, String strAlfa) throws BioException, ChangeVetoException {
		
		this.dbSequences = new HashSequenceDB();
		
		this.strAlfa = strAlfa;
		
		while (itSequences.hasNext()) {
			this.dbSequences.addSequence(itSequences.nextSequence());
		}
		
	}
	
	public ClustalWAlign (BufferedReader bufSequences, String strAlfa) throws BioException, ChangeVetoException {
		
		this.dbSequences = new HashSequenceDB();
		this.strAlfa = strAlfa;
		
		SequenceIterator itSequences = (SequenceIterator)SeqIOTools.fileToBiojava(fileFormat,strAlfa,bufSequences);	
		
		while (itSequences.hasNext()) {
			this.dbSequences.addSequence(itSequences.nextSequence());
		}		
	}
	
	public void addSequence(Sequence seqSequence) throws BioException, ChangeVetoException {
		this.dbSequences.addSequence(seqSequence);
	}
	
	public void removeSequence(String idSequence) throws BioException, ChangeVetoException {
		this.dbSequences.removeSequence(idSequence);
	}
	
	public int doMultAlign() {	
		int exitVal=999;
		
		try {
			
			FileOutputStream newFile = new FileOutputStream(clustalwPath + fileName + ".input");
			
			SeqIOTools.writeFasta(newFile,this.dbSequences);
			
			Runtime rt = Runtime.getRuntime();
			
			String [] strComando =  
								{clustalwPath+"ClustalW.EXE",
								"/infile="  + clustalwPath + fileName + ".input",
								"/outfile=" + clustalwPath + fileName + ".output",
								"/output=" + fileFormat,
								"/align"};
			
			Process proc = rt.exec(strComando);
			
			InputStream stdin = proc.getInputStream();
			BufferedReader br = new BufferedReader(new InputStreamReader(stdin));
			
			while ( (br.readLine()) != null) {
				// do nothing only read "stdout" from ClustalW
                                // you can put a System.out.print here to prints
                                // the output from ClustalW to console.
			}
			
			exitVal = proc.waitFor();
			if (exitVal == 0) {
				this.dbSequences = SeqIOTools.readFasta(
						new BufferedInputStream(
								new FileInputStream(
										clustalwPath + 
										fileName + 
								".output")),
								AlphabetManager.alphabetForName(strAlfa)
				);
				
				this.guideTree = fileToString(
										clustalwPath + 
										fileName + 
										".dnd"
										);
			}
		
		} catch (Throwable t) {
			t.printStackTrace();
		}
		return (exitVal);
	}
		
	public void setAlphabet(String strAlfa) {
		this.strAlfa = strAlfa;
	}
	
	public SequenceDB getDBSequences() {
		return this.dbSequences;
	}
	
	public SequenceIterator getIterator() {
		return this.dbSequences.sequenceIterator();
	}
	
	public String getGuideTree() {
		return guideTree;
	}
 
	public void setGuideTree(String guideTree) {
		this.guideTree = guideTree;
	}	
	
	private String fileToString(String fileName) {
		
		String fileBody = "";
		boolean endOfFile = false;
		
		try	{
			
			FileReader fileClustalW = new FileReader(fileName);
			BufferedReader fileBuffer = new BufferedReader(fileClustalW);
			
			while (!endOfFile) {
				String fileLine = fileBuffer.readLine();
				
				if (fileLine == null) {
					endOfFile = true;
				} else {
					fileBody = fileBody.concat(fileLine);
				}
			}
			fileBuffer.close();
			
		} catch (IOException e)	{
			e.printStackTrace();
		}
 
		return fileBody;
	}
}