BioJava:CookBook:Blast:Parser

From BioJava

How Do I Parse A BLAST Result?

Much of the credit for this example belongs to Keith James.

A frequent task in bioinformatics is the generation of BLAST search results. BioJava has the ability to parse "Blast-like" output such as Blast and HMMER using a trick that makes the BLAST output into SAX events that can be listened for by registered listeners.

The basic pipeline is as follows:

Blast_output -> Generate SAX events  --> Convert SAX events --> Build result objects --> Store 
them in a list.

InputStream--> BLASTLikeSAXParser --> SeqSimilartyAdapter --> BlastLikeSearchBuilder --> List

The API is very flexible however for most purposes the following simple recipe will get you what you want.

import java.io.*;
import java.util.*;
 
 
import org.biojava.bio.program.sax.*;
import org.biojava.bio.program.ssbind.*;
import org.biojava.bio.search.*;
import org.biojava.bio.seq.db.*;
import org.xml.sax.*;
import org.biojava.bio.*;
 
public class BlastParser {
  /**
   * args[0] is assumed to be the name of a Blast output file
   */
  public static void main(String[] args) {
    try {
      //get the Blast input as a Stream
      InputStream is = new FileInputStream(args[0]);
 
      //make a BlastLikeSAXParser
      BlastLikeSAXParser parser = new BlastLikeSAXParser();
 
 
      // try to parse, even if the blast version is not recognized.
      parser.setModeLazy();
 
 
      //make the SAX event adapter that will pass events to a Handler.
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
 
      //set the parsers SAX event adapter
      parser.setContentHandler(adapter);
 
      //The list to hold the SeqSimilaritySearchResults
      List results = new ArrayList();
 
      //create the SearchContentHandler that will build SeqSimilaritySearchResults
      //in the results List
      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new DummySequenceDBInstallation());
 
      //register builder with adapter
      adapter.setSearchContentHandler(builder);
 
      //parse the file, after this the result List will be populated with
      //SeqSimilaritySearchResults
      parser.parse(new InputSource(is));
 
      //output some blast details
      for (Iterator i = results.iterator(); i.hasNext(); ) {
        SeqSimilaritySearchResult result =
            (SeqSimilaritySearchResult)i.next();
 
        Annotation anno = result.getAnnotation();
 
        for (Iterator j = anno.keys().iterator(); j.hasNext(); ) {
          Object key = j.next();
          Object property = anno.getProperty(key);
          System.out.println(key+" : "+property);
        }
        System.out.println("Hits: ");
 
        //list the hits
        for (Iterator k = result.getHits().iterator(); k.hasNext(); ) {
          SeqSimilaritySearchHit hit =
              (SeqSimilaritySearchHit)k.next();
          System.out.print("\tmatch: "+hit.getSubjectID());
          System.out.println("\te score: "+hit.getEValue());
        }
 
        System.out.println("\n");
      }
 
    }
    catch (SAXException ex) {
      //XML problem
      ex.printStackTrace();
    }catch (IOException ex) {
      //IO problem, possibly file not found
      ex.printStackTrace();
    }
  }
}