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.

```java 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();
   }
 }

} ```