BioJava:Cookbook:Annotations:List2

From BioJava

When you read in a annotated sequence file such as from GenBank or EMBL there is a lot more detailed information than just the raw sequence. If the information has a sensible location then it ends up as a Feature. Each of these features can be annotated with specific information.

The following program reads in a Genbank or EMBL file and outputs annotation information about each of the CDS features

/**
 * Class to load an EMBL or Genbank sequence file and output annotation information about the CDS features.
 */
 
//Java libraries
import java.io.*;
import java.util.*;
//BioJava libraries
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
//BioJava extension libraries
import org.biojavax.*;
import org.biojavax.ontology.*;
import org.biojavax.bio.*;
import org.biojavax.bio.seq.*;
 
public class ExtractInformation {
  //Create the RichSequence object
  RichSequence richSeq;
 
  //ExtractInformation constructor
  public ExtractInformation(String fileName){
    //Load the sequence file
    try {
      richSeq = RichSequence.IOTools.readGenbankDNA(new BufferedReader(new FileReader(fileName)),null).nextRichSequence();
    }
    catch(FileNotFoundException fnfe){
      System.out.println("FileNotFoundException: " + fnfe);
    }
    catch(BioException bioe1){
      System.err.println("Not a Genbank sequence trying EMBL");
      try  {
        richSeq = RichSequence.IOTools.readEMBLDNA(new BufferedReader(new FileReader(fileName)),null).nextRichSequence();
      }
      catch(BioException bioe2){
        System.err.println("Not an EMBL sequence either");
        System.exit(1);
      }
      catch(FileNotFoundException fnfe){
        System.out.println("FileNotFoundException: " + fnfe);
      }
    }
    //Filter the sequence on CDS features
    FeatureFilter ff = new FeatureFilter.ByType("CDS");
    FeatureHolder fh = richSeq.filter(ff);
 
    //Iterate through the CDS features
    for (Iterator <Feature> i = fh.features(); i.hasNext();){
      RichFeature rf = (RichFeature)i.next();
 
      //Get the strand orientation of the feature
      char featureStrand = rf.getStrand().getToken();
 
      //Get the location of the feature
      String featureLocation = rf.getLocation().toString();
 
      //Get the annotation of the feature
      RichAnnotation ra = (RichAnnotation)rf.getAnnotation();
 
      //Use BioJava defined ComparableTerms 
      ComparableTerm geneTerm = new RichSequence.Terms().getGeneNameTerm();
      ComparableTerm synonymTerm = new RichSequence.Terms().getGeneSynonymTerm();
      //Create the required additional ComparableTerms
      ComparableTerm locusTerm = RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");
      ComparableTerm productTerm = RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");
      ComparableTerm proteinIDTerm = RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");
 
      //Create empty strings
      String gene = "";
      String locus = "";
      String product = "";
      String geneSynonym = "";
      String proteinID = "";
 
      //Iterate through the notes in the annotation 
      for (Iterator <Note> it = ra.getNoteSet().iterator(); it.hasNext();){
        Note note = it.next();
 
      //Check each note to see if it matches one of the required ComparableTerms
        if(note.getTerm().equals(locusTerm)){
          locus = note.getValue().toString();
        }
        if(note.getTerm().equals(productTerm)){
          product = note.getValue().toString();
        }
        if(note.getTerm().equals(geneTerm)){
          gene = note.getValue().toString();
        }
        if(note.getTerm().equals(synonymTerm)){
          geneSynonym = note.getValue().toString();
        }
        if(note.getTerm().equals(proteinIDTerm)){
          proteinID = note.getValue().toString();
        }
      }
      //Outout the feature information
      System.out.println(locus + "  " + gene + "  " + geneSynonym + "  " + proteinID + "  " + product + "  " + featureStrand + "  " + featureLocation);
    }
  }
 
  //Main method
  public static void main(String args []){
    if (args.length != 1){
      System.out.println("Usage: java ExtractInformation <file in Genbank or EMBL format>");
      System.exit(1);
    }
    else {
      new ExtractInformation(args[0]);
    }
  }
}