BioJava:Cookbook:Annotations:Filter

From BioJava

How do I filter sequences based on their species?

The species field of a GenBank SwissProt or EMBL file ends up as an Annotation entry. Essentially all you need to do is get the species property from a sequences Annotation and check to see if it is what you want.

The species property name depends on the source: for EMBL or SwissProt it is "OS" for GenBank it is "Organism".

The following program will read in Sequences from a file and filter them according to their species. The same general recipe with a little modification could be used for any Annotation property.

import java.io.*;
 
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
 
public class FilterEMBLBySpecies {
  public static void main(String[] args) {
 
    try {
      //read an EMBL file specified in args[0]
      BufferedReader br = new BufferedReader(new FileReader(args[0]));
      SequenceIterator iter = SeqIOTools.readEmbl(br);
 
      //the species name to search for (specified by args[1]);
      String species = args[1];
 
      //A sequenceDB to store the filtered Seqs
      SequenceDB db = new HashSequenceDB();
 
      //As each sequence is read
      while(iter.hasNext()){
        Sequence seq = iter.nextSequence();
        Annotation anno = seq.getAnnotation();
 
        //check the annotation for Embl organism field "OS"
        if(anno.containsProperty("OS")){
 
          String property = (String)anno.getProperty("OS");
 
          //check the value of the property, could also do this with a regular expression
          if(property.startsWith(species)){
            db.addSequence(seq);
          }
        }
      }
 
      //write the sequences as FASTA
      SeqIOTools.writeFasta(System.out, db);
    }
    catch (Exception ex) {
      ex.printStackTrace();
    }
  }
}