BioJava:Cookbook:Sequence:SubSequence

From BioJava

Contents 1 How do I get a subsection of a Sequence? 1.1 Getting a Sub - Sequence 1.2 Printing a Sub - Sequence 1.3 Complete Listing

How do I get a subsection of a Sequence?

Given a Sequence object we might only be interested in examining the first 10 bases or we might want to get a region between two points. You might also want to print a subsequence to an OutputStream like STDOUT how could you do this?

BioJava uses a biological coordinate system for identifying bases. The first base is numbered 1 and the last base index is equal to the length of the sequence. Note that this is different from String indexing which starts at 0 and proceedes to length -1. If you attempt to access a region outside of 1...length an IndexOutOfBoundsException will occur.

Getting a Sub - Sequence

SymbolList symL = null;
 
    //code here to generate a SymbolList
 
    //get the first Symbol
    Symbol sym = symL.symbolAt(1);
 
    //get the first three bases
    SymbolList symL2 = symL.subList(1,3);
 
    //get the last three bases
    SymbolList symL3 = symL.subList(symL.length() - 3, symL.length());

Printing a Sub - Sequence

//print the last three bases of a SymbolList or Sequence
    String s = symL.subStr(symL.length() - 3, symL.length());
    System.out.println(s);

Complete Listing

import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
 
public class SubSequencing {
  public static void main(String[] args) {
    SymbolList symL = null;
 
    //generate an RNA SymbolList
    try {
      symL = RNATools.createRNA("auggcaccguccagauu");
    }
    catch (IllegalSymbolException ex) {
      ex.printStackTrace();
    }
 
    //get the first Symbol
    Symbol sym = symL.symbolAt(1);
 
    //get the first three bases
    SymbolList symL2 = symL.subList(1,3);
 
    //get the last three bases
    SymbolList symL3 = symL.subList(symL.length() - 3, symL.length());
 
    //print the last three bases
    String s = symL.subStr(symL.length() - 3, symL.length());
    System.out.println(s);
  }
}