BioJava:Cookbook:Sequence:Edit

From BioJava

How can I Edit a Sequence?

Sometimes you will want to modify the order of Symbols in a SymbolList or Sequence. For example you may wish to delete some bases, insert some bases or overwrite some bases in a DNA Sequence. BioJava SymbolLists have a method called edit(Edit e) that takes an Edit object and performs that edit on the SymbolList. The Edit object takes arguments that specify where the edit should begin, how many residues will be changed and a SymbolList that will replace the residues.

It is worth noting that many BioJava implementations of Sequence and SymbolList do not allow edit operations as this may invalidate underlying Features or Annotations. The best strategy is to make a copy of the Symbols in the Sequence or SymbolList and operate on those.

import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
 
public class EditExamples {
  public static void main(String[] args) throws Exception{
    //you can't actually edit a sequence
    Sequence seq = DNATools.createDNASequence("atggct", "seq");
 
    //so you need to get a copy of the Symbols in it
    //using a "copy constructor"
    SimpleSymbolList syms = new SimpleSymbolList(seq);
 
    //add to the end, while overwriting 0 symbols, "cc"
    Edit e = new Edit(seq.length()+1, 0, DNATools.createDNA("cc"));
    //apply the edit
    syms.edit(e);
    //should now be atggctcc
    System.out.println(syms.seqString());
 
    //insert at the start, while overwriting 0 Symbols "tt"
    e = new Edit(1, 0, DNATools.createDNA("tt"));
    syms.edit(e);
    //should now be ttatggctcc
    System.out.println(syms.seqString());
 
    //insert at position 4, overwriting 0 symbols "aca"
    e = new Edit(4, 0, DNATools.createDNA("aca"));
    syms.edit(e);
    //should now be ttaacatggctcc
    System.out.println(syms.seqString());
 
    //overwrite at position 2, 3 bases with "ggg"
    e = new Edit(2, 3, DNATools.createDNA("ggg"));
    syms.edit(e);
    //should now be tgggcatggctcc
    System.out.println(syms.seqString());
 
    //delete from the start 5 bases (overwrite 5 bases with nothing)
    e = new Edit(1, 5, SymbolList.EMPTY_LIST);
    syms.edit(e);
    //should now be atggctcc
    System.out.println(syms.seqString());
 
    //now a more complex example
 
    //overwrite positions two and three with aa and then insert tt
    e = new Edit(2, 2, DNATools.createDNA("aatt"));
    syms.edit(e);
    //should now be aaattgctcc
    System.out.println(syms.seqString());
  }
}