How can I turn an ABI trace into a BioJava Sequence?

A lot of Bioinformatics begins with the reading of a piece of DNA (or several pieces) using a DNA sequencer. A typical output is an ABI trace. BioJava contains a Class called ABITrace that will parse either an ABITrace file or URL or a byte[] and store its values for programmatic retrieval.

The following program is modified from a version kindly supplied by Matthew Pocock. It demonstrates the creation of a BioJava Sequence from an ABI trace file.

BioJava 1.3 now contains a more generic chromatogram API that supports both ABI and SCF files. An example program that uses this API is shown below.

Reading ABI

```java import java.io.*;

import org.biojava.bio.*; import org.biojava.bio.program.abi.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.impl.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.symbol.*;

public class Trace2Seq {

 public static void main(String[] args)
 throws Exception {
   File traceFile = new File(args[0]);

   //the name of the sequence
   String name = traceFile.getName();

   //read the trace
   ABITrace trace = new ABITrace(traceFile);

   //extract the Symbols
   SymbolList symbols = trace.getSequence();
   //make a fully fledged sequence
   Sequence seq = new SimpleSequence(symbols, name, name, Annotation.EMPTY_ANNOTATION);

   //write it to STDOUT
   SeqIOTools.writeFasta(System.out, seq);
 }

} ```

Generic Solution

```java import java.io.*;

import org.biojava.bio.*; import org.biojava.bio.chromatogram.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.impl.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.symbol.*;

public class Trace2Seq {

 public static void main(String[] args)
 throws Exception {
   File traceFile = new File(args[0]);

   //the name of the sequence
   String name = traceFile.getName();

   //read the trace
   Chromatogram trace = ChromatogramFactory.create(traceFile);

   //extract the Symbols
   SymbolList symbols = ChromatogramTools.getDNASequence(trace);
   //make a fully fledged sequence
   Sequence seq = new SimpleSequence(symbols, name, name, Annotation.EMPTY_ANNOTATION);

   //write it to STDOUT
   SeqIOTools.writeFasta(System.out, seq);
 }

} ```