BioJava:Cookbook:SeqIO:ABItoSequence

From BioJava

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

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

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);
  }
}