[Biojava-l] Reading and writting Fastq files

[xyz]

Do not worry. I wrote following code:

import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.biojava.bio.program.fastq.Fastq;
import org.biojava.bio.program.fastq.FastqBuilder;
import org.biojava.bio.program.fastq.FastqReader;
import org.biojava.bio.program.fastq.FastqWriter;
import org.biojava.bio.program.fastq.IlluminaFastqReader;
import org.biojava.bio.program.fastq.IlluminaFastqWriter;

public class Fastq2Fasta {

  public static void main(String[] args) throws FileNotFoundException,
  IOException { 
    FileInputStream inputFastq = new
  FileInputStream("fastq2fasta.fastq"); FastqReader qReader = new
  IlluminaFastqReader();

    FileOutputStream outputFastq = new
    FileOutputStream("fastq2fastaTrim.fastq"); FastqWriter qWriter =
    new IlluminaFastqWriter();


    for (Fastq fastq : qReader.read(inputFastq)) {
      System.out.println(fastq.getDescription());
      System.out.println(fastq.getSequence());
      String trimSeq = fastq.getSequence().substring(0,
    fastq.getSequence().length() - 6); System.out.println(trimSeq);
      System.out.println(fastq.getQuality());
      String trimQual = fastq.getQuality().substring(0,
    fastq.getQuality().length() - 6); System.out.println(trimQual);

      FastqBuilder trimFastq = new FastqBuilder();
      trimFastq.withDescription(fastq.getDescription());
      trimFastq.appendSequence(trimSeq);
      trimFastq.appendQuality(trimQual);
      
      qWriter.write(outputFastq, trimFastq.build());
    }
  }
}

and the input fastq file is:
@HWI-EAS406:5:1:0:1390#0/1
GGGTGATGGCCGCTGCCGATGGCGTCAAAACCCACC
+HWI-EAS406:5:1:0:1390#0/1
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOAAAAAA
@HWI-EAS406:5:1:0:1390#0/1
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
+HWI-EAS406:5:1:0:1390#0/1
PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPBBBBBB
@HWI-EAS406:5:1:0:1390#0/1
GGGTGATGGCCGCTGCCGATGGCGTCAAACCCCACC
+HWI-EAS406:5:1:0:1390#0/1
QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQCCCCCC

Unfortunately, I get the following error:
HWI-EAS406:5:1:0:1390#0/1
GGGTGATGGCCGCTGCCGATGGCGTCAAAACCCACC
GGGTGATGGCCGCTGCCGATGGCGTCAAAA
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOAAAAAA
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Exception in thread "main" java.io.IOException: sequence
HWI-EAS406:5:1:0:1390#0/1 not fastq-illumina format, was fastq-sanger
at
org.biojava.bio.program.fastq.IlluminaFastqWriter.validate(IlluminaFastqWriter.java:41)
at
org.biojava.bio.program.fastq.AbstractFastqWriter.append(AbstractFastqWriter.java:67)
at
org.biojava.bio.program.fastq.AbstractFastqWriter.write(AbstractFastqWriter.java:143)
at
org.biojava.bio.program.fastq.AbstractFastqWriter.write(AbstractFastqWriter.java:125)
at Fastq2Fasta.main(Fastq2Fasta.java:37) Java Result: 1

What did I wrong?

On Sun, 28 Mar 2010 00:27:16 -0400 (EDT)
Michael Heuer wrote:

> 
> Sorry, I haven't written up an example for the Biojava Cookbook yet.
> 
> The FASTQ package javadoc API is at
> 
> http://www.biojava.org/docs/api/org/biojava/bio/program/fastq/package-summary.html
> 
> If you want to read Illumina format FASTQ files, use
> 
> FastqReader reader = new IlluminaFastqReader();
> for (Fastq fastq : reader.read(new File("in.fastq")))
> {
>   // ...
> }
> 
>    michael