[Biojava-l] Reading and writting Fastq files

[Michael Heuer]

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


On Sat, 27 Mar 2010, xyz wrote:

> Hello,
> I would like to use org.biojava.bio.program.fastq in order to read and
> write Illumina fastq files.
>
> Are there any BioJava examples how to work with fastq files?
>
> On Sat, 27 Mar 2010 17:40:21 +0530
> jitesh dundas wrote:
>
> > Hello,
> >
> > Fasta files are  normal text files. Try parsing using normal text
> > parsing methods.
> >
> > If you could be more specific & tell me the format details,then I
> > could help better.
> >
> > btw,try using biojava ,the easy & better option if you want.
> >
> > Regards,
> > Jitesh Dundas
> >
> > On 3/27/10, xyz <mitlox at op.pl> wrote:
> > > Hello,
> > > I could not find any examples how to read or write fastq files.
> > >
> > > import java.io.BufferedReader;
> > > import java.io.FileNotFoundException;
> > > import java.io.FileReader;
> > > import org.biojava.bio.program.fastq.FastqReader;
> > >
> > > public class Fastq2Fasta {
> > >   public static void main(String[] args) throws
> > > FileNotFoundException  { BufferedReader br = new BufferedReader(new
> > > FileReader("fastq2fasta.fasta"));
> > >   }
> > > }
> > >
> > > Are there any examples how to work with fastq files?
> > >
> > > Thank you in advance.
> > >
> > > Best regards,
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
>
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