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 <[email protected]> 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 - [email protected] > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
