Hello, I could create methods which can read and write fastq files. However, I downloaded the BioJava source code and in folder src/org/biojava/bio/program are following files:
* AbstractFastqReader.java * AbstractFastqWriter.java * Fastq.java * FastqBuilder.java * FastqReader.java * FastqVariant.java * FastqWriter.java * IlluminaFastqReader.java * IlluminaFastqWriter.java * SangerFastqReader.java * SangerFastqWriter.java * SolexaFastqReader.java * SolexaFastqWriter.java These looks to me that is exactly what I need, but unfortunately I do not how to use it. On Sat, 27 Mar 2010 20:13:02 +0530 jitesh dundas wrote: > Hello, > > I could not find much info on that Q.Try the Biojava API for methods. > > However, I would think of this problem as a simple text file parsing > using BufferedReader and ByteInputStream based I/p ..You have to read > the text file content byte by byte using a while loop. The loop will > detect each column using the patterns (i haven't worked on fastq or > biojava that much) in the text file, e.g. space tabs.. > Why don't you try reading this fastq file as a simple text file in > java. > > This is assuming that fastq are text files..Correct me if I am wrong.. > Java tutorial & forums have bulk of egs on that. > > Try writing the code and send the fastq file with the java code if you > face issues.. > > Hope this helps.. > > Regards, > jd _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
