Re: Is a modification of the FASTA parser for my needs easy or should I implement something else?
"Peter Troshin" <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
There is a nice FastQ parser and many other goodies available from the http://picard.sourceforge.net/command-line-overview.shtml (just download the source code) if you need one. Regards, Peter >>> Andreas Prlic 12/21/11 3:12 PM >>> The fastq parser is in the legacy biojava 1.8 and can still be downloaded if you want. Not sure how hard it would be to migrate it to biojava3. A On Wed, Dec 21, 2011 at 6:44 AM, Hannes Brandstätter-Müller wrote: > On Wed, Dec 21, 2011 at 15:21, Andreas Prlic wrote: >> Hi Hannes, >> >> if this is a more frequently used file format, would be great to get a >> parser for this... Any patches are welcome ! ;-) >> >> Andreas > > I just put together some kludgy thing that works for me now, but there > needs to be something done for this. > I mailed a bit back and forth with Peter, and he pointed me to > http://news.open-bio.org/news/2009/12/nar-fastq-format/ where Biojava > is mentioned to understand that quality information too. I guess that > got lost in the move to 3.0? > > If nothing happens until March/April, I'll pick up this as my pet > project and work to help biojava to support FASTQ and the FASTA/QUAL > format. But until then I'm totally swamped. If someone else (perhaps > the one who wrote the FASTA Parser initially) could pick that up, that > would be great. > > Hannes _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l ************************************************************ Please consider the environment. Do you really need to print this email? _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l