Re: Fwd: read fasta entry by entry
"P. Troshin" <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CAAT4F8ngW3SeqC9aQ8jZdYPYQWe=g_2bY2zbLet8ks8SAMTVgQ@mail.gmail.com> |
Hi Andreas, Sorry I am a bit short of time at the moment. I think that simply moving this code into core as is is not going to help anyone, it could just cause confusion. At a very list someone need to write a bit of documentation for the users. We need to unify different BioJava FASTA parsers. I wanted to do with someone else help, within GSOC, but the project did not go ahead. So may be next year? Regards, Peter On 12 May 2012 00:10, Andreas Prlic <[email protected]> wrote: > Hi Peter and Scooter, > > It would be great to improve the documentation for this on the wiki > and to consolidate the two Fasta parsers. Peter: utility methods are > better in -core, rather than in the specialized modules. They are hard > to find that way and create unexpected module dependencies. Any chance > to move this to the core module? > > Thanks, > > Andreas > > On Wed, May 9, 2012 at 4:41 PM, P. Troshin <[email protected]> wrote: > > Hi, > > > > Try SequenceUtil.readFasta(InputStream in). It would read sequences > > regardless of the type. > > This is a small tool in the disorder predictor package. > > > > Hope that helps, > > Regards, > > Peter > > > > > > > > On 9 May 2012 04:45, Mic <[email protected]> wrote: > > > >> Hello, > >> I have found this > >> http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example, > but > >> it looks like that the whole fasta file is stored in memory. > >> > >> Is it possible to read any fasta entry by entry i.e. without > >> to specify whether it is DNA/Protein? > >> > >> Thank you in advance. > >> > >> Mic > >> _______________________________________________ > >> 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