[Biojava-dev] Biojava3 and GenBank files

[Thiago Satake]

Hi Scooter,


Yesterday I was taking a look at FASTA Reader and I started working on
GenBank Reader using the same approach. I have created some class called
GenBankReader, GenBankReaderHelper, GenericGenBankHeaderFormat and
GenericGenBankHeaderPerse. Now, I am working on the implementation of
process method.

I not sure if it is ok for biojava project, but I would like to read
GenBank file like we are reading fasta file:
LinkedHashMap<String, DNASequence> a =
GenBankReaderHelper.readGenBankDNASequence(new File(args[0]));

I think that will be useful.

If my peace of code make sense I can share with you if you like.


Thanks



On 11 June 2012 10:28, Scooter Willis <HWillis at scripps.edu> wrote:

> Thiago
>
> We don't have GenBank support in BioJava3. I have it on my todo list and
> will see if I can make some progress this week.
>
> Thanks
>
> Scooter
>
> On 6/10/12 4:36 PM, "Thiago Satake" <maruco at gmail.com> wrote:
>
> >Hi,
> >
> >I need to read and write genbank files, gff, etc...
> >
> >Can I parse GenBank files using biojava3 or should I use biojava-legacy
> >for
> >that ?
> >
> >
> >Thanks
> >
> >--
> >Thiago Seito Satake
> >_______________________________________________
> >biojava-dev mailing list
> >biojava-dev at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


-- 
Thiago Seito Satake
Tel: (041) 88428444