[Biojava-dev] Biojava3 and GenBank files

[Scooter Willis]

That would be great. If you look at the Uniprot code that would also serve as a good template for setting features.

----- Reply message -----
From: "Thiago Satake" <maruco at gmail.com>
To: "Scooter Willis" <HWillis at scripps.edu>
Cc: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>
Subject: [Biojava-dev] Biojava3 and GenBank files
Date: Mon, Jun 11, 2012 4:43 pm



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<mailto: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<mailto: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
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--
Thiago Seito Satake
Tel: (041) 88428444