[Biojava-dev] [Fwd: large genbank data]

[Rey Vincent Babilonia]

Hi Mark,

At first it throws an out of memory exception. My workaround is to 
subdivide the sequence file into individual GenBank files.

The error now is that if a GenBank sequence has an 'empty alphabet', it 
does not get loaded to BioSQL. My workaround is to check if 
sequence.getAlphabet().getName() is DNA.

Thanks.

Mark Schreiber wrote:
> Hi -
> 
> Is the code throwing an exception or running out of memory??
> 
> Can you send an example program and the problem you encounter to the list.
> - Mark
> 
> On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia
> <rvincent at asti.dost.gov.ph> wrote:
>>
>> -------- Original Message --------
>> Subject: large genbank data
>> Date: Wed, 28 May 2008 18:02:48 +0800
>> From: Rey Vincent Babilonia <rvincent at asti.dost.gov.ph>
>> To: biojava-l at biojava.org
>>
>> hi,
>>
>> anybody tried uploading a large genbank data (e.g.
>> ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql?
>> load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and
>> it can't read the sequence (maybe because it has 30000+ sequences).
>>
>> thanks.
>>
>> --
>> /**
>>  * @author   Rey Vincent P. Babilonia
>>  * @number   +63 2 426 9760 local 1302
>>  * @pgp      0x383454CF <at> pgp.mit.edu
>>  * @project  Philippine Bioinformatics Solutions
>>  * @program  Philippine e-Science Grid
>>  * @division Research and Development Division
>>  * @agency   Advanced Science and Technology Institute
>>  * @url      http://www.psigrid.gov.ph
>>  */
>>
>>
>> --
>> /**
>>  * @author   Rey Vincent P. Babilonia
>>  * @number   +63 2 426 9760 local 1302
>>  * @pgp      0x383454CF <at> pgp.mit.edu
>>  * @project  Philippine Bioinformatics Solutions
>>  * @program  Philippine e-Science Grid
>>  * @division Research and Development Division
>>  * @agency   Advanced Science and Technology Institute
>>  * @url      http://www.psigrid.gov.ph
>>  */
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-- 
/**
  * @author   Rey Vincent P. Babilonia
  * @number   +63 2 426 9760 local 1302
  * @pgp      0x383454CF <at> pgp.mit.edu
  * @project  Philippine Bioinformatics Solutions
  * @program  Philippine e-Science Grid
  * @division Research and Development Division
  * @agency   Advanced Science and Technology Institute
  * @url      http://www.psigrid.gov.ph
  */