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

[Rey Vincent Babilonia]

Hi Mark,

What is the maximum sequence length that a RichSequence can handle?

java -Xms1024m -Xmx1256m -jar loader.jar
.
16:09:00,173  INFO Loader:296 - D:\AE005174.gbk is readable.
16:09:06,704  INFO Loader:326 - Loading sequence AE005174 with 
identifier 56384585, length 5528445 and alphabet DNA...
org.hibernate.PropertyAccessException: Exception occurred inside getter 
of org.biojavax.bio.seq.SimpleRichSequence.sequenceLength

Rey Vincent Babilonia wrote:
> 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
  */