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
<[EMAIL PROTECTED]> wrote:
-------- Original Message --------
Subject: large genbank data
Date: Wed, 28 May 2008 18:02:48 +0800
From: Rey Vincent Babilonia <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
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
*/
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