[Bioperl-l] Asking for advice on full EMBL extraction

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed May 6 23:32:32 EDT 2009

Hi Brian,
I hate to say it but it worked OK for me using rel_ann_mus_01_r99.dat.gz and simple example Bio::SeqIO code from bugzilla
It's not using more than 1GB memory on our server and doesn't segfault.

Send me your example code and I'll give it a go if you like.

Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of brian li
> Sent: Thursday, 7 May 2009 1:11 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Asking for advice on full EMBL extraction
> Dear all,
>      Recently I have to extract all EMBL entries and put them into
> relational database so that our report generation tool can access the
> data.
>      I used Bio::SeqIO::embl to get entries one by one, but can not
> move on when dealing with big million-line entries. Segmentation Fault
> popped. And as currently SeqBuilder is not integrated into
> Bio::SeqIO::embl, SeqBuilder->add_unwanted_slot can't help
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2823).
>      Is there another way to get entires one by one with BioPerl?
> Brian
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