[Bioperl-l] Re: stale links, EMBL loading

Hilmar Lapp hlapp at gmx.net
Mon Jun 16 08:03:35 EDT 2003

On Monday, June 16, 2003, at 02:19  AM, Niels Larsen wrote:

>> What costs the time is mostly building up the
>> Bio::Seq+SeqFeature+Annotation object model and populating it for 
>> every
>> entry. If you don't want the object model to be built, I wouldn't use
>> bioperl. If you do want it to be built and populated, we'd be grateful
>> for suggestions how to build it faster ...
> I meant .dat file (with 100,000) entries where I spoke "entry", sorry. 
> Ok, I
> should then write a faster non-bioperl-OO parser that creates the 
> tables in
> the biosql-schema. That way hopefully I can get my loading done and
> still use bioperl after that. I will tell you when I have it.

What I was referring to was populating the object model in memory, not 
the database, as I was talking about the SeqIO parser. You said you 
could still live with the speed of the parser. In order to speed up 
loading into biosql you may still want to try running several 
load-seqdatabase.pl in parallel on different (.dat) files and see if 
that satisfies your needs, as doing so would come almost for free ...

My $0.02 ...


Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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