[ensembl-dev] VariationAdaptor::fetch_all_by_Individual not completely deprecated

Will McLaren wm2 at ebi.ac.uk
Tue Oct 26 09:28:15 BST 2010


OK I see what you mean now. Thanks for spotting this - the method is
indeed deprecated.

I will remove it from the documentation and API.

Cheers

Will

On 25 October 2010 16:56, Ma, Man Chun John <manchunjohn-ma at uiowa.edu> wrote:
> Hi,
>
> Sorry for the confusion. I meant
> InvididualGenotypesAdaptor::fetch_all_by_by_Individual.
>
>
> John MC Ma
> Graduate Assistant
> Kwitek Lab
> Department of Internal Medicine
> 3125E MERF
> 375 Newton Road
> Iowa City IA 52242
> -----Original Message-----
> From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
> McLaren
> Sent: Monday, October 25, 2010 4:02 AM
> To: Ma, Man Chun John
> Cc: dev at ensembl.org
> Subject: Re: [ensembl-dev] VariationAdaptor::fetch_all_by_Individual not
> completely deprecated
>
> Hi John,
>
> I'm not entirely sure I know which methods you are referring to -
> neither VariationAdaptor::fetch_all_by_Individual or
> CompressedGenotypeAdaptor::fetch_all_by_Individual exist in our current
> API.
>
> You are correct, accessing individual genotypes can be slow; this is
> because the genotypes are compressed into chunks containing all
> genotypes in a 100kb block. Therefore if you are randomly accessing
> genotypes from different blocks this can be slow as each time the API
> has to retrieve a 100kb block of genotypes and filter out the
> appropriate one(s). The schema is optimised for retrieving large numbers
> of genotypes along a contiguous genomic region, so if you configure your
> scripts to access data in a similar way you should see speed increases.
>
> This is an issue we are looking into, especially since the number of
> genotypes we store is increasing rapidly - the latest release of Ensembl
> human contains ~2.5 billion genotypes!
>
> Cheers
>
> Will McLaren
> Ensembl Variation
>
> On 22 October 2010 19:26, Ma, Man Chun John <manchunjohn-ma at uiowa.edu>
> wrote:
>> Hi,
>>
>> I have noticed that CompressedGenotypeAdaptor::fetch_all_by_Individual
>> has been deprecated as of August 2007
>> (http://listserver.ebi.ac.uk/mailing-lists-archives/ensembl-dev/msg031
>> 96 .html), yet the method VariationAdaptor::fetch_all_by_Individual,
>> which directly calls
>> CompressedGenotypeAdaptor::fetch_all_by_Individual, still exists to
>> this day. There is no reason to keep a non-functional method in
>> Ensembl-Variation, and should be removed.
>>
>> On the other hand, I have noticed that, probably due to the said
>> database restructuring, accessing IndividualGenotypes through the
>> Ensembl API is very slow-- are there any way that I can improve the
>> speed?
>>
>> Any help is appreciated!
>>
>> Cheers,
>>
>> John MC Ma
>> Graduate Assistant
>> Kwitek Lab
>> Department of Internal Medicine
>> 3125E MERF
>> 375 Newton Road
>> Iowa City IA 52242
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>>
>




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