[ensembl-dev] Deleting DnaAlignFeatures?

[Dan Bolser]

Thanks Andy,

I'll just have my script output a 'DELETE' SQL file, then run that on
the database.


Cheers,
Dan.

On 17 May 2012 08:50, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi Dan,
>
> The DnaAlignFeatureAdaptor is one way only. We've never had the need to implement a remove AFAIK. Since all Ensembl DBs have a surrogate key deletion of just the feature reasonably simple thing to do. It obviously gets a little bit harder when you propagate the delete to supporting features, if your alignment features are linked to exons/transcripts.
>
>
> All the best,
>
> Andy
>
> Sent from my mobile.
>
> On 16 May 2012, at 18:38, Dan Bolser <dbolser at ebi.ac.uk> wrote:
>
>> On 16 May 2012 18:34, Dan Bolser <dbolser at ebi.ac.uk> wrote:
>>> Hi,
>>>
>>> How can I use a DnaAlignFeature adaptor and some DnaAlignFeatures
>>> retrieved from within it to delete those features from the database?
>>>
>>> Here is a snippet of code:
>>>
>>> $reg->load_registry_from_db(
>>> ...
>>>    my $dafa = $reg->
>>>      get_adaptor( $species, 'core', 'DnaAlignFeature' );
>>> ...
>>>            my $dafs = $dafa->fetch_all_by_hit_name( $hit_name );
>>>            my @best = sort { ... } @$dafs
>>>
>>>            delete_dafs_somhow( @best[1:-1] )
>>
>> Sorry, I meant to say "@best[1..$#best]" obviously ;-)
>>
>>
>>> ...
>>>
>>>
>>>
>>> Cheers,
>>> Dan.
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/