[ensembl-dev] Fwd: Re: Transcript variation alleles - - Bayesian Filter detected spam

Pontus Larsson Pontus.Larsson at ebi.ac.uk
Thu Feb 10 09:41:54 GMT 2011

Hi Andrea,

Yes, the default behavior in 61 is the same as pre-61, i.e. no failed 
variations returned. It's not strictly true to say that any methods that 
return multiple objects filters out failed variations though, if you get 
multiple objects by a call that explicitly specifies a list of objects 
to fetch (e.g. fetch_all_by_VariationFeatures on 
TranscriptVariationAdaptor or fetch_all_by_name_list on 
VariationAdaptor), you will get the failed variations irrespective of 
what the flag on the DBAdaptor says.
But the 'unspecific' fetch methods (e.g. fetch_all_by_Slice, 
fetch_all_by_Population etc.) will exclude the failed ones by default. 
Also, a minor detail: you don't specify the flag on the object adaptor 
but on the db adaptor, i.e. 
$obj_adaptor->db->include_failed_variations() (since it's a global 
property that affects all object adaptors created for the connection).

I hope this is clear

On 10/02/2011 00:01, Andrea Edwards wrote:
> Hi Will
> Just to be 100% clear about this answer, are you saying that methods 
> that return more than one object don't return failed variants (in v61 
> and all previous versions) but in v61 you can call the method 
> include_failed_variations on the adaptors? If i am reading that right 
> you dont need to check the data returned by the adaptors for failed 
> variants as they are excluded by default.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110210/0bdb1f3b/attachment.html>

More information about the Dev mailing list