[ensembl-dev] Fwd: Re: Transcript variation alleles - - Bayesian Filter detected spam
Pontus.Larsson at ebi.ac.uk
Thu Feb 10 09:41:54 GMT 2011
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.
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