[ensembl-dev] "Member adaptor" deprecated warning in Ensembl Compara perl API

[Miguel Pignatelli]

Hi Samiul,

Sorry for the outdated documentation, we will fix that.

We have split the MemberAdaptor into GeneMemberAdaptor (for genes) and 
SeqMemberAdaptor for products (protein and transcripts).
Since you are looking for an Ensembl gene, you should be using the 
GeneMemberAdaptor.

This should work without warnings:

my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 
'compara', 'GeneMember'); ## Note 'GeneMember' here instead of 'Member'

  my $member = 
$member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','ENSG00000004059');

Cheers,

M;


On 31/05/13 16:30, Samiul Hasan wrote:
> Hello,
>
> I keep receiving the following warning when trying to use the Member
> adaptor class:
>
> ------------------ DEPRECATED ---------------------
>
>              The Member adaptor is deprecated in favour of the more
> specific GeneMember and SeqMember adaptors.
>
>              Please update your code (change the adaptor) here:
>
> STACK toplevel ./test2.pl:53
>
> You are using the version 71 of the API. The old methods / objects are
> available for compatibility until version 74 (included)
>
> ---------------------------------------------------
>
> (line 42) my $member_adaptor =
> Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'Member');
>
> (line 53) my $member =
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','ENSG00000004059');
>
> Is there more specific documentation detailing what the change should
> be? I tried going through the Ensembl Compara tutorial but it still
> follows the old API methods.
>
> Best wishes, Samiul
>
> *S/amiul Hasan,/*
>
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-- 

Miguel Pignatelli, PhD

Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
Room A3-33
Phone + 44 (0) 1223 494 598
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