[ensembl-dev] Problems with transcript variation adaptor

[Will McLaren]

Hi Gavin,

The code you give works fine for me. Double check that you have all the
correct APIs installed, and that your ensembl-variation API is the same
version as the main ensembl API.

You could also see if there are any clues when you connect to the server, by
adding the verbose option:

$registry->load_registry_from_db(

    -host => 'ensembldb.ensembl.org',

    -user => 'anonymous',

    -port => 5306,

    -verbose = > 1,

);

If you're sure this is OK, try getting a variation adaptor:

my $var_adaptor = $registry->get_adaptor("human", "variation", "variation");

If this works but transcript variation doesn't, then try doing a fresh
install of the ensembl-variation API module.

Will

On 21 February 2011 15:15, Oliver, Gavin <gavin.oliver at almacgroup.com>wrote:

>  Hi,
>
>
>
> I am trying to pull variations associated with a transcript and am having a
> problem whereby the transcript variation adaptor is being flagged as
> ‘undefined’.
>
>
>
> I have tried to simplify the problem below.
>
>
>
> my $registry = 'Bio::EnsEMBL::Registry';
>
>
>
> $registry->load_registry_from_db(
>
>     -host => 'ensembldb.ensembl.org',
>
>     -user => 'anonymous',
>
>     -port => 5306,
>
> );
>
>
>
> my $trv_adaptor = $registry->get_adaptor("human", "variation",
> "transcriptvariation");
>
>
>
> print $trv_adaptor;
>
>
>
> This produces the error “Use of uninitialized value.” for $trv_adaptor in
> the print command.
>
>
>
> Why would $trv_adaptor be undefined at this stage?
>
>
>
>
>
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