[ensembl-dev] MarkerAdaptor

[Will Chow]

cheers magali for the help.

have a good weekend.

Will
On 28 Feb 2014, at 16:04, mag <mr6 at ebi.ac.uk> wrote:

> Hi Will,
> 
> The markers currently stored in the core databases are being loaded using the scripts in
> ensembl-analysis/scripts/markers
> This does not use the API.
> 
> 
> Regards,
> Magali
> 
> On 28/02/2014 16:00, Will Chow wrote:
>> Hi Dev'ers,
>> 
>> I'm trying to store some Marker data in to a ensembl schema database using the API.
>> 
>> I've created the marker features as per.
>>  $marker = Bio::EnsEMBL::Map::Marker->new
>>                             (undef, undef,
>>                  $left_primer, $right_primer, 400,
>>                  80, $ms1, [$ms1, $ms2], [$mloc1, $mloc2]);
>> added the marker synonyms and marker_map_locations (e.g. ms & msloc);
>> 
>> then i guess would use the marker_adaptor->store($marker);
>> 
>> however looking at the MarkerAdaptor.pm code for the store call, Line 405
>> 
>>     403     # Loop through all MapLocations and store if needed
>>     404     foreach my $loc( @{$marker->get_all_MapLocations} ){
>>     405       # Dunno how to implement this :( Just bomb out
>>     406       $self->throw( 'Storing of MapLocation objects is not yet implemented' )
>>     407     }
>> 
>> Does this mean the MapLocations which I've linked to the marker feature won't be stored? Has anyone used the API to store marker data?
>> 
>> Or maybe its just friday, and I've stared at the code for too long this week.
>> 
>> 
>> thanks,
>> 
>> Will
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140228/f69883b6/attachment.html>