[ensembl-dev] difference behaviour of fetch_by_region in GRCh37 and GRCH38

[mag]

Hi Duarte,

The API still relies on the information being in the database.
For GRCh38, we have stored entries in the seq_region_synonym table for 
'chr22' and the like.
For GRCh37, these entries are not stored, hence the API does not know 
what chr22 means.

I suggest using real chromosome names :-)


Regards,
Magali

On 24/03/2016 10:49, Duarte Molha wrote:
> Hi Devs
>
> I was just wondering why a strange behavior is different between the 
> GRCH37 database and GRCh38 using the same API
>
> I am currently using APIv83 and when I connect to my local GRCh37 
> database, the method:
>
> my $slice_targeted = $slice_adaptor->fetch_by_region( 'chromosome', 
> $chr, $start, $end, $strand);
>
> fails if $chr contains the prefix "chr" like in chr22
> but it works fine against my also local GRCh38 database
>
> since they are both using the same api should the behavior not be the 
> same?
>
> Best regards
>
> Duarte
>
>
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