[ensembl-dev] Plant API download?

[Dan Bolser]

On 6 January 2012 13:24, simon andrews (BI)
<simon.andrews at babraham.ac.uk> wrote:
>
>
> -----Original Message-----
>> From: Dan Staines
>> Subject: Re: [ensembl-dev] Plant API download?
>>
>> branch-ensemblgenomes-12-65 now in over ensembl-ap (missing due to internal miscommunication...) so please have another try!
>
> Thanks, it worked fine this time.
>
> A second (possibly minor) problem.  I'm trying to do some processing on the Glycine max genome, and get this warning:
>
> -------------------- WARNING ----------------------
> MSG: Using implicit mapping path between 'chromosome:1.0' and 'scaffold:1.0' coord systems.
> An explicit 'assembly.mapping' entry should be added to the meta table.
> Example: 'chromosome:1.0|chunk:1.0|scaffold:1.0'
>
> FILE: EnsEMBL/DBSQL/CoordSystemAdaptor.pm LINE: 708
> CALLED BY: EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm  LINE: 222
> Ensembl API version = 65
> ---------------------------------------------------
>
> The processing is still working, but is this something I should be concerned about?

I don't think so (unlikely to have any major effects), but we can fix
it for the next  release.


Cheers,
Dan B.

> Cheers
>
> Simon.
>
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