[ensembl-dev] database model and API versions

Duarte Molha duartemolha at gmail.com
Tue Apr 28 09:51:48 BST 2015


Ok ... thanks Magali.

I believe the latest VEP now supports an --assembly flag to allow it to
annotate against a specific assembly.
Can we not have the same flag on the registry ?
How does VEP do it?
This would be incredibly useful because I would not have to  create new
scripts to support a different assembly.

I could just download all the tables and just tell the registry which one
to use.

Please correct me if I am wrong but your proposed solution would mean I
would have to bypass the registry completely and I would need to create
each each adaptor from scratch and thus I would need to alter a lot of my
scripts to support both assemblies.

"--assembly GRCh37" would be a much more preferable route.

Best regards,

    Duarte




=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================

On 27 April 2015 at 17:48, mag <mr6 at ebi.ac.uk> wrote:

>  Hi Duarte,
>
> The mysql dumps for GRCh37 are available on the ftp site as well
> ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/
>
> I would recommend having only one copy of human for release 79.
> So if you are interested in the GRCh37 data, you can download the database
> from ftp://ftp.ensembl.org/pub/grch37/release-79/mysql/ rather than
> ftp://ftp.ensembl.org/pub/release-79/mysql/
>
> If you need both databases on the same server, you can access a given
> database directly rather than using the registry.
> my $human_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
>     -HOST => 'localhost',
>     -PORT => 3306,
>     -USER => 'user',
>     -DBNAME => 'homo_sapiens_core_79_37',
>     -SPECIES => 'homo_sapiens',
>     -GROUP => 'core'
> );
>
>
> Hope that helps,
> Magali
>
> On 27/04/2015 17:11, Duarte Molha wrote:
>
> Thanks Magali
>
>  But I think you have not understtod my question.
>
>  Assume I want to download the databases to my local computer and use the
> perl API 79 to query the latest 79_37 database instead of the default 79_38
> .
> Previously, I just had to download the mysql tables corresponding to the
> api I was using to fetch the data correctly, however, now you have broken
> that link API->Underlying_assembly
>
>  So how do I tell my scripts what database to query?
>
>  My local sql will all be under the same port.
>
>  Best regards
>
>  Duarte
>
>
>
>  =========================
>      Duarte Miguel Paulo Molha
>           http://about.me/duarte
> =========================
>
> On 27 April 2015 at 17:01, mag <mr6 at ebi.ac.uk> wrote:
>
>>  Hi Duarte,
>>
>> The archive 75 website is still based on the release 75 API.
>>
>> For the dedicated GRCh37 website though, we have used a data freeze from
>> release 75 and have since been updating the website and underlying
>> databases along with the main release.
>> The GRCh37 databases are available on our main MySQL server on port 3337
>> (instead of the default 3306 which will give you access to GRCh38 databases)
>>
>>
>> Hope that helps,
>> Magali
>>
>>
>> On 27/04/2015 16:56, Duarte Molha wrote:
>>
>>   Dear developers
>>
>>  On your GRCh37 archive site you say this:
>>
>>  ===========================
>>
>>  About this archive
>>
>> This archive is based on Ensembl Release 75 data, and gives continuing
>> access to human assembly GRCh37, as well as all our other release 75
>> species (data freeze March 2014) for comparative purposes. Human variation
>> and regulation data has since been updated in March 2015.
>>
>> The API and website will be updated in tandem with the release of the
>> main Ensembl website (*currently version 79*), and we will also
>> periodically update this site with new data human, which will be announced
>> in this panel.
>> MySQL dumps of human databases on the most recent schema version are
>> available on our FTP site <ftp://ftp.ensembl.org/pub/grch37/>.
>>
>>  =========================
>>
>>  It was my understanding that an API version was directly linked to a
>> specific assembly. So I thought that if I wanted to query the latest GRCh37
>> assembly I would need to use the api v75 and if I wanted to use a local
>> database, I would download the corresponding sql tables for that version.
>>
>>  However, according to this announcement, I can now use the V79 api and
>> query the old assembly... How is this accomplished ?
>> What you I have to do on my scripts to make sure I am querying the 37
>> version even though I am using the latest API?
>>
>>  Sorry, I hope this is not a stupid question but I am a bit confused.
>>
>>  Best regards
>>
>>  Duarte
>>
>>
>>
>>  =========================
>>      Duarte Miguel Paulo Molha
>>           http://about.me/duarte
>> =========================
>>
>>
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>
>
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