[ensembl-dev] how to use Ensembl API to fetch data from an older release?

[Andy Yates]

Hi there

Absolutely. You can get the version 67 core API from GitHub. 

https://github.com/Ensembl/ensembl/archive/release/67.zip

Or if you cloned the Ensembl API you can switch using a command such as

cd ensembl 
git branch release/67

Best regards

Andy

Sent from my mobile.

> On 5 Dec 2016, at 20:22, Tuo Zhang <taz2008 at med.cornell.edu> wrote:
> 
> Hi Andy,
> 
> Thank you for the detailed explanation. 
> 
> As you suggested, it is better to use an older version of API that was released together with old data. I'm wondering if it's possible to download an old API version for the data release 67, and if yes where to find it?
> 
> Many thanks,
> 
> Tuo
> 
> 
> 
>> On Mon, Dec 5, 2016 at 1:40 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
>> Hi
>> 
>> You can force a specific version/release when you initialise the registry e.g.
>> 
>> Bio::EnsEMBL::Registry->load_registry_from_db(
>>   -HOST => 'ensembldb.ensembl.org',
>>   -USER => 'anonymous',
>>   -DB_VERSION => '67'
>> );
>> 
>> I would urge caution in doing so. We recommend you keep API and data releases in-sync with each other as the schema/APIs may have drifted away from each other in that period. If you do use the current API and old database together then double check any data you get out from it. Should the API throws an error then they are not compatible.
>> 
>> Best regards,
>> 
>> Andy
>> 
>> ------------
>> Andrew Yates - Genomics Technology Infrastructure Team Leader
>> The European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Genome Campus
>> Hinxton, Cambridge
>> CB10 1SD, United Kingdom
>> Tel: +44-(0)1223-492538
>> Fax: +44-(0)1223-494468
>> Skype: andy.yates.ebi
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>> 
>> > On 5 Dec 2016, at 18:29, Tuo Zhang <taz2008 at med.cornell.edu> wrote:
>> >
>> > Dear support,
>> >
>> > I was trying to use the most recent Ensembl Perl API to fetch data from an older release 67 (NCBIM37 for mouse).
>> >
>> > The current API gives me an error message when I used gvf2vcf.pl:
>> > "MSG: Cannot request a slice whose start (148582227) is greater than 145441459 for 7."
>> >
>> > I guess the error is due to accessing a wrong mouse genome assembly. Is there a way I can force the API on a specific release?
>> >
>> > Thanks a lot,
>> >
>> > Tuo
>> >
>> > --
>> > Tuo Zhang, Ph.D.
>> > Research Associate
>> > Genomics Resources Core Facility
>> > Weill Cornell Medical College
>> > 1300 York Ave. Rm. A-162
>> > New York, NY 10021
>> > Tel. 212-746-5076 (O)
>> > taz2008 at med.cornell.edu
>> > _______________________________________________
>> > Dev mailing list    Dev at ensembl.org
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>> 
>> 
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> 
> 
> 
> -- 
> Tuo Zhang, Ph.D.
> Research Associate
> Genomics Resources Core Facility
> Weill Cornell Medical College
> 1300 York Ave. Rm. A-162
> New York, NY 10021
> Tel. 212-746-5076 (O)
> taz2008 at med.cornell.edu
> _______________________________________________
> 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/
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