[ensembl-dev] REST - map endpoint

[Daniel Suveges]

Hi Magali,


Thank you very much, please keep us posted!
Best,
Daniel

From: Dev <dev-bounces at ensembl.org> on behalf of mag <mr6 at ebi.ac.uk>
Reply-To: Ensembl developers list <dev at ensembl.org>
Date: Friday, 16 June 2017 at 14:56
To: "dev at ensembl.org" <dev at ensembl.org>
Subject: Re: [ensembl-dev] REST - map endpoint

Dear Daniel,

Thank you for reporting this, it is definitely not expected behaviour.
We will investigate the problem and let you know when a fix is available.


Kind regards,
Magali
On 16/06/2017 13:50, Daniel Suveges wrote:
Ok, I have to adjust my question: apparently sometimes the query returns the expected coordinates, but mostly the return is empty. I hope this helps.
(On the attached screenshot you can see that the response to the same query sometimes empty, sometimes not.)

Best,
Daniel



From: Dev <dev-bounces at ensembl.org><mailto:dev-bounces at ensembl.org> on behalf of Daniel Suveges <ds26 at sanger.ac.uk><mailto:ds26 at sanger.ac.uk>
Reply-To: Ensembl developers list <dev at ensembl.org><mailto:dev at ensembl.org>
Date: Friday, 16 June 2017 at 13:16
To: Ensembl developers list <dev at ensembl.org><mailto:dev at ensembl.org>
Subject: [ensembl-dev] REST - map endpoint

Hi Guys,


I’m trying to use the map endpoint of the REST service (to map between the human GRCh37 and 38 build) and I’m encountering some unexpected behavior:

Let’s take the variant rs11553699 for example:
it’s GRCh37 coordinates: 12:122216910
it’s GRCh38 coordinates: 12:121779004

If I want to map it’s GRCh37 coordinates to the newer build it works:
http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json

But when I’m trying to do the same in the opposite direction, the ‘mappings’ array is empty in the returned json:
http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json

For other GRCh38 coordinates mapping works, this position has coordinates in both build, so it is not clear to me why the second query seemingly fails.
Thank you very much for your help!

Best,
Daniel




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