Return structural variants by ID in Variation/VEP endpoints

[nuno-agostinho]

Description

ENSVAR-5793: Return structural variants (SVs) by their ID when using Variation/VEP endpoints.

The information displayed for SVs is based on their Ensembl Variation page: for instance, esv1815690

Requires Ensembl/ensembl-variation#1029.

Use case

Users request that these endpoints return SVs (e.g., esv1815690). Currently, they only return non-SVs (e.g., rs699).

Possible Drawbacks

If all IDs are non-SVs, the code will take the same time as before; otherwise, the code looks for the mismatched IDs in the SV table.

Also, some SVs may hit the memory limit, such as in the case of nsv3901821, and return an error message: ERROR: Cannot allocate memory.

Testing

Unit tests added (but failing because they require Ensembl/ensembl-variation#1029).

Some examples

• http://wp-np2-11.ebi.ac.uk:9300/vep/human/id/esv1815690
• http://wp-np2-11.ebi.ac.uk:9300/variation/human/esv1815690

# POST variation/human
curl -d '{ "ids" : ["esv1815690", "rs699", "cnvi0111251"] }' -H "Content-Type: application/json" http://wp-np2-11.ebi.ac.uk:9300/variation/human

# POST vep/human/id
curl -d '{ "ids" : ["esv1815690", "rs699", "cnvi0111251"] }' -H "Content-Type: application/json" http://wp-np2-11.ebi.ac.uk:9300/vep/human/id

Documentation changes

Check the following documentation updates in my sandbox:

• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/variation_id
• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/variation_post
• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/vep_id_get
• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/vep_id_post

Changelog

[/variation/:species/id] Return structural variants by their ID
[/variation/:species] Return structural variants by their ID
[/vep/:species/id] Return structural variants by their ID
[/vep/:species] Return structural variants by their ID

[dglemos]

The documentation specifies which type of ID is supported: http://rest.ensembl.org/documentation/info/vep_id_get
Maybe you could update the docs to make it clear SV IDs are also supported.

[nuno-agostinho]

Hey @dglemos, I updated documentation on the following pages to include structural variant ID examples:

• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/variation_id
• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/variation_post
• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/vep_id_get
• http://wp-np2-11.ebi.ac.uk:9300/documentation/info/vep_id_post

[nwillhoft]

Hi @nuno-agostinho, please could I check if this is for Release 111 or 112? Thanks!

[nuno-agostinho]

Hi @nwillhoft, this is for 112, so no need to rush. Still waiting for an approval from @dglemos. Thanks for asking!

[nwillhoft]

Approving PR based on code review carried out by Variation team.