[ensembl-dev] using REST to get EPO multispecies alignment

Matthieu Muffato muffato at ebi.ac.uk
Thu Mar 10 09:16:31 GMT 2016


Hi Matthew

There is a bug on 
http://rest.ensembl.org/documentation/info/compara_species_sets . 
"species_set_group" shouldn't be empty.

In your case, the group would be "mammals", and 
http://rest.ensembl.org/alignment/region/homo_sapiens/8:144276224-144276304?content-type=application/json;aligned=0&method=EPO&species_set_group=mammals 
works

In the meantime, if you follow the link from any multiple alignment on 
this page http://www.ensembl.org/info/genome/compara/analyses.html#pecan 
the stats page will give you the name of the species-set

Matthieu

On 10/03/16 08:54, mhobbs_science at optusnet.com.au wrote:
> Hi,
>
> I am trying to retrieve an EPO multispecies alignment using the REST API
> (http://rest.ensembl.org/documentation/info/genomic_alignment_region).
>
> The example on this page
> (http://rest.ensembl.org/documentation/info/compara_species_sets) gives
> allowable values for |the "species_set_group" parameter and I would like
> to use "17 eutherian mammals EPO".
>
> This is what
>
> ~: wget
> 'http://rest.ensembl.org/alignment/region/homo_sapiens/8:144276224-144276304?content-type=application/json;aligned=0&method=EPO&species_set_group=17
> eutherian mammals EPO' -O -
> --2016-03-10 19:50:30--
> http://rest.ensembl.org/alignment/region/homo_sapiens/8:144276224-144276304?content-type=application/json;aligned=0&method=EPO&species_set_group=17%20eutherian%20mammals%20EPO
> Resolving rest.ensembl.org (rest.ensembl.org)... 193.62.54.30
> Connecting to rest.ensembl.org (rest.ensembl.org)|193.62.54.30|:80...
> connected.
> HTTP request sent, awaiting response... 400 Bad Request
> 2016-03-10 19:50:33 ERROR 400: Bad Request.
> |
>
> What am I doing wrong? Thanks for any suggestions.
>
> Matthew




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