[ensembl-dev] using REST to get EPO multispecies alignment
mhobbs_science at optusnet.com.au
mhobbs_science at optusnet.com.au
Thu Mar 10 09:54:14 GMT 2016
Thanks very much Matthieu
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From: "Ensembl developers list" <dev at ensembl.org>
To:"Ensembl developers list" <dev at ensembl.org>
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Sent:Thu, 10 Mar 2016 09:16:31 +0000
Subject:Re: [ensembl-dev] using REST to get EPO multispecies alignment
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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