[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

----- Original Message -----
From: "Ensembl developers list" <dev at ensembl.org>
To:"Ensembl developers list" <dev at ensembl.org>
Cc:
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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