[ensembl-dev] newbie with Ensembl API- alignments

[Emily Pritchard]

Hi Manuel

Have you seen our API course on EBI Train Online:
http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop

The Core section will introduce you to the API itself, and the Compara 
module for alignments.

Hope this helps

Emily

On 13/01/2014 13:32, Manuel Rodríguez Pascual wrote:
> I am just starting working with Ensembl API. I am not really 
> experienced neither with Ensembl or bioinformatics itself,so I am 
> stuck in a problem that seems to be easy to solve.
>
>
> As a test and proof of concept, I am interested to retrieve 
> information of a comparison in phylip format. In particular, the 
> provided example
> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Alignments?align=548&db=core&g=ENSG00000171105&r=19%3A7112266-7294045 
> <http://www.ensembl.org/Homo_sapiens/Gene/Compara_Alignments?align=548&db=core&g=ENSG00000171105&r=19%3A7112266-7294045>
>
> when exported into a phylip format,
>
> http://www.ensembl.org/Homo_sapiens/Export/Output/Location/Alignment?align=548;db=core;g=ENSG00000171105;output=alignment;r=19:7112266-7294045;format=phylip;_format=Text 
> <http://www.ensembl.org/Homo_sapiens/Export/Output/Location/Alignment?align=548;db=core;g=ENSG00000171105;output=alignment;r=19:7112266-7294045;format=phylip;_format=Text>
>
> I have however seen that the employment of wget is discouraged and the 
> Ensembl API should be used instead.
>
> Reading the available documentation, I fell that I should use the 
> Compara API Tutorial,
> http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html 
> <http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html>
>
> but I don't really understand it or how to apply it to my objective.
>
> The question is, can anyone orient me on how to proceed?
>
>
>
> Thanks for your attention,
>
>
>
> Manuel
>
>
> -- 
> Dr. Manuel Rodríguez-Pascual
> skype: manuel.rodriguez.pascual
> phone: (+34) 913466173 // (+34) 679925108
>
> CIEMAT-Moncloa
> Edificio 22, desp. 1.25
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> 28040- MADRID
> SPAIN
>
>
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-- 
Dr Emily Pritchard
Ensembl Outreach Officer

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

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