Jason Stajich | 11 May 21:07 2012
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small project

HMMER folks have contributed a module to BioJava to simplify submission of a protein sequence to the HMMER
RESTful API
http://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/
http://hmmer.janelia.org/help/api

Perhaps a BioPerl similar module that wraps up the existing code to submit Bio::Seq objects similar to
other Bio::DB:: or probably better to do Bio::Tools interfaces for interaction with remote
webservices. The code to add this to bioperl is basically already written - the question would be if you
wanted to populate a Bio::Search object with the XML results (Writing a parser for the XML)

http://hmmer.janelia.org/help/api#sending

Jason

Jason Stajich
jason.stajich <at> gmail.com
jason <at> bioperl.org
Leon Timmermans | 14 May 14:38 2012
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Re: small project

On Fri, May 11, 2012 at 9:07 PM, Jason Stajich <jason.stajich <at> gmail.com> wrote:
> HMMER folks have contributed a module to BioJava to simplify submission of a protein sequence to the HMMER
RESTful API
> http://xfam.wordpress.com/2012/05/09/pdb-pfam-mapping/
> http://hmmer.janelia.org/help/api
>
>
> Perhaps a BioPerl similar module that wraps up the existing code to submit Bio::Seq objects similar to
other Bio::DB:: or probably better to do Bio::Tools interfaces for interaction with remote
webservices. The code to add this to bioperl is basically already written - the question would be if you
wanted to populate a Bio::Search object with the XML results (Writing a parser for the XML)
>
> http://hmmer.janelia.org/help/api#sending
>
> Jason

I rather like the Spore concept for this kind of issue. It's a
framework for RESTful webservices that only requires you to write a
description of a webservice (often in json or yaml form) and it will
then generate the code to interact with it from that. A major
advantage is that it's implemented for a range of programming
languages (currently Perl, Python, Ruby, Lua, Clojure, Javascript).
Thinking about this, a wider Bio-Spore project may be a good idea.

Leon

Gmane