[BioRuby] Ensembl API for ruby

[jan aerts (RI)]

All,

I committed the first version of a ruby API to the bioruby-annex SVN on
rubyforge. Although it is far from completed, it does already have its
uses. Thought it would be good to commit as soon as possible so you guys
get an idea of what the API would look like.
I would like to follow the excellent perl API as much as possible
(http://www.ensembl.org/info/software/core/core_tutorial.html).


What it does at the moment:
* All tables of the core database are covered by ActiveRecord classes.
* A Slice object represents a continuous region of a genome. Slices can
be used to obtain sequence, features or other information from a
particular region of interest.
* Coordinates can be transfered from one coordinate system to another. I
hope I tested this thorougly enough (but still am a bit squeemish about
it).

What is not implemented yet:
* A whole bunch of methods that are available to the perl objects that I
would like to 'copy' to the ruby API.
* The Variation and Compara databases.
* The 'project' and 'transform' methods for features and slices (as
explained on the perl tutorial mentioned above).

To get this code, please go to
http://rubyforge.org/projects/bioruby-annex/ You can export the code
using SVN with the following command (without quotes):
"svn checkout svn://rubyforge.org/var/svn/bioruby-annex". There should
be a subdirectory 'ensembl-api', containing the API itself, the sample
script, tests and of course all documentation.

I've created a gem (available in the top-directory of the SVN export),
but can't test if it actually works. Can someone please test it for me?

Toshiaki: if the code works and the gem can be installed on other
systems, could you please do a file release for the gem-file?

Others: if people are interested to help me to develop this API, please
let me know.

Thanks,
jan.

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

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