[BioRuby] The first BioRuby IRC conference on Dec 19th

Raoul Bonnal bonnalraoul at ingm.it
Fri Dec 10 11:45:16 UTC 2010

Got it.
It's a good idea.
Sorry I use the term Scaffolder but it's a different thing it's more like a scaffold generator code for developing bioruby libraries.

We can packit as a bioruby gem with my lib.

Also George wrote a library, asking for the plugin guidelines time ago, we could pack it too.

Il giorno 09/dic/2010, alle ore 19.10, Michael Barton ha scritto:

> Thanks Pjotr. I wrote it for my own needs doing genome assembly on a 7MBp
> microbe. At the moment I'm doing my own mini-code freeze so that I can finish
> the website and documentation for releasing version 0.4.
> Here's a bit more detail which may be of interest:
> The YAML format maps on to a DSL for the Scaffolder::Region class.
> ---
>  some_class:
>    some_attr: "value"
> The above YAML corresponds to a DSL which uses Ruby's metaprogramming. The top
> level name corresponds to a class and the second level indentations correspond
> to the attributes on the instance of that class. So the above YAML would fetch
> the subclass of Scaffolder::Region named SomeClass, create a new instance, and
> call 'some_method' on this instance with the parameter "value".
> All you would need to do to define this class is as follows.
> class SomeClass << Scaffolder::Region
>  attribute :some_attr
> end
> I tried to design it so that the vocabulary of the YAML scaffold definition is
> completely extensible. See the Scaffolder::Region#attribute method for more
> details - http://bit.ly/eMImcn
> Here's the slides from a short presentation I gave on it recently also:
> http://bit.ly/cwH2Xm.
> I agree that really large YAML files may be a problem with memory requirements.
> However I'm working on small increments developments so far. I've yet to
> encounter it though but hopefully will be able to solve it when I reach it.
> Any suggestions from the bioruby community are very welcome.
> Cheers
> Mike
> On Thu, Dec 09, 2010 at 06:45:53PM +0100, Pjotr Prins wrote:
>> On Thu, Dec 09, 2010 at 12:06:58PM -0500, Michael Barton wrote:
>>> I have also written a genome scaffolder in Ruby.
>>> The lastest doc is located at - http://bit.ly/ho2UtW
>>> I hope to release this within the next week or two.
>> That is a very nice idea - it would be great if we can get rid of
>> gff3. And it is perfect for a plugin.
>> I only wonder how YAML will hold up with really big files.
>> Pj.
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

More information about the BioRuby mailing list