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

Michael Barton mail at michaelbarton.me.uk
Thu Dec 9 18:10:06 UTC 2010

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_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

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:

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.



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.

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