[BioRuby] Parsing line-based formats with Ragel

[Ben Woodcroft]

Just wanted to say thanks for pointing this out Artem - can definitely see
myself using it in the future. If only you'd been a few days earlier!

Perhaps idealistically, the state machine might be written once, and then
the last mile be implemented in multiple different Bio* projects.

On 4 June 2012 00:20, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Trust a CS student to start on finite state machines. For us mere
> mortals, here is a good write-up on Ragel principles for Rubyists
>
>  http://zedshaw.com/essays/ragel_state_charts.html
>
> by the much loved Zed :)
>
> Pj.
>
> On Sat, Jun 02, 2012 at 05:06:12PM +0400, Artem Tarasov wrote:
> > Hi guys,
> >
> > I've recently discovered absolutely cool thing called Ragel (
> > http://www.complang.org/ragel/). It is a finite state machine compiler,
> its
> > applications include parsing Cucumber features in Gherkin, parsing HTTP
> > requests in Mongrel, and implementing pack/unpack functions in Rubinius.
> >
> > It can be used for creating parser for any regular language, that
> includes
> > nearly every line-based format. It generates code for C, C++, Objective
> C,
> > D(!), Java, and Go. The speed of generated code is incredible.
> >
> > I wrote a few words more about it in my blog:
> > http://lomereiter.wordpress.com/2012/06/02/ragel-and-bioinformatics/
> >
> > Basically, you write a formal grammar, define which snippets of code to
> > execute on state transitions, and everything just works. As for me, I'm
> > going to implement SAM parser with this tool.
> >
> > It can also be useful for Marjan. I wrote a GFF3 grammar, but it might be
> > incorrect in some places. Here's a basic example of usage:
> > https://github.com/lomereiter/bioragel/blob/master/examples/d/gff3.rl
> >
> >
> >
> > --
> > Artem
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> _______________________________________________
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> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 
--
Ben Woodcroft
http://ecogenomic.org/users/ben-woodcroft <http://www.ecogenomic.org/>