[BioRuby] Bio Assembly Plugin

[Chase Miller]

Francesco,

Looking over the code, it looks like I never got around to generalizing bio::assembly to work with multiple parsers. This is long overdue and I'm going to work on it today. 

Chase

On Dec 27, 2010, at 8:28 AM, Francesco Strozzi <francesco.strozzi at gmail.com> wrote:

> Hi Chase,
> I will have a look for sure. Good to know you will create a plugin for this, so it will be easy to share your code with BioRuby and add new features. A Bio::Assembly module does not exist in BioRuby at the moment, so it will make more sense also for me to keep the plugin as a general Bio::Assembly "container" where you or me or everybody else can add new parsers for different file formats.
> 
> Cheers
> 
> P.S. It seems the plugin system is getting ground very fast! :-)
> 
> On Mon, Dec 27, 2010 at 14:11, Chase Miller <chmille4 at gmail.com> wrote:
> Hi Francesco
> 
> Currently, Bio::Assembly only has an ace parser, but I it should be straightforward to add a CAF ( or whatever ) parser.  Take a look at the code (https://github.com/chmille4/bioruby) and let me know if you have any questions.
> 
> I'm in the process of turning this into a plugin. I was thinking of turning it into a standalone ace parser plugin, but maybe it makes more sense to keep it as a bio-assembly plugin, especially if we can add another parser :) .
> 
> Chase
> 
> 
> 
> On Mon, Dec 27, 2010 at 6:54 AM, Francesco Strozzi <francesco.strozzi at gmail.com> wrote:
> Thanks! I will have a look.
> 
> 
> On Mon, Dec 27, 2010 at 12:39, Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>wrote:
> 
> > Hi,
> >
> > http://github.com/chmille4/bioruby
> >
> > http://lists.open-bio.org/pipermail/bioruby/2010-September/001480.html
> >
> > On Mon, 27 Dec 2010 12:25:26 +0100
> > Francesco Strozzi <francesco.strozzi at gmail.com> wrote:
> >
> > > Hi Bioruby coders,
> > >
> > > I want to start a Bioruby Assembly Plugin, where I'd like to put parsers
> > for
> > > common used formats like ACE, CAF and maybe MAF that is used by the Mira
> > > assembler. For what I have seen the Bioruby Core does not provide this
> > type
> > > of parsers yet. If someone else is doing something similar please let me
> > > know, so we can avoid duplicate the same code...
> > >
> > > Cheers
> > >
> > > --
> > >
> > > Francesco
> > > _______________________________________________
> > > BioRuby Project - http://www.bioruby.org/
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> 
> 
> 
> --
> 
> Francesco
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
> 
> -- 
> 
> Francesco
>