[BioRuby] Bio Assembly Plugin

[George Githinji]

Hi,
This definitely is intresting as sometime back I was looking for an CAF
parser.
I have some local dirty CAF parser. It would be interesting to develop a
community CAF parser.
Thanks
George


On Mon, Dec 27, 2010 at 8:00 PM, Chase Miller <chmille4 at gmail.com> wrote:

> 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
> >
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 
---------------
Sincerely
George
KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/