[BioRuby] Bio Assembly Plugin

[Francesco Strozzi]

Iteretors will be the way, as discussed in another thread :-)

Ciao
Francesco

On Tue, Dec 28, 2010 at 11:18, Raoul Bonnal <bonnalraoul at ingm.it> wrote:

>
> On 27/dic/2010, at 19.11, George Githinji wrote:
>
> > 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.
>
> I think so.
> I agree with Francesco, I suggest to start designing a general Assembler
> and use adapters like Ace, CAF an others in the way we did with
> Bio::Sequence.
>
> Bio::Assembler
> Bio::Assembler::Ace
> Bio::Assembler::CAF
>
> and we need to keep in mind that we can not store everything in memory :-)
>
>
>
> > 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/
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
> --
> R.J.P.B.
>
>
>
>
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 

Francesco