[BioRuby] Bio Assembly Plugin

[Francesco Strozzi]

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