[BioRuby] Bio Assembly Plugin

[Raoul Bonnal]

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.