[BioRuby] Bio Assembly Plugin

[Chase Miller]

> 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
>

My code currently does this, but not in the way Bio::Sequence does. I based
my solution off this stackoverflow example (
http://stackoverflow.com/questions/746207/ruby-design-pattern-how-to-make-an-extensible-factory-class
).

I'll take look at Bio::Sequence and see if it's easy to refactor.   Here's
what I have so far (suggestions very welcome!):

code: https://github.com/chmille4/bioruby-assembly

usage example:  https://gist.github.com/615296


>  and we need to keep in mind that we can not store everything in memory :-)
>

By this do you mean streaming, where the entire file is eventually read into
memory if all the data is accessed?  Or are you talking about something
else, perhaps creating an index file similar to a project like
https://github.com/ekg/fastahack.


Cheers,
Chase




>
>
>
> > 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.
>
>
>
>
>