[Bioperl-l] [Gmod-schema] beginning work on SeqIO::chadoxml

Scott Cain cain.cshl at gmail.com
Fri Feb 2 13:05:47 EST 2007


Hi Peili,

A little bit ago I checked in Bio::SeqIO::flybase_chadoxml that is
fairly simple.  My suggestion is that when you make tweaks for different
scenarios, that you turn the things you are tweaking into methods in
BSIO::chadoxml and then override them in flybase_chadoxml (and commit at
least the chadoxml module) to make it more flexible when other people
have similar scenarios.

Scott


On Fri, 2007-02-02 at 10:56 -0500, Peili Zhang wrote:
> i 'third' Hilmar's opinion. flybase's fingerprint is shown in the module
> because i wrote it for fb's data loading task. no need to worry about
> flybase compatibility in making the module generic. in fact, at flybase,
> i tweak the module frequently to make it work for different scenarios.
> 
> cheers,
> peili
>  
> On Fri, 2007-02-02 at 10:27, Brian Osborne wrote:
> > Hilmar,
> > 
> > I second your motion, good idea. Let's keep the standard module nice and
> > clean.
> > 
> > Brian O.
> > 
> > 
> > On 2/2/07 10:09 AM, "Hilmar Lapp" <hlapp at duke.edu> wrote:
> > 
> > > and create a second
> > > module fb-chadoxml.pm that inherits from the first and merely
> > > overrides a few things so that it works for Flybase
> > 
> > 
> > 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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