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

Hilmar Lapp hlapp at duke.edu
Fri Feb 2 10:09:57 EST 2007

On Feb 1, 2007, at 2:55 PM, Scott Cain wrote:

> The second main change was to introduce a -flybase_compat argument  
> when
> initializing the Bio::SeqIO writer, so that 'old style' cv and cvterms
> (that are compatable with flybase) will be used, but now the default
> will be to use current standards:

Just my $0.02 ... obviously, Flybase may be the only organization  
that uses an 'old style' or any other way not compliant with 'current  
standards' (presumably SO), but if it's not the only one then this  
approach won't scale.

Also, an argument -flybase_compat suggests to the unsuspecting that  
this is an endorsed flavor of the standard and fine to use for  
everyone else too.

If Flybase is idiosyncratic in this way, why not make chadoxml.pm  
compliant with the standard as we all want it, keep it free from  
litter caused by usage of old versions of SO, 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. This way, other  
organizations with similar needs can follow the path and create their  
own xyz-chadoxml.pm, rather than having to muck around in the  
chadoxml.pm that comes with the distribution.

I'm not sure I fully grasp the underlying issue, so I may not make  
much sense here. Apologies if that's the case ...

: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :

More information about the Bioperl-l mailing list