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