[BioPerl] Re: [Bioperl-l] How to check the validity of an accession number ?

[Mark Wilkinson]

Well... I'm not convinced that this is the "polite" thing to do :-)   

We have to be much more forgiving in the MOBY world.  The fact that THIS
service provider does not understand the ID number, does *not* mean that
the ID number is invalid (as you are asserting by the fact that you
throw an error).  In MOBY we would then simply pass it off to another
service provider who claimed to know something about it, and so on,
until in the end we just claim "nobody knew anything about it... but
that STILL doesn't mean it is invalid!".

We certainly would never "break" due to service providers ignorance, or
we would be broken all the time :-)

Mark


On Sat, 2003-11-08 at 08:08, Heikki Lehvaslaiho wrote:
> Mark,
> 
> Jason's cvs commit note:
> 
> "properly throw an error when no sequences are retrieved for a query --
> cannot distinguish between errors and non-connections though at this
> point, but this makes t/Perl.t now properly run when network is
> disconnected [during an ice storm]"
> 
> 	-Heikki
> 
> On Sat, 2003-11-08 at 12:46, Mark Wilkinson wrote:
> > On Sat, 2003-11-08 at 03:10, Heikki Lehvaslaiho wrote:
> > 
> > > The change is in the bioperl code. It was put in almost 11 months ago
> > > for the 1.2 release. As the error message indicates, line 177 in
> > > Bio::DB::WebDBSeqI now throws an error.
> > 
> > Although I am now "getting used to it", I have to say that I found the
> > earlier behaviour much more sensible and easier to deal with... why was
> > this change made in this way?
> > 
> > Mark
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae