[Bioperl-l] bioperl-run parameter question

Sendu Bala bix at sendu.me.uk
Mon Dec 11 16:19:55 EST 2006

Chris Fields wrote:
> On Dec 11, 2006, at 12:21 PM, Sendu Bala wrote:
>> Chris Fields wrote:
>>> I am writing up a few bioperl-run modules and have a simple 
>>> question,  though I don't know if anyone knows the answer.  I was 
>>> curious as to  why parameters for most (all?) bioperl-run modules 
>>> lack the '-'  preceding them.  This came up re: StandAloneBlast last 
>>> week  (something Torsten fixed), but I noticed just about every 
>>> bioperl-run  module uses the dashless parameters.
>> I didn't follow that particular thread, but from my experience there 
>> is a useful distinction between bioperl options using the - as normal 
>> for full consistency with core (eg. -verbose), whilst the options that 
>> belong to the program the run module is a wrapper for do not take 
>> dashes. Again, this seems consistent within the run package.
> I respectfully disagree that this is a 'useful' distinction.  My main 
> point is consistency.

We're on the same page in terms of what we think would be a Good Thing, 
and allowing both ways (dashed and dashless) sounds reasonable. I was 
just suggesting why bioperl-run might be the way it was. Further to 
that, there is the practical aspect that it is a lot simpler to figure 
out which are the program options so they can be farmed out to the 
AUTOLOAD methods - again something that isn't done in core.

If you come up with some generic way of dealing with options and farming 
to AUTOLOAD, perhaps there's scope for applying it to all the run 
wrappers (ideally via one of their base classes), so they all instantly 
gain dashed-mode capability.

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