[Bioperl-l] bioperl-run parameter question

Chris Fields cjfields at uiuc.edu
Mon Dec 11 08:06:32 EST 2006

On Dec 11, 2006, at 12:44 AM, Nathan S. Haigh 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.
>> chris
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> No idea!
> Is there any reason for/against using dashed/dashless parameters? I
> suppose dshed parameters allow you to easy see which tokens on the
> command line are parameters and which are values. Should modules be  
> able
> to accept both? Should dashed be preferred?
> Nath
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I'm thinking about it from the point of consistency.  When using a  
mix of core and run modules it can be a bit confusing, particularly  
when (as pointed out in the previous thread on StandAloneBlast) you  
can use only dashed parameters with core modules, while most (all?)  
run modules only accept dashless ones (in most cases some exception  
is thrown).  Torsten fixed this in StandAloneBlast so it accepts  
both, but shouldn't this rule also apply to all run modules?

Much of this probably is probably due to the donated nature of much  
of the bioperl-run code and Jason's 'cat-herding', and I understand  
that it would be a lot of work to change this for all run modules.   
However, we could at least try to start enforcing some loose rules  
with new bioperl-run wrappers (e.g. implement WrapperBase, use core- 
like parameters, etc).


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