[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer

Chris Fields cjfields at uiuc.edu
Wed Feb 28 20:19:31 EST 2007

On Feb 28, 2007, at 6:13 PM, Sendu Bala wrote:

> Mark Johnson wrote:
>> I'm using _rearrange() now.  I'll look at _set_from_args().  Is  
>> either one
>> preferred to the other?
> _set_from_args() is implemented using _rearrange() iirc. In any case,
> they do different things but _set_from_args() just makes creating
> wrapper modules a lot simpler. Another example: compare revisions 1.15
> and 1.16 of Bio::Tools::Run::Alignment::Lagan where I reimplemented it
> to use _set_from_args() and _setparams().
> http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-run/Bio/Tools/Run/ 
> Alignment/Lagan.pm.diff? 
> r1=text&tr1=1.15&r2=text&tr2=1.16&diff_format=h
> So, its new, but I'd recommend new modules, especially wrappers, make
> use of it.

Agreed; I think it allows for parameter variations (dashed, dashless,  
etc) and can create on-the-fly simple get/setters, so is particularly  
suited for wrappers.

_rearrange() will always have use in situations where using named  
parameters helps (long arg lists) but you don't want get/setters,  
just values.

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