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

Sendu Bala bix at sendu.me.uk
Wed Feb 28 19:13:29 EST 2007


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.


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