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

Mark Johnson johnsonm at gmail.com
Thu Mar 1 17:46:12 EST 2007

Now that I'm using _set_from_args() and trying to get all the options and
switches working that I never use, it occurs to me that a 4-in-1 module for
Glimmer2/Glimmer3/GlimmerM/GllimmerHMM is not going to fly due to the
options and switches being different.  At this point, I think I'm going to
end up with a Genemark module, a Glimmer2 module, and a Glimmer3 module.

On 2/28/07, Sendu Bala <bix at sendu.me.uk> 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.

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