[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer
cjfields at uiuc.edu
Thu Mar 1 18:08:46 EST 2007
I have been working on an Infernal wrapper (not finished yet but
getting there) which does this:
# when run() is called, cmsearch is the program run...
my $factory = Bio::Tools::Run::Infernal->new('-program' =>'cmsearch',
# for each program...
my %INFERNAL_PROGRAM = (
cmsearch => [qw(h W informat toponly local noalign dumptrees
thresh X inside
null2 learninserts hmmfb hmmweinberg hmmpad hmmonly
hthresh beta noqdb
qdbfile hbanded hbandp banddump sums scan2bands)],
then set in new() based on only the parameters listed for the
program; I'm still toying with whether the program needs to be
specified in the constructor prior to a run. There are prob. other
variations on this using AUTOLOAD and _set_from_args() etc.
On Mar 1, 2007, at 4:46 PM, Mark Johnson wrote:
> 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. Feh.
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