[Bioperl-l] run RNAfold in perl
arvindvanam at gmail.com
Sat Nov 24 02:29:11 EST 2007
i have seen the documentation for Bio::Tools::Run::AnalysisFactory::Pise and
i used it exactly as it was mentioned in it.
i just want that instead of running its perl version "RNAfold.pl" I can use
the functions associated with RNAfold with a perl program without having to
call the program using system() command.
if you can just tell me how to use these wrapper modules it would b of gr8
help...like while using clustalw or clustalx we define the environment
variable for it ..do we have to do the same for RNAfold or Mfold
Chris Fields wrote:
> The Pise wrappers run the programs remotely; see
> Bio::Tools::Run::AnalysisFactory::Pise on how to run it. As for a
> local RNAfold wrapper, I had planned on making Bioperl-based Vienna/
> mfold wrappers but haven't done so yet. The Vienna tools do have a
> Perl-based (non-BioPerl-based) module included which uses libRNA, and
> is well worth a look. Try 'perldoc RNA' if you have installed the
> tools locally, or look here for other Perl-based tools:
> On Nov 23, 2007, at 3:26 PM, vanam wrote:
>> how to run RNAfold using Bio::Tools::Run::AnalysisFactory::Pise?????
>> my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
>> my $rnafold = $factory->program('rnafold');
>> my $job=$rnafold->run(-rnafold =>
>> I installed Vienna package and then i tried using Pise to create an
>> for the program but its giving the following error
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Bio::Tools::Run::PiseJob terminated: URL missing
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> STACK: Bio::Tools::Run::PiseJob::terminated
>> STACK: Bio::Tools::Run::PiseApplication::submit
>> STACK: Bio::Tools::Run::PiseApplication::run
>> STACK: evaluate.pl:12
>> how to make the program RNAfold run in perl...
>> IS THERE ANY NEED TO SPECIFY WHERE MY rnafold program is???
>> plz reply soon
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> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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