[Bioperl-l] run RNAfold in perl

vanam arvindvanam at gmail.com
Fri Nov 23 16:26:06 EST 2007


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 =>
'UUUGACGACAGACGACUCAAUGUCAGCUAGCUAGUACGAUCGAUC');

I installed Vienna package and then i tried using Pise to create an object
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
/usr/local/share/perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Tools::Run::PiseJob::terminated
/usr/local/share/perl/5.8.8/Bio/Tools/Run/PiseJob.pm:460
STACK: Bio::Tools::Run::PiseApplication::submit
/usr/local/share/perl/5.8.8/Bio/Tools/Run/PiseApplication.pm:416
STACK: Bio::Tools::Run::PiseApplication::run
/usr/local/share/perl/5.8.8/Bio/Tools/Run/PiseApplication.pm:352
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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