[Bioperl-l] BLAST example doesn't work

Enzyme arlett.wrona at c-lecta.de
Tue Feb 21 04:16:21 EST 2012


Hi,

i'm new to BioPerl and wanna use it for BLAST. But the example doesn't work.
I tried some possible solutions and at the moment i don't know if the code
is wrong or my bio perl package don't work how it should:

use Bio::Tools::Run::StandAloneBlast;
my $factory = Bio::Tools::Run::StandAloneBlast->new(p => 'blastn',
                                                    d => 'nr',
                                                    e => '1e-5');
my $seq = Bio::PrimarySeq->new(-id => 'test1',
                               -seq => 'AGATCAGTAGATGATAGGGGTAGA');
my $report = $factory->blastall($seq); # get back a {{PM|Bio::SearchIO}}
report

I get this error:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Command 'run' not registered
STACK: Error::throw
STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::set_parameters
C:/Perl/site/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1203
STACK: Bio::Tools::Run::WrapperBase::new
C:/Perl/site/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:505
STACK: Bio::Tools::Run::StandAloneBlast::new
C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:366
STACK: Bio::Tools::Run::StandAloneNCBIBlast::new
C:/Perl/site/lib/Bio\Tools\Run\StandAloneNCBIBlast.pm:166
STACK: C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:382

Any ideas?
I downloaded the database "nr" correctly. The environment paths were
created.

Thanks! Enzyme
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