Bioperl: Using BioPerl modules

[Aaron J Mackey]

I apologize, I thought we had discussed removing Bio::Search::* from the
release ... but I guess if it's out there already, I should make it
functional ... give me a week or so to see what I can get together.

-Aaron

On Sat, 8 Apr 2000, Ewan Birney wrote:

> On Fri, 7 Apr 2000, Nicolas Tourasse wrote:
> 
> > Hi everyone,
> > 
> > I got an error message when trying to use the 
> > Bio::Search::Processor and Bio::Search::Result::ResultI
> > modules and I really don't see why. The program crashes when
> > I try to call the get_query_id() method.
> 
> The Bio::Search stuff is not functional (really) at the moment. At least I
> have not tested it heavily and it needs reworking.
> 
> Apologies for not either removing it or documenting this better. My
> suggestion is to email aaron mackay directly and see if he will help you
> and if not dig around the code.
> 
> 
> 
> > 
> > Can any one help me to find where is the error ?
> > I would be so grateful.
> > Below is a sample of the code and the error message:
> > 
> > use Bio::Search::Processor;
> > my $processor;
> > 
> > $processor = Bio::Search::Processor->new(-file => $filename,
> > -algorithm => 'Fasta');
> > $result = $processor->next_result();
> > $qid = $result->get_query_id();
> > 
> > 
> > -------------------- EXCEPTION --------------------
> > MSG: Abstract interface call.
> > CONTEXT: Error in uNKNOWN CONTEXT
> > SCRIPT: fasta.perl
> > STACK: 
> > Bio::Search::Result::ResultI::get_query_id(105)
> > main::fasta.perl(64)
> > ---------------------------------------------------
> > 
> > 
> > Thanks,
> > 
> > Nicolas Tourasse.
> > Biotechnology Centre of Oslo, Norway.
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
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-- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o


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