Bioperl: Using BioPerl modules

[Ewan Birney]

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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